@article {pmid40286509,
year = {2025},
author = {Torres-Tamayo, N and Bastir, M and VanSickle, C and García-Tabernero, A and de la Rasilla, M and Rosas, A},
title = {New insights into the Neanderthal pelvis morphology based on a partial os coxae from El Sidrón (Asturias, Spain).},
journal = {Journal of human evolution},
volume = {203},
number = {},
pages = {103666},
doi = {10.1016/j.jhevol.2025.103666},
pmid = {40286509},
issn = {1095-8606},
abstract = {The Neanderthal pelvis exhibits distinctive features compared to modern humans, including wider and more flared iliac blades, a more anteriorly positioned sacrum, and a longer and thinner, outwardly oriented pubic bone. Each new addition to the pelvic fossil record is significant for enhancing our understanding of Neanderthal morphology and variation. Here, we present SD-1663, the most complete adult os coxae fragment recovered from the El Sidrón site in Asturias (Spain), dated to approximately 49 ka. We carried out a detailed description and quantitative analysis of SD-1663 within a comparative framework that includes other notable pelvic fossil specimens. Utilizing traditional and three-dimensional morphometric techniques, we assessed the morphological characteristics of SD-1663 focusing on dimensions and anatomical landmarks that distinguish Neanderthal pelves from those of other hominins. The analyses reveal that SD-1663 was a young adult male with features and size that clustered with other Neanderthals in our comparative sample. However, SD-1663 also shares significant morphological affinities with earlier Pleistocene Homo specimens such as KNM-ER 3228 (Homo erectus), suggesting a broader range of pelvic variation within Neanderthals than previously recognized. This discovery contributes to expanding the Neanderthal range of anatomical diversity, indicating that the Neanderthal pelvis may have been more variable than the current fossil record suggests. It also underscores the importance of continued excavation and analysis of Neanderthal remains to fully comprehend the scope of their anatomical adaptations and evolutionary history. SD-1663 thus represents a valuable addition to the fossil record, offering new perspectives on Neanderthal pelvis morphology and its variation.},
}

@article {pmid40214099,
year = {2025},
author = {Owen-Smith, N},
title = {Reconciling Species Concepts: An Ecological Perspective.},
journal = {American journal of biological anthropology},
volume = {186},
number = {4},
pages = {e70047},
doi = {10.1002/ajpa.70047},
pmid = {40214099},
issn = {2692-7691},
mesh = {Animals ; *Biological Evolution ; Humans ; Fossils ; *Hominidae/classification ; Ecosystem ; Phylogeny ; },
abstract = {Species concepts remain contentious, both in paleoanthropology and in modern taxonomy. The lineage-based concept emphasizing evolutionary independence is most fundamental, but in practice is generally represented by proxy evidence of morphological or genetic divergence. This has resulted in a troubling proliferation of species names in the hominin fossil record. Pseudo-extinctions where lineages persisted under a new species name need to be distinguished from cases where lineages ended terminally-the implications for ecological adaptability are diametrically opposed. Furthermore, the ecological criterion for species coexistence is widely overlooked. The competitive exclusion principle holds that species sharing closely similar niches cannot continue to coexist in the same place at the same time. Notably, the largely vegetarian Paranthropus lineage remained distinct from the diverging, more versatile Homo lineage until fading from the fossil record during the later Pleistocene. Claims that additional hominin species existed are ecologically suspect unless supported by evidence of adequate niche separation. Modern examples where there has been equivocation in lineage recognition are illustrated for bovids, giraffids, baboons, and elephants. Furthermore, the mechanisms that resulted in the displacement of Neanderthals by modern humans are reappraised from an ecological perspective. Representations of evolutionary divergence as a bushy tree need to be superseded by the emerging paradigm of reticulate lineages diverging and coalescing through time and space.},
}

Animals
*Biological Evolution
Humans
Fossils
*Hominidae/classification
Ecosystem
Phylogeny

@article {pmid40175549,
year = {2025},
author = {Salem, N and van de Loosdrecht, MS and Sümer, AP and Vai, S and Hübner, A and Peter, B and Bianco, RA and Lari, M and Modi, A and Al-Faloos, MFM and Turjman, M and Bouzouggar, A and Tafuri, MA and Manzi, G and Rotunno, R and Prüfer, K and Ringbauer, H and Caramelli, D and di Lernia, S and Krause, J},
title = {Ancient DNA from the Green Sahara reveals ancestral North African lineage.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40175549},
issn = {1476-4687},
abstract = {Although it is one of the most arid regions today, the Sahara Desert was a green savannah during the African Humid Period (AHP) between 14,500 and 5,000 years before present, with water bodies promoting human occupation and the spread of pastoralism in the middle Holocene epoch[1]. DNA rarely preserves well in this region, limiting knowledge of the Sahara's genetic history and demographic past. Here we report ancient genomic data from the Central Sahara, obtained from two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya. The majority of Takarkori individuals' ancestry stems from a previously unknown North African genetic lineage that diverged from sub-Saharan African lineages around the same time as present-day humans outside Africa and remained isolated throughout most of its existence. Both Takarkori individuals are closely related to ancestry first documented in 15,000-year-old foragers from Taforalt Cave, Morocco[2], associated with the Iberomaurusian lithic industry and predating the AHP. Takarkori and Iberomaurusian-associated individuals are equally distantly related to sub-Saharan lineages, suggesting limited gene flow from sub-Saharan to Northern Africa during the AHP. In contrast to Taforalt individuals, who have half the Neanderthal admixture of non-Africans, Takarkori shows ten times less Neanderthal ancestry than Levantine farmers, yet significantly more than contemporary sub-Saharan genomes. Our findings suggest that pastoralism spread through cultural diffusion into a deeply divergent, isolated North African lineage that had probably been widespread in Northern Africa during the late Pleistocene epoch.},
}

@article {pmid40163722,
year = {2025},
author = {Ruan, QJ and Li, H and Xiao, PY and Li, B and Monod, H and Sumner, A and Zhao, KL and Liu, JH and Jia, ZX and Wang, CX and Fan, AC and Moncel, MH and Marwick, B and Peresani, M and Wang, YP and Chen, FH and Delpiano, D},
title = {Quina lithic technology indicates diverse Late Pleistocene human dynamics in East Asia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {14},
pages = {e2418029122},
doi = {10.1073/pnas.2418029122},
pmid = {40163722},
issn = {1091-6490},
support = {TPESER202210//Open Research Fund of TPESER/ ; 41988101//National Natural Science Foundation of China BSCTPES/ ; 42471180//National Natural Science Foundation of China/ ; DP210100717//Australian Research Council/ ; FAR2023//University of Ferrara/ ; },
mesh = {Humans ; *Neanderthals ; *Archaeology ; Animals ; *Technology/history ; *Fossils ; China ; Asia, Eastern ; History, Ancient ; },
abstract = {The Late Pleistocene of Eurasia is key for understanding interactions between early modern humans and different types of archaic human groups. During this period, lithic technology shows more diversity and complexity, likely indicating flexible adaptative strategies. However, cultural variability as expressed by technological types remains vague in large parts of eastern Eurasia, like in China. Here, we report a complete Quina technological system identified from the study of the Longtan site in Southwest China. The site has been securely dated to ca. 60 to 50 thousand years ago (ka), with compelling evidence of core exploitation, production of large and thick flakes, shaping and maintenance of scrapers exhibiting the whole Quina concept, typical of contemporary European Middle Paleolithic technologies developed by Neanderthal groups adapted to climatic oscillations during Marine Isotope Stage (MIS) 4 and early MIS 3. The finding of a Quina lithic assemblage in China not only demonstrates the existence of a Middle Paleolithic technology in the region but also shows large-scale analogies with Neanderthal behaviors in western Europe. Longtan substantially extends the geographic distribution of this technical behavior in East Asia. Although its origin remains unclear, implications for Pleistocene hominin dispersal and adaptation to diverse ecological settings are considered. The Longtan lithic evidence also provides perspectives for understanding the cultural evolutionary situation before the large-scale arrivals of early modern humans in East Asia predating ~45 ka.},
}

Humans
*Neanderthals
*Archaeology
Animals
*Technology/history
*Fossils
China
Asia, Eastern
History, Ancient

@article {pmid40163477,
year = {2025},
author = {Ragsdale, AP},
title = {Archaic introgression and the distribution of shared variation under stabilizing selection.},
journal = {PLoS genetics},
volume = {21},
number = {3},
pages = {e1011623},
doi = {10.1371/journal.pgen.1011623},
pmid = {40163477},
issn = {1553-7404},
abstract = {Many phenotypic traits are under stabilizing selection, which maintains a population's mean phenotypic value near some optimum. The dynamics of traits and trait architectures under stabilizing selection have been extensively studied for single populations at steady state. However, natural populations are seldom at steady state and are often structured in some way. Admixture and introgression events may be common, including over human evolutionary history. Because stabilizing selection results in selection against the minor allele at a trait-affecting locus, alleles from the minor parental ancestry will be selected against after admixture. We show that the site-frequency spectrum can be used to model the genetic architecture of such traits, allowing for the study of trait architecture dynamics in complex multi-population settings. We use a simple deterministic two-locus model to predict the reduction of introgressed ancestry around trait-contributing loci. From this and individual-based simulations, we show that introgressed-ancestry is depleted around such loci. When introgression between two diverged populations occurs in both directions, as has been inferred between humans and Neanderthals, the locations of such regions with depleted introgressed ancestry will tend to be shared across populations. We argue that stabilizing selection for shared phenotypic optima may explain recent observations in which regions of depleted human-introgressed ancestry in the Neanderthal genome overlap with Neanderthal-ancestry deserts in humans.},
}

@article {pmid40161630,
year = {2025},
author = {Casten, LG and Koomar, T and Thomas, TR and Koh, JY and Hofamman, D and Thenuwara, S and Momany, A and O'Brien, M and Murray, JC and Tomblin, JB and Michaelson, JJ},
title = {Rapidly evolved genomic regions shape individual language abilities in present-day humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.07.641231},
pmid = {40161630},
issn = {2692-8205},
abstract = {1 Minor genetic changes have produced profound differences in cognitive abilities between humans and our closest relatives, particularly in language. Despite decades of research, ranging from single-gene studies to broader evolutionary analyses[1, 2, 3, 4, 5], key questions about the genomic foundations of human language have persisted, including which sequences are involved, how they evolved, and whether similar changes occur in other vocal learning species. Here we provide the first evidence directly linking rapidly evolved genomic regions to language abilities in contemporary humans. Through extensive analysis of 65 million years of evolutionary events in over 30,000 individuals, we demonstrate that Human Ancestor Quickly Evolved Regions (HAQERs)[5] - sequences that rapidly accumulated mutations after the human-chimpanzee split - specifically influence language but not general cognition. These regions evolved to shape language development by altering binding of Forkhead domain transcription factors, including FOXP2 . Strikingly, language-associated HAQER variants show higher prevalence in Neanderthals than modern humans, have been stable throughout recent human history, and show evidence of convergent evolution across other mammalian vocal learners. An unexpected pattern of balancing selection acting on these apparently beneficial alleles is explained by their pleiotropic effects on prenatal brain development contributing to birth complications, reflecting an evolutionary trade-off between language capability and reproductive fitness. By developing the Evolution Stratified-Polygenic Score analysis, we show that language capabilities likely emerged before the human-Neanderthal split - far earlier than previously thought[3, 6, 7]. Our findings establish the first direct link between ancient genomic divergence and present-day variation in language abilities, while revealing how evolutionary constraints continue to shape human cognitive development.},
}

@article {pmid40134218,
year = {2025},
author = {Janivara, R and Hazra, U and Pfennig, A and Harlemon, M and Kim, MS and Eaaswarkhanth, M and Chen, WC and Ogunbiyi, A and Kachambwa, P and Petersen, LN and Jalloh, M and Mensah, JE and Adjei, AA and Adusei, B and Joffe, M and Gueye, SM and Aisuodionoe-Shadrach, OI and Fernandez, PW and Rohan, TE and Andrews, C and Rebbeck, TR and Adebiyi, AO and Agalliu, I and Lachance, J},
title = {Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men.},
journal = {HGG advances},
volume = {},
number = {},
pages = {100428},
doi = {10.1016/j.xhgg.2025.100428},
pmid = {40134218},
issn = {2666-2477},
abstract = {Androgenetic alopecia is a highly heritable trait. However, much of our understanding about the genetics of male pattern baldness comes from individuals of European descent. Here, we examined a dataset comprising 2,136 men from Ghana, Nigeria, Senegal, and South Africa that were genotyped using the MADCaP Array. We first tested how genetic predictions of baldness generalize from Europe to Africa and found that polygenic scores from European GWAS yielded AUC statistics that ranged from 0.513 to 0.546, indicating that genetic predictions of baldness generalized poorly from European to African populations. Subsequently, we conducted an African GWAS of androgenetic alopecia, focusing on self-reported baldness patterns at age 45. After correcting for age at recruitment, population structure, and study site, we identified 266 moderately significant associations, 51 of which were independent (p-value < 10[-5], r[2] < 0.2). Most baldness associations were autosomal, and the X chromosome does not appear to have a large impact on baldness in African men. Although Neanderthal alleles have previously been associated with skin and hair phenotypes, within the limits of statistical power, we did not find evidence that continental differences in the genetic architecture of baldness are due to Neanderthal introgression. While most loci that are associated with androgenetic alopecia do not have large iHS or FST statistics, multiple baldness-associated SNPs near the EDA2R and AR genes have large allele frequency differences between continents. Collectively, our findings illustrate how population genetic differences contribute to the limited portability of polygenic predictions across ancestries.},
}

@article {pmid40132491,
year = {2025},
author = {Schuh, A and Gunz, P and Villa, C and Maureille, B and Toussaint, M and Abrams, G and Hublin, JJ and Freidline, SE},
title = {Human midfacial growth pattern differs from that of Neanderthals and chimpanzees.},
journal = {Journal of human evolution},
volume = {202},
number = {},
pages = {103667},
doi = {10.1016/j.jhevol.2025.103667},
pmid = {40132491},
issn = {1095-8606},
abstract = {Present-day humans have small and retracted midfaces, while Neanderthals possess large and forwardly projected midfaces. To understand the ontogenetic patterns underlying these characteristic morphologies, we compared maxillary growth and development from birth to adulthood in present-day humans (Homo sapiens; n = 128), Neanderthals (Homo neanderthalensis; n = 13), and chimpanzees (Pan troglodytes verus; n = 33) using macroscopic (i.e., geometric morphometrics) and microscopic (i.e., surface histology) approaches. Using geometric morphometrics to quantify macroscopic patterns of growth and development, we found that the midfaces of present-day humans are on average already smaller at birth than those of Neanderthals and grow more slowly after birth. In particular, we find an early cessation of growth around adolescence, which is unique to our species. Microscopically, this is reflected in reduced amounts of bone resorption, indicative of decreased cellular activities linked to bone development. Greater amounts of bone formation in the infraorbital and nasal regions and faster growth rates are responsible for the large Neanderthal midface. These results highlight the importance of postnatal ontogeny (especially in late stages) for explaining facial differences between Neanderthals and present-day humans, as well as part of the gracilization process characteristic of present-day humans.},
}

@article {pmid40102687,
year = {2025},
author = {Cousins, T and Scally, A and Durbin, R},
title = {A structured coalescent model reveals deep ancestral structure shared by all modern humans.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40102687},
issn = {1546-1718},
support = {207492/Z/17/Z//Wellcome Trust (Wellcome)/ ; 108864/B/15/Z//Wellcome Trust (Wellcome)/ ; },
abstract = {Understanding the history of admixture events and population size changes leading to modern humans is central to human evolutionary genetics. Here we introduce a coalescence-based hidden Markov model, cobraa, that explicitly represents an ancestral population split and rejoin, and demonstrate its application on simulated and real data across multiple species. Using cobraa, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ~1.5 million years ago came together in an admixture event ~300 thousand years ago, in a ratio of ~80:20%. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human-Neanderthal or human-Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.},
}

@article {pmid40069367,
year = {2025},
author = {Zaidner, Y and Prévost, M and Shahack-Gross, R and Weissbrod, L and Yeshurun, R and Porat, N and Guérin, G and Mercier, N and Galy, A and Pécheyran, C and Barbotin, G and Tribolo, C and Valladas, H and White, D and Timms, R and Blockley, S and Frumkin, A and Gaitero-Santos, D and Ilani, S and Ben-Haim, S and Pedergnana, A and Pietraszek, AV and García, P and Nicosia, C and Lagle, S and Varoner, O and Zeigen, C and Langgut, D and Crouvi, O and Borgel, S and Sarig, R and May, H and Hershkovitz, I},
title = {Evidence from Tinshemet Cave in Israel suggests behavioural uniformity across Homo groups in the Levantine mid-Middle Palaeolithic circa 130,000-80,000 years ago.},
journal = {Nature human behaviour},
volume = {},
number = {},
pages = {},
pmid = {40069367},
issn = {2397-3374},
support = {2229/23//Israel Science Foundation (ISF)/ ; 91/6391//Israel Science Foundation (ISF)/ ; 1458/19//Israel Science Foundation (ISF)/ ; 1084/23//Israel Science Foundation (ISF)/ ; NGS-72344R-20//National Geographic Society/ ; NGS-51135R-18//National Geographic Society/ ; },
abstract = {The south Levantine mid-Middle Palaeolithic (mid-MP; ~130-80 thousand years ago (ka)) is remarkable for its exceptional evidence of human morphological variability, with contemporaneous fossils of Homo sapiens and Neanderthal-like hominins. Yet, it remains unclear whether these hominins adhered to discrete behavioural sets or whether regional-scale intergroup interactions could have homogenized mid-MP behaviour. Here we report on our discoveries at Tinshemet Cave, Israel. The site yielded articulated Homo remains in association with rich assemblages of ochre, fauna and stone tools dated to ~100 ka. Viewed from the perspective of other key regional sites of this period, our findings indicate consolidation of a uniform behavioural set in the Levantine mid-MP, consisting of similar lithic technology, an increased reliance on large-game hunting and a range of socially elaborated behaviours, comprising intentional human burial and the use of ochre in burial contexts. We suggest that the development of this behavioural uniformity is due to intensified inter-population interactions and admixture between Homo groups ~130-80 ka.},
}

@article {pmid40063818,
year = {2025},
author = {Ma, X and Lu, Y and Stoneking, M and Xu, S},
title = {Neanderthal adaptive introgression shaped LCT enhancer region diversity without linking to lactase persistence in East Asian populations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {11},
pages = {e2404393122},
doi = {10.1073/pnas.2404393122},
pmid = {40063818},
issn = {1091-6490},
support = {2023YFC2605400//MOST | National Key Research and Development Program of China (NKPs)/ ; 32030020 32288101//MOST | National Natural Science Foundation of China (NSFC)/ ; 23JS1410100//shanghai science and technology commission program/ ; Key Projects Development Fund//the office of global partnerships/ ; },
mesh = {*Lactase/genetics/metabolism ; Humans ; Animals ; *Enhancer Elements, Genetic/genetics ; *Haplotypes ; *Neanderthals/genetics ; *Asian People/genetics ; Genetic Introgression ; Selection, Genetic ; Black People/genetics ; East Asian People ; },
abstract = {Positive selection at the 2q21.3 enhancer region for lactase gene (LCT) expression in Europeans and Africans has long been attributed to selection for lactase persistence (LP), the capacity of adults to digest lactose in milk, presumably because of the benefits associated with milk consumption. While considered a classic example of gene-culture coevolution, recently doubts have been raised about the link between selection at 2q21.3 and LP. Analysis of additional populations could shed further light; here, we demonstrate that a haplotype spanning ~467 kb at the 2q21.3 locus has risen to high frequency in East Asians (~25%) but is absent from Africans and Europeans. This haplotype likely derived from Neanderthals and has been under positive selection in East Asians. The East Asian-specific haplotype is associated with alterations in LCT expression and promoter methylation in certain cell types, similar to what is observed with LP-associated haplotypes in Europeans. Moreover, its frequency is comparable to that of LP in East Asians, suggesting a potential association with LP in East Asians. However, it is highly unlikely that selection in East Asians was related to milk-drinking habits. We find that this haplotype impacts the expression of UBXN4, DARS1, and DARS1-AS1 in immune cells and is associated with neutrophil and white blood cell counts. Hence, the selection might be linked to certain aspects of immune function. This implies that selection on 2q21.3 has thus either occurred for different reasons in different populations or the selection observed in other populations is also not due to LP.},
}

*Lactase/genetics/metabolism
Humans
Animals
*Enhancer Elements, Genetic/genetics
*Haplotypes
*Neanderthals/genetics
*Asian People/genetics
Genetic Introgression
Selection, Genetic
Black People/genetics
East Asian People

@article {pmid40053588,
year = {2025},
author = {Linscott, B and Devièse, T and Duarte, C and Trinkaus, E and Zilhão, J},
title = {Direct hydroxyproline radiocarbon dating of the Lapedo child (Abrigo do Lagar Velho, Leiria, Portugal).},
journal = {Science advances},
volume = {11},
number = {10},
pages = {eadp5769},
doi = {10.1126/sciadv.adp5769},
pmid = {40053588},
issn = {2375-2548},
mesh = {*Radiometric Dating/methods ; Humans ; Portugal ; *Hydroxyproline/analysis ; *Archaeology/methods ; Animals ; Bone and Bones/chemistry ; Fossils ; Neanderthals ; Child, Preschool ; Child ; },
abstract = {The 1998 discovery of a nearly intact Gravettian human burial in the Lapedo Valley (Leiria, Portugal) propelled the Lagar Velho rockshelter to worldwide fame. The ochre-stained skeleton of the Lapedo child, a juvenile aged around four or five, exhibited a mosaic of Neanderthal and anatomically modern human features argued to reflect admixture between the two human populations. Here, we present direct compound-specific radiocarbon dates for the child's skeleton [27,780 to 28,550 calibrated years before present (cal B.P.)] and five associated bones from the burial and underlying contexts. We reassess the chronology and archaeological interpretation of the burial in light of these new dates and demonstrate the suitability of hydroxyproline radiocarbon dating for poorly preserved Paleolithic samples that otherwise fail routine radiocarbon pretreatment methods.},
}

*Radiometric Dating/methods
Humans
Portugal
*Hydroxyproline/analysis
*Archaeology/methods
Animals
Bone and Bones/chemistry
Fossils
Neanderthals
Child, Preschool
Child

@article {pmid40022290,
year = {2025},
author = {Adegboyega, MT and Grote, MN and Weaver, TD},
title = {Predicting the Position of Hip Bones Within the Pelvic Girdle: A Case Study of the Kebara 2 Neanderthal.},
journal = {American journal of biological anthropology},
volume = {186},
number = {2},
pages = {e70014},
doi = {10.1002/ajpa.70014},
pmid = {40022290},
issn = {2692-7691},
support = {//University of California, Davis, Department of Anthropology/ ; },
mesh = {Animals ; *Pelvic Bones/anatomy & histology/diagnostic imaging ; *Neanderthals/anatomy & histology ; *Fossils ; Female ; Male ; Humans ; Pelvis/anatomy & histology/diagnostic imaging ; Adult ; Anthropology, Physical ; Regression Analysis ; Tomography, X-Ray Computed ; },
abstract = {OBJECTIVES: Poor preservation of hominin pelvises and the lack of soft tissue in the fossil record inhibits researchers' abilities to ascertain the true geometry of hominin pelvic girdles. The reconstruction process becomes subjective, largely relying on researchers' anatomical expertise, particularly, when the sacrum is absent or cannot be used to orient the hip bones. The bilateral symmetry of the pelvis, however, offers an opportunity to use one side to reconstruct potentially missing data on the other side.

METHODS: We developed a regression model to predict the translation and rotation actions that are needed to transform a hip bone onto the location of its pair. We collected landmarks and curve semilandmarks on a training sample of medical CT scans of 103 adult humans. A reduced rank regression model was trained to predict the values that would fit each right hip bone on its left pair. Then, we applied the model to two reconstructions of the Kebara 2 Neanderthal pelvis and assessed how well, it predicted the reconstructions (assuming the sacrum was absent), which were made using the preserved sacrum.

RESULTS: Euclidean errors from the model were significantly lower than errors from a mean form model and an observed form pairwise model.

CONCLUSION: Regression modeling that takes advantage of bilateral symmetry can be used to reliably predict "missing" human hip bones and Kebara 2's reconstructed left hip bones. This method can be employed in conjunction with a researcher's anatomical expertise and other techniques to reduce subjectivity in the fossil pelvis reconstruction process.},
}

Animals
*Pelvic Bones/anatomy & histology/diagnostic imaging
*Neanderthals/anatomy & histology
*Fossils
Female
Male
Humans
Pelvis/anatomy & histology/diagnostic imaging
Adult
Anthropology, Physical
Regression Analysis
Tomography, X-Ray Computed

@article {pmid40009574,
year = {2025},
author = {Degioanni, A and Cabut, S and Condemi, S and Smith, RS},
title = {Climate change in Europe between 90 and 50 kyr BP and Neanderthal territorial habitability.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0308690},
doi = {10.1371/journal.pone.0308690},
pmid = {40009574},
issn = {1932-6203},
mesh = {*Neanderthals ; Animals ; *Climate Change ; Europe ; Humans ; Fossils ; Ecosystem ; },
abstract = {After having lived as the dominant human species in Europe for over 200 kyr, Homo neanderthalensis (the Neanderthals) disappeared around 40 kyr BP (Before Present) Higham T (2014). Competition with Homo sapiens, who arrived in Europe around the same time, is often invoked to explain this extinction. Others have argued that climate change may have reduced the living space of this population making its disappearance more rapid. In order to test the climate change hypothesis we modelled the Neanderthals' ecological niches in Europe between 90 and 50 kyr BP through paleoenvironmental reconstructions and Eco-Cultural Niche Modelling. We selected five environmental variables (orographic height, mean annual precipitation, mean temperature of the coldest month, carrying capacity and friction, see below) from climate model simulations of 5 periods between 90 and 50 kyr BP in Europe. We used Structural Similarity (SSIM) index to compare the probability maps of suitable niches to Neanderthals performed by Maxent. After a strong initial environmental change between the first (P1 = 90 to 83 kyr BP) and second (P2 = 83 to 69 kyr BP) periods, our results show that large areas highly suitable for Neanderthal occupation persisted across Europe. As our results show an increase/stability of the areas suitable to Neanderthals, the question of the cause of the decrease or displacement of the Neanderthal population towards southern Europe after this climatic change remains open.},
}

*Neanderthals
Animals
*Climate Change
Europe
Humans
Fossils
Ecosystem

@article {pmid39999512,
year = {2025},
author = {Olsen, ST and White, S},
title = {Facial morphologies of Middle Pleistocene Europe: Morphological mosaicism and the evolution of Homo neanderthalensis.},
journal = {Journal of human evolution},
volume = {201},
number = {},
pages = {103645},
doi = {10.1016/j.jhevol.2024.103645},
pmid = {39999512},
issn = {1095-8606},
abstract = {The phylogeny of the Middle Pleistocene hominins is a matter of intense scientific debate. Important phylogenetic and taxonomic uncertainties remain, not least due to conflicting results of phylogenetic analyses when methodologies or morphological focus differ. Geography has been proposed to play a key role in Middle Pleistocene hominin diversity, with a European group potentially ancestral to Neanderthals (Homo neanderthalensis) and an African group possibly ancestral to Homo sapiens, but the evidence is equivocal. In this study, we explore the connection between geography and facial morphology in Middle Pleistocene hominins with a particular emphasis on the potential Neanderthal affinities of the European group. Furthermore, to assess the impact of methodology on the results, we use a multimethod approach in which morphological affinities in both facial shape and discrete facial traits are assessed on a dataset consisting of 38 fossil and 20 recent hominin skulls divided into five groups (European and non-European Middle Pleistocene hominins, H. sapiens, H. neanderthalensis, and Homo erectus/Homo ergaster). Two main conclusions emerge from these analyses. First, methodological approach has a marked impact on the recorded pattern of morphological affinity, which may explain result discrepancies among previous studies. Second, this disparity may be caused by morphological mosaicism and polymorphism in the facial region of Middle Pleistocene hominins. The results provide some support for a closer connection between European Middle Pleistocene hominins and Neanderthals in terms of discrete facial traits, but not in overall facial shape, raising questions about the process of evolution of the Neanderthal facial phenotype. As a consequence of these results, we argue that greater attention needs to be paid to clarifying the broader evolutionary processes guiding hominin evolution during this period.},
}

@article {pmid39979299,
year = {2025},
author = {Urciuoli, A and Martínez, I and Quam, R and Arsuaga, JL and Keeling, BA and Diez-Valero, J and Conde-Valverde, M},
title = {Semicircular canals shed light on bottleneck events in the evolution of the Neanderthal clade.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {972},
pmid = {39979299},
issn = {2041-1723},
mesh = {Animals ; *Neanderthals/anatomy & histology/genetics ; *Semicircular Canals/anatomy & histology ; *Biological Evolution ; *Fossils ; *Phylogeny ; Humans ; },
abstract = {Revealing the evolutionary processes which resulted in the derived morphologies that characterize the Neanderthal clade has been an important task for paleoanthropologists. One critical method to quantify evolutionary changes in the morphology of hominin populations is through evaluating morphological phenotypic diversity (i.e., disparity) in phylogenetically informative bones as a close proxy to neutral evolutionary processes. The goal of this study is to quantify the degree of disparity in the Neanderthal clade. We hypothesize that a reduction in bony labyrinth disparity is indicative of the underlying genetic variation resulting from bottleneck events. We apply a deformation-based geometric morphometric approach to investigate semicircular canal and vestibule shape of a chronologically broad sample of individuals belonging to the Neanderthal lineage. Our results identify a significant reduction in disparity after the start of Marine Isotope Stage 5 supporting our hypothesis of a late bottleneck, possibly leading to the derived morphology of Late Pleistocene Neanderthals.},
}

Animals
*Neanderthals/anatomy & histology/genetics
*Semicircular Canals/anatomy & histology
*Biological Evolution
*Fossils
*Phylogeny
Humans

@article {pmid39971893,
year = {2025},
author = {Breton, É and Kaufmann, T},
title = {An evolutionary perspective on the genetics of anorexia nervosa.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {59},
pmid = {39971893},
issn = {2158-3188},
support = {323961//Norges Forskningsråd (Research Council of Norway)/ ; },
mesh = {*Anorexia Nervosa/genetics ; Humans ; Female ; *Menarche/genetics ; *Body Mass Index ; *Genome-Wide Association Study ; *Biological Evolution ; Adolescent ; Multifactorial Inheritance/genetics ; Animals ; Phenotype ; },
abstract = {Anorexia nervosa (AN) typically emerges around adolescence and predominantly affects females. Recent progress has been made in identifying biological correlates of AN, but more research is needed to pinpoint the specific mechanisms that lead to its development and maintenance. There is a known phenotypic link between AN, growth and sexual maturation, yet the genetic overlap between these phenotypes remains enigmatic. One may hypothesize that shared factors between AN, energy metabolism and reproductive functions may have been under recent evolutionary selection. Here, we characterize the genetic overlap between AN, BMI and age at menarche, and aimed to reveal recent evolutionary factors that may help explain the origin of AN. We obtained publicly available GWAS summary statistics of AN, BMI and age at menarche and studied the polygenic overlap between them. Next, we used Neandertal Selective Sweep scores to explore recent evolutionary selection. We found 22 loci overlapping between AN and BMI, and 9 loci between AN and age at menarche, with 7 of these not previously associated with AN. We found that loci associated with AN may have been under particular evolutionary dynamic. Chronobiology appeared relevant to the studied genetic overlaps and prone to recent evolutionary selection, offering a promising avenue for future research. Taken together, our findings contribute to the understanding of the genetic underpinning of AN. Ultimately, better knowledge of the biological origins of AN may help to target specific biological processes and facilitate early intervention in individuals who are most at risk.},
}

*Anorexia Nervosa/genetics
Humans
Female
*Menarche/genetics
*Body Mass Index
*Genome-Wide Association Study
*Biological Evolution
Adolescent
Multifactorial Inheritance/genetics
Animals
Phenotype

@article {pmid39962554,
year = {2025},
author = {Liang, SA and Ren, T and Zhang, J and He, J and Wang, X and Jiang, X and He, Y and McCoy, RC and Fu, Q and Akey, JM and Mao, Y and Chen, L},
title = {A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {32},
pmid = {39962554},
issn = {1474-760X},
mesh = {*Neanderthals/genetics ; Humans ; Animals ; *Genome, Human ; Genetic Introgression ; },
abstract = {BACKGROUND: Leveraging long-read sequencing technologies, the first complete human reference genome, T2T-CHM13, corrects assembly errors in previous references and resolves the remaining 8% of the genome. While studies on archaic admixture in modern humans have so far relied on the GRCh37 reference due to the availability of archaic genome data, the impact of T2T-CHM13 in this field remains unexplored.

RESULTS: We remap the sequencing reads of the high-quality Altai Neanderthal and Denisovan genomes onto GRCh38 and T2T-CHM13. Compared to GRCh37, we find that T2T-CHM13 significantly improves read mapping quality in archaic samples. We then apply IBDmix to identify Neanderthal-introgressed sequences in 2504 individuals from 26 geographically diverse populations using different reference genomes. We observe that commonly used pre-phasing filtering strategies in public datasets substantially influence archaic ancestry determination, underscoring the need for careful filter selection. Our analysis identifies approximately 51 Mb of Neanderthal sequences unique to T2T-CHM13, predominantly in genomic regions where GRCh38 and T2T-CHM13 assemblies diverge. Additionally, we uncover novel instances of population-specific archaic introgression in diverse populations, spanning genes involved in metabolism, olfaction, and ion-channel function. Finally, to facilitate the exploration of archaic alleles and adaptive signals in human genomics and evolutionary research, we integrate these introgressed sequences and adaptive signals across all reference genomes into a visualization database, ASH (www.arcseqhub.com).

CONCLUSIONS: Our study enhances the detection of archaic variations in modern humans, highlights the importance of utilizing the T2T-CHM13 reference, and provides novel insights into the functional consequences of archaic hominin admixture.},
}

*Neanderthals/genetics
Humans
Animals
*Genome, Human
Genetic Introgression

@article {pmid39953642,
year = {2025},
author = {Abood, S and Oota, H},
title = {Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations.},
journal = {Journal of physiological anthropology},
volume = {44},
number = {1},
pages = {5},
pmid = {39953642},
issn = {1880-6805},
mesh = {Humans ; *Human Migration ; Animals ; *Adaptation, Physiological/genetics ; Genome, Human/genetics ; Neanderthals/genetics ; Anthropology, Physical ; Biological Evolution ; },
abstract = {Humans have long pondered their genesis. The answer to the great question of where Homo sapiens come from has evolved in conjunction with biotechnologies that have allowed us to more brightly illuminate our distant past. The "Multiregional Evolution" model was once the hegemonic theory of Homo sapiens origins, but in the last 30 years, it has been supplanted by the "Out of Africa" model. Here, we review the major findings that have resulted in this paradigmatic shift. These include hominin brain expansion, classical insight from the mitochondrial genome (mtDNA) regarding the timing of the divergence point between Africans and non-Africans, and next-generation sequencing (NGS) of the Neanderthal and Denisovan genomes. These findings largely bolstered the "Out of Africa" model, although they also revealed a small degree of introgression of the Neanderthal and Denisovan genomes into those of non-African Homo sapiens. We also review paleogenomic studies for which migration route, north or south, early migrants to East Eurasia most likely traversed. Whichever route was taken, the migrants moved to higher latitudes, which necessitated adaptation for lower light conditions, colder clines, and pro-adipogenic mechanisms to counteract food scarcity. Further genetic and epigenetic investigations of these physiological adaptations constitute an integral aspect of the story of human origins and human migration to East Asia.},
}

Humans
*Human Migration
Animals
*Adaptation, Physiological/genetics
Genome, Human/genetics
Neanderthals/genetics
Anthropology, Physical
Biological Evolution

@article {pmid39868299,
year = {2025},
author = {Khouri-Farah, N and Winchester, EW and Schilder, BM and Robinson, K and Curtis, SW and Skene, NG and Leslie-Clarkson, EJ and Cotney, J},
title = {Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.18.633396},
pmid = {39868299},
issn = {2692-8205},
abstract = {Craniofacial development gives rise to the complex structures of the face and involves the interplay of diverse cell types. Despite its importance, our understanding of human-specific craniofacial developmental mechanisms and their genetic underpinnings remains limited. Here, we present a comprehensive single-nucleus RNA sequencing (snRNA-seq) atlas of human craniofacial development from craniofacial tissues of 24 embryos that span six key time points during the embryonic period (4-8 post-conception weeks). This resource resolves the transcriptional dynamics of seven major cell types and uncovers distinct major cell types, including muscle progenitors and cranial neural crest cells (CNCCs), as well as dozens of subtypes of ectoderm and mesenchyme. Comparative analyses reveal substantial conservation of major cell types, alongside human biased differences in gene expression programs. CNCCs, which play a crucial role in craniofacial morphogenesis, exhibit the lowest marker gene conservation, underscoring their evolutionary plasticity. Spatial transcriptomics further localizes cell populations, providing a detailed view of their developmental roles and anatomical context. We also link these developmental processes to genetic variation, identifying cell type-specific enrichments for common variants associated with facial morphology and rare variants linked to orofacial clefts. Intriguingly, Neanderthal-introgressed sequences are enriched near genes with biased expression in cartilage and specialized ectodermal subtypes, suggesting their contribution to modern human craniofacial features. This atlas offers unprecedented insights into the cellular and genetic mechanisms shaping the human face, highlighting conserved and distinctly human aspects of craniofacial biology. Our findings illuminate the developmental origins of craniofacial disorders, the genetic basis of facial variation, and the evolutionary legacy of ancient hominins. This work provides a foundational resource for exploring craniofacial biology, with implications for developmental genetics, evolutionary biology, and clinical research into congenital anomalies.},
}

@article {pmid39848961,
year = {2025},
author = {Mazières, S and Condemi, S and El Nemer, W and Chiaroni, J},
title = {Rapid change in red cell blood group systems after the main Out of Africa of Homo sapiens.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1597},
pmid = {39848961},
issn = {2045-2322},
support = {ANR-20-CE03-0002//Agence Nationale de la Recherche/ ; },
mesh = {Humans ; Animals ; *Blood Group Antigens/genetics ; *Neanderthals/genetics ; *Genetic Variation ; Haplotypes ; Phylogeny ; Erythrocytes ; Alleles ; Africa ; },
abstract = {Despite the advances in paleogenomics, red cell blood group systems in ancient human populations remain scarcely known. Pioneer attempts showed that Neandertal and Denisova, two archaic hominid populations inhabiting Eurasia, expressed blood groups currently found in sub-Saharans and a rare "rhesus", part of which is found in Oceanians. Herein we fully pictured the blood group genetic diversity of 22 Homo sapiens and 14 Neandertals from Eurasia living between 120,000 and 20,000 years before present (yBP). From the ABO, Rh, Kell, Duffy, Kidd, MNS, Diego, H, secretor and Indian systems, we noted that the blood group allele diversity in the Neandertals remained unchanged since 120,000 yBP, while H. sapiens conquered Eurasia with blood group alleles presently exclusive to non-African populations, suggesting they may have differentiated right after the Out of Africa, between 70,000 and 45,000 yBP. Notably, Ust'Ishim possessed unknown alleles that may illustrate the lost genetic heritage of the early Eurasians. Lastly, Neandertals shared a unique Rh haplotype from which we updated the current RHD phylogeny. The contribution of this study is twofold. It enlightens the expansion patterns of H sapiens and recalls the anthropological effectiveness of genetic polymorphisms currently being surveyed for transfusion safety and pregnancy monitoring.},
}

Humans
Animals
*Blood Group Antigens/genetics
*Neanderthals/genetics
*Genetic Variation
Haplotypes
Phylogeny
Erythrocytes
Alleles
Africa

@article {pmid39836586,
year = {2025},
author = {Casanova, EL and Feltus, FA},
title = {Neandertal DNA and the Human Mind: DNA inherited from our extinct relatives may affect modern human cognition.},
journal = {Scientific American},
volume = {332},
number = {2},
pages = {42},
doi = {10.1038/scientificamerican022025-ZJUzYFHXtbEy09x2LIFMa},
pmid = {39836586},
issn = {0036-8733},
}

@article {pmid39836570,
year = {2025},
author = {Bryner, J},
title = {Blobs and Green Monsters: Our February issue covers new Alzheimer's guidelines, teens' transcendent thinking, Neandertal DNA in all of us, and more.},
journal = {Scientific American},
volume = {332},
number = {2},
pages = {4},
doi = {10.1038/scientificamerican022025-SEPEKDBlVCyUKCmn5na3F},
pmid = {39836570},
issn = {0036-8733},
}

@article {pmid39807710,
year = {2025},
author = {Blessing, MA},
title = {Behavioural modernity is dead: Long live behavioural modernity.},
journal = {The Behavioral and brain sciences},
volume = {48},
number = {},
pages = {e5},
doi = {10.1017/S0140525X24001018},
pmid = {39807710},
issn = {1469-1825},
mesh = {Humans ; Animals ; *Neanderthals ; Cognition/physiology ; Biological Evolution ; Symbolism ; Cultural Evolution ; },
abstract = {Using Neanderthal symbolism, I extend on Stibbard-Hawkes to show that reconsidering the link between cognitive capacity and material culture extends beyond matters of preservation. A reconceptualization of behavioural modernity inclusive of both extant and extinct populations must begin with an honest theoretical separation of biological and behavioural modernity, which requires to critically engage with how we frame the underlying questions.},
}

Humans
Animals
*Neanderthals
Cognition/physiology
Biological Evolution
Symbolism
Cultural Evolution

@article {pmid39801370,
year = {2025},
author = {Sandroni, V and Chaumette, B},
title = {Understanding the Emergence of Schizophrenia in the Light of Human Evolution: New Perspectives in Genetics.},
journal = {Genes, brain, and behavior},
volume = {24},
number = {1},
pages = {e70013},
doi = {10.1111/gbb.70013},
pmid = {39801370},
issn = {1601-183X},
support = {//Institut National de la Santé et de la Recherche Médicale/ ; //Agence Régionale de Santé Île-de-France/ ; //Agence Nationale de la Recherche/ ; //French Congress of Psychiatry/ ; },
mesh = {Humans ; *Schizophrenia/genetics ; Animals ; Biological Evolution ; Evolution, Molecular ; Hominidae/genetics ; },
abstract = {Schizophrenia is a frequent and disabling disease. The persistence of the disorder despite its harmful consequences represents an evolutionary paradox. Based on recent discoveries in genetics, scientists have formulated the "price-to-pay" hypothesis: schizophrenia would be intimately related to human evolution, particularly to brain development and human-specific higher cognitive functions. The objective of the present work is to question scientific literature about the relationship between schizophrenia and human evolution from a genetic point of view. In the last two decades, research investigated the association between schizophrenia and a few genetic evolutionary markers: Human accelerated regions, segmental duplications, and highly repetitive DNA such as the Olduvai domain. Other studies focused on the action of natural selection on schizophrenia-associated genetic variants, also thanks to the complete sequencing of archaic hominins' genomes (Neanderthal, Denisova). Results suggested that a connection between human evolution and schizophrenia may exist; nonetheless, much research is still needed, and it is possible that a definitive answer to the evolutionary paradox of schizophrenia will never be found.},
}

Humans
*Schizophrenia/genetics
Animals
Biological Evolution
Evolution, Molecular
Hominidae/genetics

@article {pmid39788103,
year = {2025},
author = {Kun, E and Sohail, M and Narasimhan, VM},
title = {The trait-specific timing of accelerated genomic change in the human lineage.},
journal = {Cell genomics},
volume = {5},
number = {1},
pages = {100740},
doi = {10.1016/j.xgen.2024.100740},
pmid = {39788103},
issn = {2666-979X},
mesh = {Humans ; Animals ; *Genome-Wide Association Study ; Neanderthals/genetics ; Evolution, Molecular ; Genome, Human/genetics ; Macaca mulatta/genetics ; Phenotype ; Genomics/methods ; Epigenesis, Genetic ; },
abstract = {Humans exhibit distinct characteristics compared to our primate and ancient hominin ancestors. To investigate genomic bursts in the evolution of these traits, we use two complementary approaches to examine enrichment among genome-wide association study loci spanning diseases and AI-based image-derived brain, heart, and skeletal tissue phenotypes with genomic regions reflecting four evolutionary divergence points. These regions cover epigenetic differences among humans and rhesus macaques, human accelerated regions (HARs), ancient selective sweeps, and Neanderthal-introgressed alleles. Skeletal traits such as pelvic width and limb proportions showed enrichment in evolutionary annotations that mirror morphological changes in the primate fossil record. Additionally, we observe enrichment of loci associated with the longitudinal fasciculus in human-gained epigenetic elements since macaques, the visual cortex in HARs, and the thalamus proper in Neanderthal-introgressed alleles, implying that associated cognitive functions such as language processing, decision-making, sensory signaling, and motor control are enriched at different evolutionary depths.},
}

Humans
Animals
*Genome-Wide Association Study
Neanderthals/genetics
Evolution, Molecular
Genome, Human/genetics
Macaca mulatta/genetics
Phenotype
Genomics/methods
Epigenesis, Genetic

@article {pmid39766821,
year = {2024},
author = {Shimada, MK and Nishida, T},
title = {Haplotype-Based Approach Represents Locus Specificity in the Genomic Diversification Process in Humans (Homo sapiens).},
journal = {Genes},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/genes15121554},
pmid = {39766821},
issn = {2073-4425},
support = {23101506, 20H05139, 22H04454, 18K06452, 21K06366//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Haplotypes ; *Genome, Human ; *Neanderthals/genetics ; Evolution, Molecular ; Animals ; Genomics/methods ; Genetics, Population ; Genetic Variation ; },
abstract = {BACKGROUND/OBJECTIVES: Recent progress in evolutionary genomics on human (Homo sapiens) populations has revealed complex demographic events and genomic changes. These include population expansion with complicated migration, substantial population structure, and ancient introgression from other hominins, as well as human characteristics selections. Nevertheless, the genomic regions in which such evolutionary events took place have remained unclear.

METHODS: Here, we focused on eight loci containing the haplotypes that were previously presented as atypical for the mutation pattern in sequence and/or geographic distribution pattern with the model of recent African origin, which constitute two major clusters: African only, and global. This was the consensus model before information regarding introgression from Neanderthal (Homo neanderthalensis) was available. We compared diversity in identical datasets of the modern human population genome, with the 1000 Genomes project among them.

RESULTS/CONCLUSIONS: This study identified representative genomic regions that show traces of various demographic events and genomic changes that modern humans have undergone by categorizing the relationships in sequence similarity and in worldwide geographic distribution among haplotypes.},
}

Humans
*Haplotypes
*Genome, Human
*Neanderthals/genetics
Evolution, Molecular
Animals
Genomics/methods
Genetics, Population
Genetic Variation

@article {pmid39765216,
year = {2025},
author = {Stringer, C},
title = {Human evolution: The lonely Neanderthal?.},
journal = {Current biology : CB},
volume = {35},
number = {1},
pages = {R29-R31},
doi = {10.1016/j.cub.2024.11.043},
pmid = {39765216},
issn = {1879-0445},
mesh = {*Neanderthals/genetics ; Animals ; *Fossils ; *Biological Evolution ; Humans ; France ; },
abstract = {A recently excavated Neanderthal skeleton from southern France has yielded DNA from a distinct lineage, different from other late Neanderthals. This suggests Neanderthals expanded and diversified about 120,000 years ago, and some of that diversity persisted in Europe until near the time of their extinction.},
}

*Neanderthals/genetics
Animals
*Fossils
*Biological Evolution
Humans
France

@article {pmid24146934,
year = {2013},
author = {Lozano, M and Subirà, ME and Aparicio, J and Lorenzo, C and Gómez-Merino, G},
title = {Toothpicking and periodontal disease in a Neanderthal specimen from Cova Foradà site (Valencia, Spain).},
journal = {PloS one},
volume = {8},
number = {10},
pages = {e76852},
pmid = {24146934},
issn = {1932-6203},
mesh = {Animals ; *Fossils ; Geography ; Humans ; Maxilla/pathology ; Neanderthals ; Periodontal Diseases/*pathology ; Spain ; Tooth/*pathology ; },
abstract = {We present a Neanderthal maxilla (CF-1) from Cova Foradà site (Oliva, Valencia, Spain) with periodontal disease and evidence of attempts to alleviate pain with the use of a toothpick. Two interproximal grooves have been found on the distal surfaces of the upper left Pm(3) and M(1) of CF-1 maxilla. The location, morphology and size of the grooves coincide with other interproximal grooves found on the teeth of other fossil specimens. Heavy dental wear and periodontal disease would have caused the Cova Foradà Neanderthal specimen pain and discomfort, which the individual attempted to mitigate using some kind of dental probe.},
}

Animals
*Fossils
Geography
Humans
Maxilla/pathology
Neanderthals
Periodontal Diseases/*pathology
Spain
Tooth/*pathology

@article {pmid39729880,
year = {2024},
author = {Henrion, J and Maureille, B and Beauval, C and Vanderesse, N and Hublin, JJ and Hardy, M},
title = {The Grotte du Bison Neandertals (Arcy-sur-Cure, France).},
journal = {Journal of human evolution},
volume = {199},
number = {},
pages = {103631},
doi = {10.1016/j.jhevol.2024.103631},
pmid = {39729880},
issn = {1095-8606},
abstract = {The Grotte du Bison, in Arcy-sur-Cure (Yonne, France), yielded a large assemblage of 49 Neandertal remains from late Mousterian layers, offering critical insights for the study of Middle to Upper Paleolithic populations of Western Europe. Previous studies described the external morphology of 13 isolated teeth and a partial maxilla. Building on this previous work, the current study provides further descriptions and analyses of the remains, including one postcranial fragment, six cranial fragments, two maxillary fragments, and 40 isolated teeth. The dental remains are examined for a more detailed assessment of the metric and nonmetric variability of their external and internal morphologies. We focus our description on preservation, health status, and age at death, and we assess the minimum number of individuals. The dental variability is also compared to that of Middle and Upper Pleistocene hominins. Our results indicate that the collection represents at least nine to 17 individuals, comprising mostly children and adolescents. Five to seven pairings are identified based on shared dental traits, developmental criteria, such as perikymata and pitted hypoplasia, wear patterns, and taphonomic alterations. This collection exhibits characteristic Neandertal features, including occasionally markedly expressed traits (e.g., I[1] and P[3] ridging and tubercular expressions), as well as a homogenous expression of accessory structures (particularly for the molars). The highest morphological variability is observed on maxillary premolar roots, which display different stages of root fusion, mesially placed hypercementosis, and pulp cavity extension. This collection also reflects the morphological and behavioral diversity observed in the other Arcy-sur-Cure caves.},
}

@article {pmid39672950,
year = {2024},
author = {Tournebize, R and Chikhi, L},
title = {Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {39672950},
issn = {2397-334X},
support = {ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events-such as ancient bottlenecks or admixture-is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation.},
}

@article {pmid39672157,
year = {2024},
author = {Li, Q and Faux, P and Wentworth Winchester, E and Yang, G and Chen, Y and Ramírez, LM and Fuentes-Guajardo, M and Poloni, L and Steimetz, E and Gonzalez-José, R and Acuña, V and Bortolini, MC and Poletti, G and Gallo, C and Rothhammer, F and Rojas, W and Zheng, Y and Cox, JC and Patel, V and Hoffman, MP and Ding, L and Peng, C and Cotney, J and Navarro, N and Cox, TC and Delgado, M and Adhikari, K and Ruiz-Linares, A},
title = {PITX2 expression and Neanderthal introgression in HS3ST3A1 contribute to variation in tooth dimensions in modern humans.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.11.027},
pmid = {39672157},
issn = {1879-0445},
abstract = {Dental morphology varies greatly throughout evolution, including in the human lineage, but little is known about the biology of this variation. Here, we use multiomics analyses to examine the genetics of variation in tooth crown dimensions. In a human cohort with mixed continental ancestry, we detected genome-wide significant associations at 18 genome regions. One region includes EDAR, a gene known to impact dental features in East Asians. Furthermore, we find that EDAR variants increase the mesiodistal diameter of all teeth, following an anterior-posterior gradient of decreasing strength. Among the 17 novel-associated regions, we replicate 7/13 in an independent human cohort and find that 4/12 orthologous regions affect molar size in mice. Two association signals point to compelling candidate genes. One is ∼61 kb from PITX2, a major determinant of tooth development. Another overlaps HS3ST3A1, a paralogous neighbor of HS3ST3B1, a tooth enamel knot factor. We document the expression of Pitx2 and Hs3st3a1 in enamel knot and dental epithelial cells of developing mouse incisors. Furthermore, associated SNPs in PITX2 and HS3ST3A1 overlap enhancers active in these cells, suggesting a role for these SNPs in gene regulation during dental development. In addition, we document that Pitx2 and Hs3st3a1/Hs3st3b1 knockout mice show alterations in dental morphology. Finally, we find that associated SNPs in HS3ST3A1 are in a DNA tract introgressed from Neanderthals, consistent with an involvement of HS3ST3A1 in tooth size variation during human evolution.},
}

@article {pmid39667410,
year = {2024},
author = {Sümer, AP and Rougier, H and Villalba-Mouco, V and Huang, Y and Iasi, LNM and Essel, E and Mesa, AB and Furtwaengler, A and Peyrégne, S and de Filippo, C and Rohrlach, AB and Pierini, F and Mafessoni, F and Fewlass, H and Zavala, EI and Mylopotamitaki, D and Bianco, RA and Schmidt, A and Zorn, J and Nickel, B and Patova, A and Posth, C and Smith, GM and Ruebens, K and Sinet-Mathiot, V and Stoessel, A and Dietl, H and Orschiedt, J and Kelso, J and Zeberg, H and Bos, KI and Welker, F and Weiss, M and McPherron, S and Schüler, T and Hublin, JJ and Velemínský, P and Brůžek, J and Peter, BM and Meyer, M and Meller, H and Ringbauer, H and Hajdinjak, M and Prüfer, K and Krause, J},
title = {Earliest modern human genomes constrain timing of Neanderthal admixture.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-024-08420-x},
pmid = {39667410},
issn = {1476-4687},
abstract = {Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals[1-4]. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlatý kůň, Czechia[3] and Bacho Kiro, Bulgaria[2]. Here we deepen our understanding of early modern humans by analyzing one high-coverage genome and five low-coverage genomes from ~45,000 year-old remains from Ilsenhöhle in Ranis, Germany[4], and a further high-coverage genome from Zlatý kůň. We show that distant familial relationships link the Ranis and Zlatý kůň individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbor Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to ~45,000-49,000 years ago. This implies that ancestors of all non-Africans sequenced to-date resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.},
}

@article {pmid39667186,
year = {2024},
author = {López-Rey, JM and García-Martínez, D and Bastir, M},
title = {Shanidar 3 'rings the bell': Virtual ribcage reconstruction and its implications for understanding the Neanderthal bauplan.},
journal = {Journal of human evolution},
volume = {199},
number = {},
pages = {103629},
doi = {10.1016/j.jhevol.2024.103629},
pmid = {39667186},
issn = {1095-8606},
abstract = {The study of the ribcage is fundamental to understanding hominin evolution. However, ribs and vertebrae are scarce in the fossil record. Although Neanderthals are one of the most represented and, therefore, one of the most studied fossil Homo species, it is controversial whether there is a standardized Neanderthal ribcage morphotype that could differ from modern humans. Hence, we used three-dimensional geometric morphometrics to reconstruct and compare the Neanderthal ribcage of Shanidar 3 with another Neanderthal specimen, Kebara 2, and with 58 Homo sapiens individuals of worldwide distribution. Shape differences among the Neanderthal and H. sapiens ribcages were analyzed by a hierarchical cluster using the Euclidean distances among the permuted Procrustes distances between groups. Size differences between the Neanderthal and H. sapiens ribcages were examined using a permutation test on centroid size. To examine the potential for allometry, we performed a linear regression of Procrustes coordinates on centroid size of the sample, followed by a principal component analysis in form space. Our results show that Shanidar 3 has the 'bell-shaped' thorax typically described for Neanderthals. In fact, the shapes of both Shanidar 3 and Kebara 2 ribcages cluster apart from that of H. sapiens, being closer to cold-adapted individuals. The study of the centroid size supports similarities between Neanderthals and cold-adapted H. sapiens since significant size differences were found only between Neanderthals and temperate/tropical recent humans. The linear regression and principal component analysis showed an allometric relationship between ribcage size and shape, suggesting Neanderthals had larger and stockier ribcages than most H. sapiens, although they fall within the H. sapiens range of variation. Finally, ribcage similarities found between Shanidar 3 and Kebara 2, both inhabiting warm Levantine locations during the Upper Pleistocene, could challenge the conventional idea of a cold-adapted bauplan in Neanderthals.},
}

@article {pmid39666853,
year = {2024},
author = {Iasi, LNM and Chintalapati, M and Skov, L and Mesa, AB and Hajdinjak, M and Peter, BM and Moorjani, P},
title = {Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6727},
pages = {eadq3010},
doi = {10.1126/science.adq3010},
pmid = {39666853},
issn = {1095-9203},
mesh = {*Neanderthals/genetics ; Animals ; *Gene Flow ; Humans ; *Genome, Human ; *Selection, Genetic ; DNA, Ancient/analysis ; },
abstract = {Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. We generated a catalog of Neanderthal ancestry segments in more than 300 genomes spanning the past 50,000 years. We examined how Neanderthal ancestry is shared among individuals over time. Our analysis revealed that the vast majority of Neanderthal gene flow is attributable to a single, shared extended period of gene flow that occurred between 50,500 to 43,500 years ago, as evidenced by ancestry correlation, colocalization of Neanderthal segments across individuals, and divergence from the sequenced Neanderthals. Most natural selection-positive and negative-on Neanderthal variants occurred rapidly after the gene flow. Our findings provide new insights into how contact with Neanderthals shaped modern human origins and adaptation.},
}

*Neanderthals/genetics
Animals
*Gene Flow
Humans
*Genome, Human
*Selection, Genetic
DNA, Ancient/analysis

@article {pmid39577372,
year = {2024},
author = {Tagore, D and Akey, JM},
title = {Archaic hominin admixture and its consequences for modern humans.},
journal = {Current opinion in genetics & development},
volume = {90},
number = {},
pages = {102280},
doi = {10.1016/j.gde.2024.102280},
pmid = {39577372},
issn = {1879-0380},
abstract = {As anatomically modern humans dispersed out of Africa, they encountered and mated with now extinct hominins, including Neanderthals and Denisovans. It is now well established that all non-African individuals derive approximately 2% of their genome from Neanderthal ancestors and individuals of Melanesian and Australian aboriginal ancestry inherited an additional 2%-5% of their genomes from Denisovan ancestors. Attention has started to shift from documenting amounts of archaic admixture and identifying introgressed segments to understanding their molecular, phenotypic, and evolutionary consequences and refining models of human history. Here, we review recent insights into admixture between modern and archaic humans, emphasizing methodological innovations and the functional and phenotypic effects Neanderthal and Denisovan sequences have in contemporary individuals.},
}

@article {pmid39565777,
year = {2024},
author = {Richards, MP and Mannino, MA and Jaouen, K and Dozio, A and Hublin, JJ and Peresani, M},
title = {Correction: Strontium isotope evidence for Neanderthal and modern human mobility at the upper and middle palaeolithic site of Fumane Cave (Italy).},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0314425},
pmid = {39565777},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0254848.].},
}

@article {pmid39523570,
year = {2024},
author = {Lozano, M and Soler, J and López-Onaindia, D and Solés, A and Julià, R and Ceperuelo, D and Lorenzo, C and Soler, N},
title = {Middle Pleistocene teeth from Arbreda Cave (Serinyà, northeastern Iberian Peninsula).},
journal = {American journal of biological anthropology},
volume = {185},
number = {4},
pages = {e25037},
doi = {10.1002/ajpa.25037},
pmid = {39523570},
issn = {2692-7691},
support = {PACEA-UMR5199//EVODIBIO and EURAPAL/ ; PID2021-122355NB-C32//the Spanish Ministry of Science and Innovation through the "María de Maeztu" excellence accreditation (CEX2019-000945- M), from the FEDER/Ministerio de Ciencia e Innovación-Agencia Estatal de Investigación/ ; N°895713Neander-TALe//Marie Skłodowska-Curie Actions/ ; CLT009/18/00092//Departament de Cultura de la Generalitat de Catalunya/ ; IdEx "Investments for the Future" program / GPR Hu//University of Bordeaux/ ; POS_2019_1_0024//Basque Government postdoctoral Fellowship/ ; 2017SGR-1688//AGAUR/ ; 22021SGR01239//AGAUR/ ; },
mesh = {Spain ; Animals ; *Neanderthals/anatomy & histology ; *Fossils ; Humans ; *Caves ; *Tooth/anatomy & histology/chemistry ; Adult ; Infant ; Paleodontology ; X-Ray Microtomography ; Molar/anatomy & histology/chemistry ; },
abstract = {OBJECTIVES: We report the discovery and description of three human teeth from the Middle Paleolithic archaeological levels of Arbreda Cave (Serinyà, Catalonia, NE Iberian Peninsula).

MATERIALS AND METHODS: The teeth, two molars (one right dm2 and one right M2) from Level N (older than 120 kyr) and one P[3] from Level J (dated between 71 and 44 kyr), were morphologically described based on microCT images and compared with Neanderthal and Homo sapiens specimens.

RESULTS: The teeth belong to a minimum of three individuals: one adult and one infant from Level N and one juvenile from Level J. The premolar from Mousterian Level J, the best preserved of the three teeth, exhibits characteristics to those from our comparative sample of Homo neanderthalensis, such as the crown measurements, EDJ traits, enamel thickness and volume of the pulp cavity.

DISCUSSION: In contrast to the clear Neanderthal characteristics observed in the P[3] from Level J, the high degree of dental wear and poor state of preservation precludes definitive taxonomic designations of the two teeth from Level N. However, the crown dimensions and some tissue proportions are consistent with a probable assignation to Homo neanderthalensis. The teeth from Level N come from a context of long and recurrent occupations of the cave, whereas the archaeological context of the tooth from Level J is indicative of short and seasonal occupations of the cave, which may indicate a change in the lifestyle strategies of the last Neanderthals of the Iberian Peninsula.},
}

Spain
Animals
*Neanderthals/anatomy & histology
*Fossils
Humans
*Caves
*Tooth/anatomy & histology/chemistry
Adult
Infant
Paleodontology
X-Ray Microtomography
Molar/anatomy & histology/chemistry

@article {pmid39502191,
year = {2024},
author = {Pilliol, V and Mahmoud Abdelwadoud, B and Aïcha, H and Lucille, T and Gérard, A and Hervé, T and Michel, D and Ghiles, G and Elodie, T},
title = {Methanobrevibacter oralis: a comprehensive review.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2415734},
pmid = {39502191},
issn = {2000-2297},
abstract = {Methanobrevibacter oralis (M. oralis) has predominated human oral microbiota methanogenic archaea as far back as the Palaeolithic era in Neanderthal populations and gained dominance from the 18[th] century onwards. M. oralis was initially isolated from dental plaque samples collected from two apparently healthy individuals allowing its first characterization. The culture of M. oralis is fastidious and has been the subject of several studies to improve its laboratory growth. Various PCR methods are used to identify M. oralis, targeting either the 16S rRNA gene or the mcrA gene. However, only one RTQ-PCR system, based on a chaperonin gene, offers specificity, and allows for microbial load quantification. Next-generation sequencing contributed five draft genomes, each approximately 2.08 Mb (±0.052 Mb) with a 27.82 (±0.104) average GC%, and two ancient metagenomic assembled genomes. M. oralis was then detected in various oral cavity sites in healthy individuals and those diagnosed with oral pathologies, notably periodontal diseases, and endodontic infections. Transmission pathways, possibly involving maternal milk and breastfeeding, remain to be clarified. M. oralis was further detected in brain abscesses and respiratory tract samples, bringing its clinical significance into question. This review summarizes the current knowledge about M. oralis, emphasizing its prevalence, associations with dysbiosis and pathologies in oral and extra-oral situations, and symbiotic relationships, with the aim of paving the way for further investigations.},
}

@article {pmid39501127,
year = {2024},
author = {Ongaro, L and Huerta-Sanchez, E},
title = {A history of multiple Denisovan introgression events in modern humans.},
journal = {Nature genetics},
volume = {56},
number = {12},
pages = {2612-2622},
pmid = {39501127},
issn = {1546-1718},
mesh = {Humans ; Animals ; *Genome, Human ; *Hominidae/genetics ; *Fossils ; Genetic Introgression ; Neanderthals/genetics ; Phylogeny ; Selection, Genetic ; Evolution, Molecular ; Biological Evolution ; Genetics, Population ; },
abstract = {The identification of a new hominin group in the Altai mountains called Denisovans was one of the most exciting discoveries in human evolution in the last decade. Unlike Neanderthal remains, the Denisovan fossil record consists of only a finger bone, jawbone, teeth and skull fragments. Leveraging the surviving Denisovan segments in modern human genomes has uncovered evidence of at least three introgression events from distinct Denisovan populations into modern humans in the past. Each of them presents different levels of relatedness to the sequenced Altai Denisovan, indicating a complex relationship between these sister lineages. Here we review the evidence suggesting that several Denisovan populations, who likely had an extensive geographical range, were adapted to distinct environments and introgressed into modern humans multiple times. We further discuss how archaic variants have been affected by demographic history, negative and positive selection and close by proposing possible new lines of future research.},
}

Humans
Animals
*Genome, Human
*Hominidae/genetics
*Fossils
Genetic Introgression
Neanderthals/genetics
Phylogeny
Selection, Genetic
Evolution, Molecular
Biological Evolution
Genetics, Population

@article {pmid39429655,
year = {2024},
author = {Farhud, DD and Azari, M and Rahbar, M},
title = {Tuberculosis in Human Bones from 4000 Years Ago, Iran.},
journal = {Iranian journal of public health},
volume = {53},
number = {9},
pages = {2103-2112},
pmid = {39429655},
issn = {2251-6093},
abstract = {BACKGROUND: Tuberculosis is caused by a bacterium called Mycobacterium tuberculosis, which is a contagious and infectious disease; in the first stage, it destroys the lungs and in the next stage other body organs, such as the spine and long bones. This disease is transmitted through an infected person and due to the weakness of the immune system, the infection intensifies. Tuberculosis has two stages: low activity and high activity. In this article, we have discussed the signs of tuberculosis destruction with high intensity on the bones of prehistory human remains.

METHODS: The examples of our research are related to human remains from the ancient cemetery of 4000 years ago from Sagezabad region of Qazvin Province of Iran. That period of history coincides with the Iron Age 2 and 3 in the region. People inside the Sagezabad cemetery were very near to early urban (the late rural) society.

RESULTS: By matching the form of bone destruction with international atlases for tuberculosis, we have reached a satisfactory result in this article. Due to the strong penetration of the infection into the bones, destruction in the remains was high, so it has simplified the diagnosis for us.

CONCLUSION: We found tuberculosis among the bones. This common ancient disease existed even among Neanderthals.},
}

@article {pmid39357284,
year = {2024},
author = {Fuchs, J and García-Tabernero, A and Rosas, A and Camus, H and Metz, L and Slimak, L and Zanolli, C},
title = {The dentition of a new adult Neanderthal individual from Grotte Mandrin, France.},
journal = {Journal of human evolution},
volume = {196},
number = {},
pages = {103599},
doi = {10.1016/j.jhevol.2024.103599},
pmid = {39357284},
issn = {1095-8606},
mesh = {*Neanderthals/anatomy & histology/genetics ; Animals ; France ; *Fossils/anatomy & histology ; Male ; Tooth/anatomy & histology ; Dentition ; X-Ray Microtomography ; },
abstract = {Grotte Mandrin is located in the middle Rhône River Valley, in Mediterranean France, and has yielded 11 Pleistocene archeological and paleoanthropological layers (ranging from the oldest layer J to the youngest layer B) dating from Marine Isotope Stage (MIS) 5 to MIS 3. We report here the nearly complete dentition of an adult Neanderthal individual, nicknamed 'Thorin,' associated to the last phase of the Post-Neronian II, in layer B2 (∼44.50-42.25 ka). A previous paleogenetic analysis revealed that Thorin is a male individual and that he shows a deep genetic divergence with other penecontemporaneous Neanderthals from western Europe that possibly occurred ∼105 ka. The 31 teeth of Thorin (including two distomolars) are described and analyzed using microcomputed tomography imaging and are compared with other Neanderthals and modern humans. Based on direct observation and measurements on the fossil remains, and using microtomographic imaging, tooth wear, nonmetric characters, crown dimensions, and dental tissue proportions were investigated, and the shape of the enamel-dentine junction of the M[2], M2, and M3 was analyzed by geometric morphometrics. Our results indicate that Thorin's teeth show dental characteristics typical of MIS 5-3 Neanderthals. It is also the first time that the presence of two distomolars is reported in a Neanderthal individual, a trait that is rare among modern human populations. Combined with the genetic peculiarities of this individual, the results of the present study imply either a process of morphological convergence among the latest Neanderthal groups or an underestimation of the genetic variability of recent Neanderthal groups.},
}

*Neanderthals/anatomy & histology/genetics
Animals
France
*Fossils/anatomy & histology
Male
Tooth/anatomy & histology
Dentition
X-Ray Microtomography

@article {pmid39333171,
year = {2024},
author = {Sánchez-Yustos, P and Marín-Arroyo, AB and Arnold, LJ and Luque, L and Kehl, M and López-Sáez, JA and Carrancho Alonso, Á and Demuro, M and Sanz-Royo, A and Buckley, M and Maíllo-Fernández, JM and Cuartero-Monteagudo, F and Llamazares-González, J and Ruiz-Alonso, M and Luelmo-Lautenschlaeger, R and García-Soto, E and Alcaraz-Castaño, M},
title = {Initial Upper Palaeolithic lithic industry at Cueva Millán in the hinterlands of Iberia.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21705},
pmid = {39333171},
issn = {2045-2322},
support = {818299//the European Research Council/ ; 805478/ERC_/European Research Council/International ; },
mesh = {*Archaeology ; Animals ; Humans ; *Neanderthals ; Spain ; Fossils/history ; Industry/history ; History, Ancient ; },
abstract = {The extended period of coexistence between Neanderthals and Homo sapiens in Europe coincided with the emergence of regionally distinctive lithic industries, signalling the onset of the Upper Palaeolithic. The Iberian Peninsula was on the periphery of pioneering Upper Palaeolithic developments, with archaeological remains primarily found in northern territories. We report the discovery of an initial Upper Palaeolithic lithic industry at Cueva Millán in the hinterlands of Iberia. This industry, termed here Arlanzian, not only represents the earliest and southernmost evidence of such industries in Iberia but also lacks a direct counterpart. However, it exhibits chronological and technological parallels with the lithic industries associated with the earliest expansion of Homo sapiens throughout Eurasia. We interpret this as potential evidence of its intrusive nature, but not necessarily associated with a migration event, as more complex scenarios derived from inter-population connectivity must be also considered. The biological identity of the Arlanzian makers remains unknown, but they coexisted with declining Neanderthal groups from neighbouring territories.},
}

*Archaeology
Animals
Humans
*Neanderthals
Spain
Fossils/history
Industry/history
History, Ancient

@article {pmid39288002,
year = {2024},
author = {Relethford, JH},
title = {Craniometric variation and the ancestry of modern humans.},
journal = {American journal of biological anthropology},
volume = {185},
number = {4},
pages = {e25028},
doi = {10.1002/ajpa.25028},
pmid = {39288002},
issn = {2692-7691},
mesh = {Animals ; Female ; Humans ; Male ; Africa South of the Sahara/ethnology ; Anthropology, Physical ; *Cephalometry ; *Neanderthals/genetics ; *Skull/anatomy & histology ; White People ; Sub-Saharan African People ; Asian People ; },
abstract = {OBJECTIVES: Ancient and contemporary DNA provide information about geographic variation in the ancestry of present-day humans. All living populations have ancestry from early Homo sapiens originating in sub-Saharan Africa. Populations of Eurasian descent also have a small amount of Neandertal ancestry. This study examines whether craniometric distances between recent modern human samples reflect this geographic variation in ancestry. Among recent modern humans, Eurasians are expected to be more similar to Neandertals, whereas both sub-Saharan Africans and Eurasians are expected to be equidistant from early H. sapiens.

MATERIALS AND METHODS: Data on 33 craniometric traits from 2524 recent modern humans were compared with data from the literature for Neandertals and early H. sapiens. Mahalanobis distances were computed for each modern specimen to both the Neandertal and early H. sapiens means. These distances were examined for differences between recent humans from sub-Saharan Africa (N = 373) and those of Eurasian descent (N = 2151).

RESULTS: Eurasians as a group are significantly closer than sub-Saharan Africans to Neandertals. There is no significant difference between the distances of sub-Saharan Africans and Eurasians to early H. sapiens.

DISCUSSION: The differences between sub-Saharan Africans and Eurasians for both Neandertals and early H. sapiens are as expected. Although there has been geographic differentiation among recent modern humans, including differences in Neandertal admixture, these differences have not affected overall similarity of recent modern sub-Saharan Africans and Eurasians to the earliest samples of H. sapiens.},
}

Animals
Female
Humans
Male
Africa South of the Sahara/ethnology
Anthropology, Physical
*Cephalometry
*Neanderthals/genetics
*Skull/anatomy & histology
White People
Sub-Saharan African People
Asian People

@article {pmid39271648,
year = {2024},
author = {Higham, T and Frouin, M and Douka, K and Ronchitelli, A and Boscato, P and Benazzi, S and Crezzini, J and Spagnolo, V and McCarty, M and Marciani, G and Falcucci, A and Rossini, M and Arrighi, S and Dominici, C and Devièse, T and Schwenninger, JL and Martini, I and Moroni, A and Boschin, F},
title = {Chronometric data and stratigraphic evidence support discontinuity between Neanderthals and early Homo sapiens in the Italian Peninsula.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8016},
pmid = {39271648},
issn = {2041-1723},
support = {324139//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science-European Research Council)/ ; },
mesh = {*Neanderthals ; Italy ; Animals ; Humans ; *Bayes Theorem ; *Fossils ; Radiometric Dating/methods ; Archaeology/methods ; History, Ancient ; },
abstract = {The process by which Palaeolithic Europe was transformed from a Neanderthal-dominated region to one occupied exclusively by Homo sapiens has proven challenging to diagnose. A blurred chronology has made it difficult to determine when Neanderthals disappeared and whether modern humans overlapped with them. Italy is a crucial region because here we can identify not only Late Mousterian industries, assumed to be associated with Neanderthals, but also early Upper Palaeolithic industries linked with the appearance of early H. sapiens, such as the Uluzzian and the Aurignacian. Here, we present a chronometric dataset of 105 new determinations (74 radiocarbon and 31 luminescence ages) from four key southern Italian sites: Cavallo, Castelcivita, Cala, and Oscurusciuto. We built Bayesian-based chronometric models incorporating these results alongside the relative stratigraphic sequences at each site. The results suggest; 1) that the disappearance of Neanderthals probably pre-dated the appearance of early modern humans in the region and; 2) that there was a partial overlap in the chronology of the Uluzzian and Protoaurignacian, suggesting that these industries may have been produced by different human groups in Europe.},
}

*Neanderthals
Italy
Animals
Humans
*Bayes Theorem
*Fossils
Radiometric Dating/methods
Archaeology/methods
History, Ancient

@article {pmid39265525,
year = {2024},
author = {Slimak, L and Vimala, T and Seguin-Orlando, A and Metz, L and Zanolli, C and Joannes-Boyau, R and Frouin, M and Arnold, LJ and Demuro, M and Devièse, T and Comeskey, D and Buckley, M and Camus, H and Muth, X and Lewis, JE and Bocherens, H and Yvorra, P and Tenailleau, C and Duployer, B and Coqueugniot, H and Dutour, O and Higham, T and Sikora, M},
title = {Long genetic and social isolation in Neanderthals before their extinction.},
journal = {Cell genomics},
volume = {4},
number = {9},
pages = {100593},
pmid = {39265525},
issn = {2666-979X},
mesh = {*Neanderthals/genetics ; Animals ; *Fossils ; Social Isolation ; Humans ; Genome ; Extinction, Biological ; France ; },
abstract = {Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations' structure that mostly indicates that late European Neanderthals belonged to a single metapopulation with no significant evidence of population structure. Here, we report the discovery of a late Neanderthal individual, nicknamed "Thorin," from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of Neanderthal final technological traditions in this region ∼50-42 thousand years ago. Thorin's genome reveals a relatively early divergence of ∼105 ka with other late Neanderthals. Thorin belonged to a population with a small group size that showed no genetic introgression with other known late European Neanderthals, revealing some 50 ka of genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the disappearance of the Neanderthals.},
}

*Neanderthals/genetics
Animals
*Fossils
Social Isolation
Humans
Genome
Extinction, Biological
France

@article {pmid39261722,
year = {2024},
author = {Sun, W and Yang, T and Sun, F and Liu, P and Gao, J and Lan, X and Xu, W and Pang, Y and Li, T and Li, C and Liang, Q and Chen, H and Liu, X and Tan, W and Zhu, H and Wang, F and Cheng, F and Zhai, W and Kim, HN and Zhang, J and Zhang, L and Lu, L and Xi, Q and Deng, G and Huang, Y and Jin, X and Chen, X and Liu, W},
title = {An IGHG1 variant exhibits polarized prevalence and confers enhanced IgG1 antibody responses against life-threatening organisms.},
journal = {Nature immunology},
volume = {25},
number = {10},
pages = {1809-1819},
pmid = {39261722},
issn = {1529-2916},
support = {2021YFC2300503//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2021YFC2302403//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32141004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81825010//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81930061//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; Animals ; *Immunoglobulin G/immunology ; *COVID-19/immunology/genetics ; *SARS-CoV-2/immunology ; Mice ; *Immunoglobulin Heavy Chains/genetics/immunology ; Linkage Disequilibrium ; Antibody Formation/genetics/immunology ; Haplotypes ; Memory B Cells/immunology ; Female ; Genetic Variation ; Male ; },
abstract = {Evolutionary pressures sculpt population genetics, whereas immune adaptation fortifies humans against life-threatening organisms. How the evolution of selective genetic variation in adaptive immune receptors orchestrates the adaptation of human populations to contextual perturbations remains elusive. Here, we show that the G396R coding variant within the human immunoglobulin G1 (IgG1) heavy chain presents a concentrated prevalence in Southeast Asian populations. We uncovered a 190-kb genomic linkage disequilibrium block peaked in close proximity to this variant, suggestive of potential Darwinian selection. This variant confers heightened immune resilience against various pathogens and viper toxins in mice. Mechanistic studies involving severe acute respiratory syndrome coronavirus 2 infection and vaccinated individuals reveal that this variant enhances pathogen-specific IgG1[+] memory B cell activation and antibody production. This G396R variant may have arisen on a Neanderthal haplotype background. These findings underscore the importance of an IGHG1 variant in reinforcing IgG1 antibody responses against life-threatening organisms, unraveling the intricate interplay between human evolution and immune adaptation.},
}

Humans
Animals
*Immunoglobulin G/immunology
*COVID-19/immunology/genetics
*SARS-CoV-2/immunology
Mice
*Immunoglobulin Heavy Chains/genetics/immunology
Linkage Disequilibrium
Antibody Formation/genetics/immunology
Haplotypes
Memory B Cells/immunology
Female
Genetic Variation
Male

@article {pmid39241178,
year = {2024},
author = {Caporale, AL and Cinalli, AR and Rubinstein, M and Franchini, LF},
title = {The Human Accelerated Region HAR202 Controls NPAS3 Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences.},
journal = {Molecular biology and evolution},
volume = {41},
number = {10},
pages = {},
pmid = {39241178},
issn = {1537-1719},
support = {//Agencia Nacional de Promoción Científica y Tecnológica/ ; },
mesh = {Animals ; Humans ; *Prosencephalon/metabolism ; *Nerve Tissue Proteins/genetics/metabolism ; *Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism ; Mice ; *Zebrafish/genetics ; *Enhancer Elements, Genetic ; Evolution, Molecular ; Mice, Transgenic ; Gene Expression Regulation, Developmental ; },
abstract = {It has been proposed that the phenotypic differences in cognitive abilities between humans and our closest living relatives, chimpanzees, are largely due to changes in the regulation of neurodevelopmental genes. We have previously found that the neurodevelopmental transcription factor gene NPAS3 accumulates the largest number of human accelerated regions (HARs), suggesting it may play some role in the phenotypic evolution of the human nervous system. In this work, we performed a comparative functional analysis of NPAS3-HAR202 using enhancer reporter assays in transgenic zebrafish and mice. We found that the Homo sapiens HAR202 ortholog failed to drive reporter expression to the zebrafish nervous system, in high contrast to the strong expression displayed by the rest of the vertebrate ortholog sequences tested. Remarkably, the HAR202 ortholog from archaic humans (Neanderthals/Denisovans) also displayed a pan-vertebrate expression pattern, despite the fact that archaic and modern humans have only one nucleotide substitution. Moreover, similar results were found when comparing enhancer activity in transgenic mice, where we observed a loss of activity of the modern human version in the mouse developing brain. To investigate the functional importance of HAR202, we generated mice lacking HAR202 and found a remarkable decrease of Npas3 expression in the forebrain during development. Our results place HAR202 as one of the very few examples of a neurodevelopmental transcriptional enhancer displaying functional evolution in the brain as a result of a fast molecular evolutionary process that specifically occurred in the human lineage.},
}

Animals
Humans
*Prosencephalon/metabolism
*Nerve Tissue Proteins/genetics/metabolism
*Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism
Mice
*Zebrafish/genetics
*Enhancer Elements, Genetic
Evolution, Molecular
Mice, Transgenic
Gene Expression Regulation, Developmental

@article {pmid39227658,
year = {2024},
author = {Richard, M and Del Val, M and Fewlass, H and Sinet-Mathiot, V and Lanos, P and Pons-Branchu, E and Puaud, S and Hublin, JJ and Moncel, MH},
title = {Multi-method dating reveals 200 ka of Middle Palaeolithic occupation at Maras rock shelter, Rhône Valley, France.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20474},
pmid = {39227658},
issn = {2045-2322},
mesh = {*Neanderthals ; *Archaeology ; Animals ; *Radiometric Dating/methods ; France ; Humans ; Fossils ; Tooth/anatomy & histology ; Geologic Sediments/analysis ; Bayes Theorem ; Bone and Bones/anatomy & histology ; Electron Spin Resonance Spectroscopy/methods ; Uranium/analysis ; History, Ancient ; },
abstract = {The emergence of the Middle Palaeolithic, and its variability over time and space are key questions in the field of prehistoric archaeology. Many sites have been documented in the south-eastern margins of the Massif central and the middle Rhône valley, a migration path that connects Northern Europe with the Mediterranean. Well-dated, long stratigraphic sequences are essential to understand Neanderthals dynamics and demise, and potential interactions with Homo sapiens in the area, such as the one displayed at the Maras rock shelter ("Abri du Maras"). The site is characterised by exceptional preservation of archaeological remains, including bones dated using radiocarbon ([14]C) and teeth using electron spin resonance combined with uranium series (ESR/U-series). Optically stimulated luminescence was used to date the sedimentary deposits. By combining the new ages with previous ones using Bayesian modelling, we are able to clarify the occupation time over a period spanning 200,000 years. Between ca. 250 and 40 ka, the site has been used as a long-term residence by Neanderthals, specifically during three interglacial periods: first during marine isotopic stage (MIS) 7, between 247 ± 34 and 223 ± 33 ka, and then recurrently during MIS 5 (between 127 ± 17 and 90 ± 9 ka) and MIS 3 (up to 39,280 cal BP).},
}

*Neanderthals
*Archaeology
Animals
*Radiometric Dating/methods
France
Humans
Fossils
Tooth/anatomy & histology
Geologic Sediments/analysis
Bayes Theorem
Bone and Bones/anatomy & histology
Electron Spin Resonance Spectroscopy/methods
Uranium/analysis
History, Ancient

@article {pmid39227643,
year = {2024},
author = {Guran, SH and Yousefi, M and Kafash, A and Ghasidian, E},
title = {Reconstructing contact and a potential interbreeding geographical zone between Neanderthals and anatomically modern humans.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20475},
pmid = {39227643},
issn = {2045-2322},
support = {402379177//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Neanderthals ; Animals ; Humans ; *Fossils ; Archaeology ; Geography ; },
abstract = {While the interbreeding of Homo neanderthalensis (hereafter Neanderthal) and Anatomically modern human (AMH) has been proven, owing to the shortage of fossils and absence of appropriate DNA, the timing and geography of their interbreeding are not clearly known. In this study, we applied ecological niche modelling (maximum entropy approach) and GIS to reconstruct the palaeodistribution of Neanderthals and AMHs in Southwest Asia and Southeast Europe and identify their contact and potential interbreeding zone during marine isotope stage 5 (MIS 5), when the second wave of interbreeding occurred. We used climatic variables characterizing the environmental conditions of MIS 5 ca. 120 to 80 kyr (averaged value) along with the topography and coordinates of Neanderthal and modern human archaeological sites to characterize the palaeodistribution of each species. Overlapping the models revealed that the Zagros Mountains were a contact and potential interbreeding zone for the two human species. We believe that the Zagros Mountains acted as a corridor connecting the Palearctic/Afrotropical realms, facilitating northwards dispersal of AMHs and southwards dispersal of Neanderthals during MIS 5. Our analyses are comparable with archaeological and genetic evidence collected during recent decades.},
}

*Neanderthals
Animals
Humans
*Fossils
Archaeology
Geography

@article {pmid39160167,
year = {2024},
author = {Mateo-Lomba, P and Ollé, A and Fernández-Marchena, JL and Saladié, P and Marín, J and Chacón, MG and Vallverdú, J and Cáceres, I},
title = {First identification of a Neanderthal bone spear point through an interdisciplinary analysis at Abric Romaní (NE Iberian Peninsula).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19160},
pmid = {39160167},
issn = {2045-2322},
support = {CEX2019-000945-M//Spanish Ministry of Science and Innovation/ ; PID2021-122355NB-C32//MCIN/AEI/10.13039/501100011033 and by ERDF A way of making Europe/ ; PID2022-138590NB-C41//MCIN/AEI/10.13039/501100011033 and by ERDF A way of making Europe/ ; SGR 2021 01239//AGAUR/ ; SGR 2021 01237//AGAUR/ ; SGR 2021 01238//AGAUR/ ; 2023PFR-URV-01239//URV/ ; URV, 2023PFR-URV-0127//URV/ ; 2022PFR-URV- 64//URV/ ; 2023PFR-URV-01238//URV/ ; PRE2019-087734//MICINN/ ; ARQ001SOL-201-2022//Departament de Cultura of the Generalitat de Catalunya/ ; CIAPOS/2022/022//Generalitat Valenciana/ ; },
mesh = {Animals ; *Neanderthals/anatomy & histology ; Spain ; *Fossils ; *Bone and Bones/anatomy & histology ; *Archaeology ; Humans ; History, Ancient ; },
abstract = {Osseous industry has been observed at an increasing number of Neanderthal sites. Bone fragments were used for practical purposes, and a range of bone shaping techniques were employed. The variability of bone tools observed in different assemblages reflects considerable functional diversity. However, no bone spear points have been reported from these contexts. A comprehensive analysis of a bone spear point from the Middle Palaeolithic site of Abric Romaní (Barcelona, Spain) is presented. Through an interdisciplinary, multi-technique, and multi-scale approach combining technology, taphonomy, and functional analysis, compelling evidence for manufacture, use, and hafting was uncovered. The specimen exhibits clear signs of intentional knapping. The presence of microscopic linear impact marks, an impact fracture at the tip and potential internal stress fractures indicate its use as a spear. Furthermore, the observed wear pattern and a morphological adjustment of the trabecular tissue support the hafting hypothesis. Abric Romaní contributes to our understanding of Neanderthal hunting behaviour and the significance of composite bone tools in their technological repertoire 50,000 years ago. This discovery highlights the flexibility and adaptability of Neanderthal technology, providing evidence of bone technology that is sometimes obscured in the archaeological record and offering valuable insights into their hunting strategies during the Middle Palaeolithic.},
}

Animals
*Neanderthals/anatomy & histology
Spain
*Fossils
*Bone and Bones/anatomy & histology
*Archaeology
Humans
History, Ancient

@article {pmid39144742,
year = {2024},
author = {Zhao, W},
title = {Reconstructing human history from ancient genomes: an interview with Nobel laureate Svante Pääbo.},
journal = {National science review},
volume = {11},
number = {9},
pages = {nwae120},
doi = {10.1093/nsr/nwae120},
pmid = {39144742},
issn = {2053-714X},
abstract = {Professor Svante Pääbo, Director of the Max Planck Institute for Evolutionary Anthropology, won the Nobel Prize in Physiology or Medicine in 2022 for his discoveries in ancient hominine genomes and human evolution. His pioneering work in sequencing and interpreting the paleo genomes of Neanderthals and Denisovans, as well as their relationship with the modern human genome, was groundbreaking in terms of our understanding of human origins. Nowadays, we can even use commercial kits to easily detect the proportion of Neanderthal genes in our own genomes. Recently, NSR conducted an interview with Professor Pääbo to learn about his interesting work chasing the ancient genomes and reconstructing human evolutionary and migration history from the DNA evidence, as well as his perspective on paleo genome studies and his advice to young researchers: follow your interests and be ready to try some crazy things.},
}

@article {pmid39132848,
year = {2024},
author = {Richards, GD and Jabbour, RS and Guipert, G and Defleur, A},
title = {Early Neanderthal mandibular remains from Baume Moula-Guercy (Soyons, Ardèche).},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25550},
pmid = {39132848},
issn = {1932-8494},
support = {03-Activity-059//Arthur A. Dugoni/ ; },
abstract = {We provide an ontogenetically-based comparative description of mandibular remains from Last Interglacial deposits (MIS 5e) at Baume Moula-Guercy and examine their affinities to European and Middle Eastern Middle-to-Late Pleistocene (≈MIS 14-MIS 1) Homo. Description of the M-G2-419 right partial mandibular corpus with M1-3 (15-16.0 years ±0.5 years) and mandibular fragments M-F4-77 and M-S-TNN1 is with reference to original fossils, casts, CT scans, literature descriptions, and virtual reconstructions. Our comparative sample is ontogenetically based and divided into a Preneanderthal-Neanderthal group and a Homo sapiens group. These groups are subdivided into (1) Preneanderthals (≈MIS 14-9), Early Neanderthals (MIS 7-5e), and Late Neanderthals (MIS 5d-3), and (2) Middle (MIS 5) and Upper (MIS 3-Pre-MIS 1) Paleolithic and recent H. sapiens. Standard techniques were employed for developmental age and sex determinations and measurements. The M-G2-419 mandible possesses corpus features that link it most closely with the Sima de los Huesos Preneanderthal and Early Neanderthal groups. These include mental foramen position, number, and height on the corpus, anterior marginal tubercle position, and mylohyoid line orientation. Metrically, the M-G2-419 mandibular corpus is small relative to adults in all groups, but the thickness/height relationship is like the adult condition. The thickness of the corpus is more like Neanderthal children than adolescents. Molar crown features suggest affinities with the Preneanderthal-Neanderthal group. The Moula-Guercy mandibles possess a combination of Neanderthal-associated features that provides insights into MIS 7-5e paleodeme variation and the timing of appearance of MIS 5d-3 Neanderthal facial features.},
}

@article {pmid39091830,
year = {2024},
author = {Pfennig, A and Lachance, J},
title = {The evolutionary fate of Neanderthal DNA in 30,780 admixed genomes with recent African-like ancestry.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39091830},
issn = {2692-8205},
support = {R35 GM133727/GM/NIGMS NIH HHS/United States ; },
abstract = {Following introgression, Neanderthal DNA was initially purged from non-African genomes, but the evolutionary fate of remaining introgressed DNA has not been explored yet. To fill this gap, we analyzed 30,780 admixed genomes with African-like ancestry from the All of Us research program, in which Neanderthal alleles encountered novel genetic backgrounds during the last 15 generations. Observed amounts of Neanderthal DNA approximately match expectations based on ancestry proportions, suggesting neutral evolution. Nevertheless, we identified genomic regions that have significantly less or more Neanderthal ancestry than expected and are associated with spermatogenesis, innate immunity, and other biological processes. We also identified three novel introgression desert-like regions in recently admixed genomes, whose genetic features are compatible with hybrid incompatibilities and intrinsic negative selection. Overall, we find that much of the remaining Neanderthal DNA in human genomes is not under strong selection, and complex evolutionary dynamics have shaped introgression landscapes in our species.},
}

@article {pmid39032165,
year = {2024},
author = {Seghi, F and Sorrentino, R and Bailey, SE and Piccirilli, E and Vazzana, A and Bortolini, E and Higgins, OA and Marciani, G and Orlando, MA and Spinapolice, EE and Moroni, A and Benazzi, S},
title = {Morphological and morphometric study of the hominin dental casts from Grotta-Riparo di Uluzzo C (Apulia, southern Italy).},
journal = {American journal of biological anthropology},
volume = {185},
number = {1},
pages = {e24998},
doi = {10.1002/ajpa.24998},
pmid = {39032165},
issn = {2692-7691},
support = {European Union - Next Generation EU PRIN 2022 TRAC//European Commission/ ; PNRR PE5 - CHANGES - SPOKE 5//European Commission/ ; European Union - Next Generation EU PRIN 2022 TRACE//European Commission/ ; },
mesh = {Italy ; Animals ; *Fossils ; *Hominidae/anatomy & histology ; Humans ; Tooth, Deciduous/anatomy & histology ; Neanderthals/anatomy & histology ; Tooth/anatomy & histology ; Molar/anatomy & histology ; Paleodontology ; Models, Dental ; },
abstract = {OBJECTIVES: Grotta-Riparo di Uluzzo C (Apulia, southern Italy) is a pivotal site for investigating the evolution of the Middle Paleolithic and the earliest phases of the Upper Paleolithic in southern Italy, as the extensive stratigraphic record of this site includes a thick Mousterian sequence followed by the Uluzzian. Here, we investigate the taxonomic affinity of seven unpublished deciduous human teeth retrieved from the site of Uluzzo C in 1960.

MATERIALS AND METHODS: The teeth are represented by seven plaster dental casts, which are housed at the Museo Civico di Paleontologia e Paletnologia in Maglie (Lecce, Apulia). The location of the original specimens remains unknown, rendering these casts the only human remains evidence yielded by Uluzzo C to date. Based on occlusal-view photographs and digital models of the casts, we examined the external morphology and morphometry of the teeth, comparing them to Homo sapiens and H. neanderthalensis samples. Through geometric morphometric methods and statistical analyses, we analyzed the crown outline of the deciduous molars.

RESULTS: The teeth show morphological and morphometric features that are variably found in H. neanderthalensis, H. sapiens, or both. Specifically, crown outline analysis shows that all molars fall within H. neanderthalensis variability, except for Uluzzo 853 (lower right deciduous first molar), which falls within H. sapiens variability.

DISCUSSION: This study provides the first taxonomic assessment of the hominin teeth from Uluzzo C. The results contribute additional insights into the Paleolithic peopling of southern Italy during a crucial period marked by the persistence of post-Tyrrhenian Neanderthal techno-complexes and the arrival of H. sapiens.},
}

Italy
Animals
*Fossils
*Hominidae/anatomy & histology
Humans
Tooth, Deciduous/anatomy & histology
Neanderthals/anatomy & histology
Tooth/anatomy & histology
Molar/anatomy & histology
Paleodontology
Models, Dental

@article {pmid39029412,
year = {2024},
author = {Dodat, PJ and Albalat, E and Balter, V and Couture-Veschambre, C and Hardy, M and Henrion, J and Holliday, T and Maureille, B},
title = {Diverse bone-calcium isotope compositions in Neandertals suggest different dietary strategies.},
journal = {Journal of human evolution},
volume = {193},
number = {},
pages = {103566},
doi = {10.1016/j.jhevol.2024.103566},
pmid = {39029412},
issn = {1095-8606},
mesh = {Animals ; *Neanderthals ; *Diet ; *Bone and Bones/chemistry ; *Calcium Isotopes/analysis ; France ; Fossils ; },
abstract = {Zooarcheological and geochemical evidence suggests Neanderthals were top predators, but their adherence to a strictly carnivorous diet has been questioned. Recent studies have demonstrated the potential of calcium-stable isotopes to evaluate trophic and ecological relationships. Here, we measure the δ[44/42]Ca values in bone samples from Mousterian contexts at Grotte du Bison (Marine Isotope Stage 3, Yonne, France) and Regourdou (Marine Isotope Stage 5, Dordogne, France) in two new Neanderthal individuals, associated fauna, and living local plants. We use a Bayesian mixing model to estimate the dietary composition of these Neanderthal individuals, plus a third one already analyzed. The results reveal three distinct diets: a diet including accidental or voluntary consumption of bone-based food, an intermediate diet, and a diet without consumption of bone-based food. This finding is the first demonstration of diverse subsistence strategies among Neanderthals and as such, reconciles archaeological and geochemical dietary evidence.},
}

Animals
*Neanderthals
*Diet
*Bone and Bones/chemistry
*Calcium Isotopes/analysis
France
Fossils

@article {pmid39011558,
year = {2024},
author = {Ma, X and Lu, Y and Xu, S},
title = {Adaptive Evolution of Two Distinct Adaptive Haplotypes of Neanderthal Origin at the Immunoglobulin Heavy-chain Locus in East Asian and European Populations.},
journal = {Molecular biology and evolution},
volume = {41},
number = {7},
pages = {},
pmid = {39011558},
issn = {1537-1719},
support = {2023YFC2605400//National Key Research and Development Program of China/ ; 32030020//National Natural Science Foundation of China/ ; //Office of Global Partnerships/ ; //Human Phenome Data Center of Fudan University/ ; },
mesh = {*Neanderthals/genetics ; Animals ; *Haplotypes ; Humans ; Europe ; Asia, Eastern ; Asian People/genetics ; Immunoglobulin Heavy Chains/genetics ; White People/genetics ; Evolution, Molecular ; Genetic Introgression ; Selection, Genetic ; East Asian People ; },
abstract = {Immunoglobulins (Igs) have a crucial role in humoral immunity. Two recent studies have reported a high-frequency Neanderthal-introgressed haplotype throughout Eurasia and a high-frequency Neanderthal-introgressed haplotype specific to southern East Asia at the immunoglobulin heavy-chain (IGH) gene locus on chromosome 14q32.33. Surprisingly, we found the previously reported high-frequency Neanderthal-introgressed haplotype does not exist throughout Eurasia. Instead, our study identified two distinct high-frequency haplotypes of putative Neanderthal origin in East Asia and Europe, although they shared introgressed alleles. Notably, the alleles of putative Neanderthal origin reduced the expression of IGHG1 and increased the expression of IGHG2 and IGHG3 in various tissues. These putatively introgressed alleles also affected the production of IgG1 upon antigen stimulation and increased the risk of systemic lupus erythematosus. Additionally, the greatest genetic differentiation across the whole genome between southern and northern East Asians was observed for the East Asian haplotype of putative Neanderthal origin. The frequency decreased from southern to northern East Asia and correlated positively with the genome-wide proportion of southern East Asian ancestry, indicating that this putative positive selection likely occurred in the common ancestor of southern East Asian populations before the admixture with northern East Asian populations.},
}

*Neanderthals/genetics
Animals
*Haplotypes
Humans
Europe
Asia, Eastern
Asian People/genetics
Immunoglobulin Heavy Chains/genetics
White People/genetics
Evolution, Molecular
Genetic Introgression
Selection, Genetic
East Asian People

@article {pmid38997559,
year = {2024},
author = {Eisenstein, M},
title = {Neanderthal-human baby-making was recent - and brief.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-024-01452-3},
pmid = {38997559},
issn = {1476-4687},
}

@article {pmid38991054,
year = {2024},
author = {Li, L and Comi, TJ and Bierman, RF and Akey, JM},
title = {Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6705},
pages = {eadi1768},
doi = {10.1126/science.adi1768},
pmid = {38991054},
issn = {1095-9203},
mesh = {Animals ; Humans ; *Gene Flow ; Genetic Introgression ; *Genome, Human ; *Neanderthals/genetics ; Population Density ; Whole Genome Sequencing ; Extinction, Biological ; },
abstract = {Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.},
}

Animals
Humans
*Gene Flow
Genetic Introgression
*Genome, Human
*Neanderthals/genetics
Population Density
Whole Genome Sequencing
Extinction, Biological

@article {pmid38956433,
year = {2024},
author = {Yaghmouri, M and Safdari Lord, J and Amini, M and Yekaninejad, MS and Izadi, P},
title = {The association of rs17713054 with Neanderthal origin at 3p21.31 locus with the severity of COVID-19 in Iranian patients.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {15058},
pmid = {38956433},
issn = {2045-2322},
support = {58558//Tehran University of Medical Sciences/ ; },
mesh = {Humans ; *COVID-19/genetics/virology/epidemiology ; Iran/epidemiology ; *Neanderthals/genetics ; Male ; Female ; *Polymorphism, Single Nucleotide ; Middle Aged ; *Severity of Illness Index ; *Genetic Predisposition to Disease ; Animals ; *SARS-CoV-2/genetics/isolation & purification ; Adult ; Haplotypes ; Chromosomes, Human, Pair 3/genetics ; Alleles ; Genome-Wide Association Study ; Genotype ; Aged ; },
abstract = {Since the COVID-19 pandemic, the diversity of clinical manifestations in patients has been a tremendous challenge. It seems that genetic variations, as one of the players, contribute to the variety of symptoms. Genome-wide association studies have demonstrated the influence of certain genomic regions on the disease prognosis. Particularly, a haplotype at 3p21.31 locus, inherited from Neanderthals, showed an association with COVID-19 severity. Despite several studies regarding this haplotype, some key variants are not sufficiently addressed. In the present study, we investigated the association of rs17713054 at 3p21.31 with COVID-19 severity. We analyzed the genotype of 251 Iranian COVID-19 patients (151 patients with asymptomatic to mild form as control and 100 patients with severe to critical symptoms without any comorbidities as case group) using the ARMS-PCR method. Results demonstrated that the A allele confers an almost twofold increased risk for COVID-19 severity (P value = 0.008). The AA genotype also raises the risk by more than 11 times following the recessive model (P value = 0.013). In conclusion, the A allele in rs17713054 was a risk allele in Iranian patients and was independently associated with COVID-19 severity. More studies are beneficial to confirm these findings in other populations and to develop strategies for risk assessment, prevention, and personalized medicine.},
}

Humans
*COVID-19/genetics/virology/epidemiology
Iran/epidemiology
*Neanderthals/genetics
Male
Female
*Polymorphism, Single Nucleotide
Middle Aged
*Severity of Illness Index
*Genetic Predisposition to Disease
Animals
*SARS-CoV-2/genetics/isolation & purification
Adult
Haplotypes
Chromosomes, Human, Pair 3/genetics
Alleles
Genome-Wide Association Study
Genotype
Aged

@article {pmid38932149,
year = {2024},
author = {Ferreira, RC and Alves, GV and Ramon, M and Antoneli, F and Briones, MRS},
title = {Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data.},
journal = {Viruses},
volume = {16},
number = {6},
pages = {},
pmid = {38932149},
issn = {1999-4915},
support = {20/08943-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; },
mesh = {Animals ; *Neanderthals/genetics/virology ; *Genome, Viral ; *DNA, Ancient/analysis ; Evolution, Molecular ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Humans ; Phylogeny ; DNA Viruses/genetics/classification/isolation & purification ; Fossils/virology ; },
abstract = {DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10[-5] to 10[-8] substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.},
}

Animals
*Neanderthals/genetics/virology
*Genome, Viral
*DNA, Ancient/analysis
Evolution, Molecular
DNA, Viral/genetics
Sequence Analysis, DNA/methods
Humans
Phylogeny
DNA Viruses/genetics/classification/isolation & purification
Fossils/virology

@article {pmid38924400,
year = {2024},
author = {Conde-Valverde, M and Quirós-Sánchez, A and Diez-Valero, J and Mata-Castro, N and García-Fernández, A and Quam, R and Carretero, JM and García-González, R and Rodríguez, L and Sánchez-Andrés, Á and Arsuaga, JL and Martínez, I and Villaverde, V},
title = {The child who lived: Down syndrome among Neanderthals?.},
journal = {Science advances},
volume = {10},
number = {26},
pages = {eadn9310},
pmid = {38924400},
issn = {2375-2548},
mesh = {*Down Syndrome/psychology ; Humans ; Animals ; *Neanderthals ; Child ; Female ; Male ; Child, Preschool ; },
abstract = {Caregiving for disabled individuals among Neanderthals has been known for a long time, and there is a debate about the implications of this behavior. Some authors believe that caregiving took place between individuals able to reciprocate the favor, while others argue that caregiving was produced by a feeling of compassion related to other highly adaptive prosocial behaviors. The study of children with severe pathologies is particularly interesting, as children have a very limited possibility to reciprocate the assistance. We present the case of a Neanderthal child who suffered from a congenital pathology of the inner ear, probably debilitating, and associated with Down syndrome. This child would have required care for at least 6 years, likely necessitating other group members to assist the mother in childcare.},
}

*Down Syndrome/psychology
Humans
Animals
*Neanderthals
Child
Female
Male
Child, Preschool

@article {pmid38916350,
year = {2024},
author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G},
title = {Exploring antimicrobial resistance determinants in the Neanderthal microbiome.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0266223},
pmid = {38916350},
issn = {2165-0497},
support = {20/2022-ECR-II//Indian Council of Medical Research (ICMR)/ ; },
mesh = {Animals ; *Microbiota/genetics/drug effects ; *Neanderthals/genetics/microbiology ; *DNA, Ancient/analysis ; *Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; Feces/microbiology ; Metagenome ; Drug Resistance, Microbial/genetics ; Europe ; Fossils/microbiology ; },
abstract = {UNLABELLED: This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.

IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.},
}

Animals
*Microbiota/genetics/drug effects
*Neanderthals/genetics/microbiology
*DNA, Ancient/analysis
*Metagenomics
*Bacteria/genetics/drug effects/classification/isolation & purification
*Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Humans
Feces/microbiology
Metagenome
Drug Resistance, Microbial/genetics
Europe
Fossils/microbiology

@article {pmid38889149,
year = {2024},
author = {Yermakovich, D and André, M and Brucato, N and Kariwiga, J and Leavesley, M and Pankratov, V and Mondal, M and Ricaut, FX and Dannemann, M},
title = {Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {26},
pages = {e2405889121},
pmid = {38889149},
issn = {1091-6490},
support = {TK214//HM | Estonian Research Competency Council (Research Competency Council)/ ; 810645//EC | Horizon Europe | WPSERA | HORIZON EUROPE Reforming and enhancing the European Research and Innovation system (REERIS)/ ; MOBEC008//EC | European Regional Development Fund (ERDF)/ ; PAPUAEVOL 20-CE12-0003-01//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; NA//French Ministry of Foreign and European Affairs/ ; NA//Laboratoire d'Excellence TULIP (Labex TULIP)/ ; NA//Leakey Foundation (The Leakey Foundation)/ ; },
mesh = {Papua New Guinea ; Humans ; Animals ; *Haplotypes ; *Neanderthals/genetics ; Adaptation, Physiological/genetics ; Genetics, Population ; },
abstract = {Neandertals and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 y, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that PNG highlanders carry higher levels of Denisovan DNA compared to PNG lowlanders. Among the Denisovan-like haplotypes with higher frequencies in highlander populations, those exhibiting the greatest frequency difference compared to lowlander populations also demonstrate more pronounced differences in population frequencies than frequency-matched nonarchaic variants. Two of the five most highly differentiated of those haplotypes reside in genomic areas linked to brain development genes. Conversely, Denisovan-like haplotypes more frequent in lowlanders overlap with genes associated with immune response processes. Our findings suggest that Denisovan DNA has provided genetic variation associated with brain biology and immune response to PNG genomes, some of which might have facilitated adaptive processes to environmental challenges.},
}

Papua New Guinea
Humans
Animals
*Haplotypes
*Neanderthals/genetics
Adaptation, Physiological/genetics
Genetics, Population

@article {pmid38840007,
year = {2024},
author = {Callaway, E},
title = {These Neanderthal fire pits offer an extraordinarily precise snapshot of ancient life.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38840007},
issn = {1476-4687},
}

@article {pmid38802968,
year = {2024},
author = {Roca-Ayats, N and Maceda, I and Bruque, CD and Martínez-Gil, N and Garcia-Giralt, N and Cozar, M and Mellibovsky, L and Van Hul, W and Lao, O and Grinberg, D and Balcells, S},
title = {Evolutionary and functional analyses of LRP5 in archaic and extant modern humans.},
journal = {Human genomics},
volume = {18},
number = {1},
pages = {53},
pmid = {38802968},
issn = {1479-7364},
support = {SAF 2016-75948R and PID2019-107188RB-C21//Ministerio de Ciencia e Innovación/ ; GRC 2017 SGR 937//Generalitat de Catalunya/ ; 2017SGR:00738//Catalan Government/ ; PGC2018-098574-B-I00//Ministerio de Economía y Competitividad/ ; },
mesh = {Humans ; *Low Density Lipoprotein Receptor-Related Protein-5/genetics ; *Evolution, Molecular ; Animals ; *Neanderthals/genetics ; Selection, Genetic/genetics ; Hominidae/genetics ; Haplotypes/genetics ; Bone Density/genetics ; Genome, Human/genetics ; },
abstract = {BACKGROUND: The human lineage has undergone a postcranial skeleton gracilization (i.e. lower bone mass and strength relative to body size) compared to other primates and archaic populations such as the Neanderthals. This gracilization has been traditionally explained by differences in the mechanical load that our ancestors exercised. However, there is growing evidence that gracilization could also be genetically influenced.

RESULTS: We have analyzed the LRP5 gene, which is known to be associated with high bone mineral density conditions, from an evolutionary and functional point of view. Taking advantage of the published genomes of archaic Homo populations, our results suggest that this gene has a complex evolutionary history both between archaic and living humans and within living human populations. In particular, we identified the presence of different selective pressures in archaics and extant modern humans, as well as evidence of positive selection in the African and South East Asian populations from the 1000 Genomes Project. Furthermore, we observed a very limited evidence of archaic introgression in this gene (only at three haplotypes of East Asian ancestry out of the 1000 Genomes), compatible with a general erasing of the fingerprint of archaic introgression due to functional differences in archaics compared to extant modern humans. In agreement with this hypothesis, we observed private mutations in the archaic genomes that we experimentally validated as putatively increasing bone mineral density. In particular, four of five archaic missense mutations affecting the first β-propeller of LRP5 displayed enhanced Wnt pathway activation, of which two also displayed reduced negative regulation.

CONCLUSIONS: In summary, these data suggest a genetic component contributing to the understanding of skeletal differences between extant modern humans and archaic Homo populations.},
}

Humans
*Low Density Lipoprotein Receptor-Related Protein-5/genetics
*Evolution, Molecular
Animals
*Neanderthals/genetics
Selection, Genetic/genetics
Hominidae/genetics
Haplotypes/genetics
Bone Density/genetics
Genome, Human/genetics

@article {pmid38798350,
year = {2024},
author = {Iasi, LNM and Chintalapati, M and Skov, L and Mesa, AB and Hajdinjak, M and Peter, BM and Moorjani, P},
title = {Neandertal ancestry through time: Insights from genomes of ancient and present-day humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38798350},
issn = {2692-8205},
support = {R35 GM142978/GM/NIGMS NIH HHS/United States ; },
abstract = {Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify the location and size of introgressed Neandertal ancestry segments in more than 300 genomes spanning the last 50,000 years. We study how Neandertal ancestry is shared among individuals to infer the time and duration of the Neandertal gene flow. We find the correlation of Neandertal segment locations across individuals and their divergence to sequenced Neandertals, both support a model of single major Neandertal gene flow. Our catalog of introgressed segments through time confirms that most natural selection-positive and negative-on Neandertal ancestry variants occurred immediately after the gene flow, and provides new insights into how the contact with Neandertals shaped human origins and adaptation.},
}

@article {pmid38782948,
year = {2024},
author = {Limmer, LS and Santon, M and McGrath, K and Harvati, K and El Zaatari, S},
title = {Differences in childhood stress between Neanderthals and early modern humans as reflected by dental enamel growth disruptions.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11293},
pmid = {38782948},
issn = {2045-2322},
support = {353106138//Deutsche Forschungsgemeinschaft/ ; EP/X020819/1//Engineering and Physical Sciences Research Council/ ; State Research Award 2014//Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg/ ; 101019659//H2020 European Research Council/ ; 101001889//H2020 European Research Council/ ; },
mesh = {Animals ; *Neanderthals ; Humans ; *Dental Enamel/growth & development ; Child ; *Dental Enamel Hypoplasia ; Bayes Theorem ; Child, Preschool ; Male ; Fossils ; Female ; Stress, Physiological ; Infant ; },
abstract = {Neanderthals' lives were historically portrayed as highly stressful, shaped by constant pressures to survive in harsh ecological conditions, thus potentially contributing to their extinction. Recent work has challenged this interpretation, leaving the issue of stress among Paleolithic populations highly contested and warranting in-depth examination. Here, we analyze the frequency of dental enamel hypoplasia, a growth disruption indicator of early life stress, in the largest sample of Neanderthal and Upper Paleolithic dentitions investigated to date for these features. To track potential species-specific patterns in the ontogenetic distribution of childhood stress, we present the first comprehensive Bayesian modelling of the likelihood of occurrence of individual and matched enamel growth disruptions throughout ontogeny. Our findings support similar overall stress levels in both groups but reveal species-specific patterns in its ontogenetic distribution. While Neanderthal children faced increasing likelihoods of growth disruptions starting with the weaning process and culminating in intensity post-weaning, growth disruptions in Upper Paleolithic children were found to be limited around the period of weaning and substantially dropping after its expected completion. These results might, at least in part, reflect differences in childcare or other behavioral strategies between the two taxa, including those that were advantageous for modern humans' long-term survival.},
}

Animals
*Neanderthals
Humans
*Dental Enamel/growth & development
Child
*Dental Enamel Hypoplasia
Bayes Theorem
Child, Preschool
Male
Fossils
Female
Stress, Physiological
Infant

@article {pmid38782905,
year = {2024},
author = {Yee, SW and Ferrández-Peral, L and Alentorn-Moron, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Wolfreys, FD and Yang, J and Gestwicki, JE and Capra, JA and Artursson, P and Newman, JW and Marquès-Bonet, T and Giacomini, KM},
title = {Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4380},
pmid = {38782905},
issn = {2041-1723},
support = {GM117163//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 EY032161/EY/NEI NIH HHS/United States ; R01 GM139875/GM/NIGMS NIH HHS/United States ; GM139875//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM117163/GM/NIGMS NIH HHS/United States ; EY032161//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; },
mesh = {Animals ; Humans ; Amino Acid Sequence ; Estradiol/metabolism ; HEK293 Cells ; Hominidae/genetics/metabolism ; Mutation, Missense ; Organic Cation Transport Proteins/metabolism/genetics ; *Primates/genetics ; Pseudogenes ; Substrate Specificity ; },
abstract = {SLC22A10 is an orphan transporter with unknown substrates and function. The goal of this study is to elucidate its substrate specificity and functional characteristics. In contrast to orthologs from great apes, human SLC22A10, tagged with green fluorescent protein, is not expressed on the plasma membrane. Cells expressing great ape SLC22A10 orthologs exhibit significant accumulation of estradiol-17β-glucuronide, unlike those expressing human SLC22A10. Sequence alignments reveal a proline at position 220 in humans, which is a leucine in great apes. Replacing proline with leucine in SLC22A10-P220L restores plasma membrane localization and uptake function. Neanderthal and Denisovan genomes show proline at position 220, akin to modern humans, indicating functional loss during hominin evolution. Human SLC22A10 is a unitary pseudogene due to a fixed missense mutation, P220, while in great apes, its orthologs transport sex steroid conjugates. Characterizing SLC22A10 across species sheds light on its biological role, influencing organism development and steroid homeostasis.},
}

Animals
Humans
Amino Acid Sequence
Estradiol/metabolism
HEK293 Cells
Hominidae/genetics/metabolism
Mutation, Missense
Organic Cation Transport Proteins/metabolism/genetics
*Primates/genetics
Pseudogenes
Substrate Specificity

@article {pmid38779339,
year = {2024},
author = {Gennai, J},
title = {The Mousterian in North-Western Tuscany: publishing fieldwork documentation leads to a new stratigraphical interpretation of the Piano di Mommio sites.},
journal = {Open research Europe},
volume = {4},
number = {},
pages = {37},
pmid = {38779339},
issn = {2732-5121},
abstract = {BACKGROUND: The Mousterian technocomplex is commonly associated with Neanderthals and therefore serves as a proxy for their presence across Europe. Stratified archaeological sites are the most informative because they can yield information about artefacts' spatial distribution and dating. Only a few of the Mousterian sites in Tuscany (Italy) met these conditions and most of these sites are concentrated in the North-Western area, with three specific sites situated in proximity to the village of Piano di Mommio, on the slopes of a small river canyon. Nevertheless, research on the sites stopped early on due to their small extent and complete excavation, which does not allow for additional fieldwork.

METHODS: This article presents previously unpublished field notes, reports, and images, which are then correlated with recent archaeological surveys.

RESULTS: This combination of historical and contemporary data aims to provide a more detailed understanding of the context in which the assemblages at these sites were found. The insights gained from this research shed light on the arrangement and positioning of artefacts at these locations, offering valuable information to guide future investigations on the assemblages.

CONCLUSIONS: The proposed stratigraphical interpretation adheres to the available information and therefore contributes to a future baseline for new research on the sites and on Neanderthal presence in the area.},
}

@article {pmid38778167,
year = {2024},
author = {Marinelli, F and Moncel, MH and Lemorini, C},
title = {The use of bones as tools in Late Lower Paleolithic of Central Italy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11666},
pmid = {38778167},
issn = {2045-2322},
support = {ANR-19-CE27-0011-01//Neandroots project/ ; },
mesh = {Italy ; Animals ; *Fossils ; *Bone and Bones ; *Archaeology ; Humans ; Neanderthals ; Hominidae ; History, Ancient ; Tool Use Behavior ; },
abstract = {The Latium area in Italy has yielded rich evidence of Lower Paleolithic sites with both faunal remains, artefacts, and human fossil remains, such as the Ceprano human skull. Many are the sites where lithic industry has been found in association with bone industry. Medium and large animals were a key resource because they provided an enormous amount of meat and fat. However, they were extensively exploited for their bones, rich in marrow, and as raw material for tool production. Bone tools are so far few documented for early period of time and especially for the Middle Pleistocene in Western Europe. We report here evidence of bone tools and their efficiency of use for hominin groups living in the Frosinone-Ceprano basin during the MIS 11/10, a key period which records behavioral innovations and onset of the Neanderthal behaviors. In three sites, Isoletta, Colle Avarone and Selvotta, several bone tools and bone flakes have been discovered (MIS 11/10). They were associated to stone artefacts part of the hominins tool-kit. Technological and use-wear analyses conducted on these bone industries, dated between 410 and 430 ka, yield relevant results to understand the effectiveness of the bones tools found associated with lithic series, including handaxes.},
}

Italy
Animals
*Fossils
*Bone and Bones
*Archaeology
Humans
Neanderthals
Hominidae
History, Ancient
Tool Use Behavior

@article {pmid38771659,
year = {2024},
author = {Hubáček, JA and Šedová, L and Hellerová, V and Adámková, V and Tóthová, V},
title = {Increased prevalence of the COVID-19 associated Neanderthal mutations in the Central European Roma population.},
journal = {Annals of human biology},
volume = {51},
number = {1},
pages = {2341727},
doi = {10.1080/03014460.2024.2341727},
pmid = {38771659},
issn = {1464-5033},
mesh = {Humans ; *COVID-19/genetics/epidemiology ; *Roma/genetics ; Male ; *SARS-CoV-2 ; Female ; Animals ; *Neanderthals/genetics ; Mutation ; Middle Aged ; Czech Republic/epidemiology ; Adult ; Prevalence ; 2',5'-Oligoadenylate Synthetase/genetics ; Genetic Predisposition to Disease ; Polymorphism, Single Nucleotide ; Transcription Factors/genetics ; Aged ; },
abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and subsequent COVID-19 has spread world-wide and become pandemic with about 7 million deaths reported so far. Interethnic variability of the disease has been described, but a significant part of the differences remain unexplained and may be attributable to genetic factors.

AIM: To analyse genetic factors potentially influencing COVID-19 susceptibility and severity in European Roma minority.

SUBJECTS AND METHODS: Two genetic determinants, within OAS-1 (2-prime,5-prime-oligoadenylate synthetase 1, a key protein in the defence against viral infection; it activates RNases that degrade viral RNAs; rs4767027 has been analysed) and LZTFL1 (leucine zipper transcription factor-like 1, expressed in the lung respiratory epithelium; rs35044562 has been analysed) genes were screened in a population-sample of Czech Roma (N = 302) and majority population (N = 2,559).

RESULTS: For both polymorphisms, Roma subjects were more likely carriers of at least one risky allele for both rs4767027-C (p < 0.001) and rs35044562-G (p < 0.00001) polymorphism. There were only 5.3% Roma subjects without at least one risky allele in comparison with 10.1% in the majority population (p < 0.01).

CONCLUSIONS: It is possible that different genetic background plays an important role in increased prevalence of COVID-19 in the Roma minority.},
}

Humans
*COVID-19/genetics/epidemiology
*Roma/genetics
Male
*SARS-CoV-2
Female
Animals
*Neanderthals/genetics
Mutation
Middle Aged
Czech Republic/epidemiology
Adult
Prevalence
2',5'-Oligoadenylate Synthetase/genetics
Genetic Predisposition to Disease
Polymorphism, Single Nucleotide
Transcription Factors/genetics
Aged

@article {pmid38760502,
year = {2024},
author = {Pauly, R and Johnson, L and Feltus, FA and Casanova, EL},
title = {Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings.},
journal = {Molecular psychiatry},
volume = {29},
number = {11},
pages = {3452-3461},
pmid = {38760502},
issn = {1476-5578},
mesh = {Animals ; Female ; Humans ; Male ; *Autistic Disorder/genetics ; Genetic Association Studies/methods ; *Genetic Predisposition to Disease ; Genome, Human ; Genotype ; Hispanic or Latino/genetics ; *Neanderthals/genetics ; *Polymorphism, Single Nucleotide ; *Siblings ; United States ; White/genetics ; Black or African American/genetics ; },
abstract = {Homo sapiens and Neanderthals underwent hybridization during the Middle/Upper Paleolithic age, culminating in retention of small amounts of Neanderthal-derived DNA in the modern human genome. In the current study, we address the potential roles Neanderthal single nucleotide polymorphisms (SNP) may be playing in autism susceptibility in samples of black non-Hispanic, white Hispanic, and white non-Hispanic people using data from the Simons Foundation Powering Autism Research (SPARK), Genotype-Tissue Expression (GTEx), and 1000 Genomes (1000G) databases. We have discovered that rare variants are significantly enriched in autistic probands compared to race-matched controls. In addition, we have identified 25 rare and common SNPs that are significantly enriched in autism on different ethnic backgrounds, some of which show significant clinical associations. We have also identified other SNPs that share more specific genotype-phenotype correlations but which are not necessarily enriched in autism and yet may nevertheless play roles in comorbid phenotype expression (e.g., intellectual disability, epilepsy, and language regression). These results strongly suggest Neanderthal-derived DNA is playing a significant role in autism susceptibility across major populations in the United States.},
}

Animals
Female
Humans
Male
*Autistic Disorder/genetics
Genetic Association Studies/methods
*Genetic Predisposition to Disease
Genome, Human
Genotype
Hispanic or Latino/genetics
*Neanderthals/genetics
*Polymorphism, Single Nucleotide
*Siblings
United States
White/genetics
Black or African American/genetics

@article {pmid38739836,
year = {2024},
author = {Helmbrecht, N and Lackner, M and Maricic, T and Pääbo, S},
title = {The modern human aryl hydrocarbon receptor is more active when ancestralized by genome editing.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {22},
pages = {e2402159121},
pmid = {38739836},
issn = {1091-6490},
support = {PAABO//NOMIS Stiftung (NOMIS Foundation)/ ; },
mesh = {*Receptors, Aryl Hydrocarbon/genetics/metabolism ; Humans ; *Gene Editing/methods ; Animals ; *Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism ; Evolution, Molecular ; Pan troglodytes/genetics ; Neanderthals/genetics ; Ligands ; },
abstract = {The aryl hydrocarbon receptor (AHR) is a transcription factor that has many functions in mammals. Its best known function is that it binds aromatic hydrocarbons and induces the expression of cytochrome P450 genes, which encode enzymes that metabolize aromatic hydrocarbons and other substrates. All present-day humans carry an amino acid substitution at position 381 in the AHR that occurred after the divergence of modern humans from Neandertals and Denisovans. Previous studies that have expressed the ancestral and modern versions of AHR from expression vectors have yielded conflicting results with regard to their activities. Here, we use genome editing to modify the endogenous AHR gene so that it encodes to the ancestral, Neandertal-like AHR protein in human cells. In the absence of exogenous ligands, the expression of AHR target genes is higher in cells expressing the ancestral AHR than in cells expressing the modern AHR, and similar to the expression in chimpanzee cells. Furthermore, the modern human AHR needs higher doses of three ligands than the ancestral AHR to induce the expression of target genes. Thus, the ability of AHR to induce the expression of many of its target genes is reduced in modern humans.},
}

*Receptors, Aryl Hydrocarbon/genetics/metabolism
Humans
*Gene Editing/methods
Animals
*Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism
Evolution, Molecular
Pan troglodytes/genetics
Neanderthals/genetics
Ligands

@article {pmid38714790,
year = {2024},
author = {Schmidt, P and Tennie, C},
title = {Problems with two recent Petri net analyses of Neanderthal adhesive technology.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10481},
pmid = {38714790},
issn = {2045-2322},
}

@article {pmid38714734,
year = {2024},
author = {Fajardo, S and Kozowyk, PRB and Langejans, GHJ},
title = {Reply to: Problems with two recent Petri net analyses of Neanderthal adhesive technology.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10489},
pmid = {38714734},
issn = {2045-2322},
support = {804151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
}

@article {pmid38683367,
year = {2024},
author = {Mansueto, A and Good, DJ},
title = {Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis.},
journal = {Journal of molecular evolution},
volume = {92},
number = {3},
pages = {266-277},
pmid = {38683367},
issn = {1432-1432},
mesh = {Animals ; *Evolution, Molecular ; *Exons/genetics ; *Phylogeny ; *Primates/genetics ; *Mutation/genetics ; Humans ; *L-Gulonolactone Oxidase/genetics ; *Chromosome Inversion/genetics ; Pseudogenes/genetics ; Conserved Sequence/genetics ; },
abstract = {Ascorbic acid functions as an antioxidant and facilitates other biochemical processes such as collagen triple helix formation, and iron uptake by cells. Animals which endogenously produce ascorbic acid have a functional gulonolactone oxidase gene (GULO); however, humans have a GULO pseudogene (GULOP) and depend on dietary ascorbic acid. In this study, the conservation of GULOP sequences in the primate haplorhini suborder were investigated and compared to the GULO sequences belonging to the primates strepsirrhini suborder. Phylogenetic analysis suggested that the conserved GULOP exons in the haplorhini primates experienced a high rate of mutations following the haplorhini/strepsirrhini divergence. This high mutation rate has decreased during the evolution of the haplorhini primates. Additionally, indels of the haplorhini GULOP sequences were conserved across the suborder. A separate analysis for GULO sequences and well-conserved GULOP sequences focusing on placental mammals identified an in-frame GULO sequence in the Brazilian guinea pig, and a potential GULOP sequence in the pika. Similar to haplorhini primates, the guinea pig and lagomorph species have experienced a high substitution rate when compared to the mammals used in this study. A shared synteny to examine the conservation of local genes near GULO/GULOP identified a conserved inversion around the GULO/GULOP locus between the haplorhini and strepsirrhini primates. Fischer's exact test did not support an association between GULOP and the chromosomal inversion. Mauve alignment showed that the inversion of the length of the syntenic block that the GULO/GULOP genes belonged to was variable. However, there were frequent rearrangements around ~ 2 million base pairs adjacent to GULOP involving the KIF13B and MSRA genes. These data may suggest that genes acquiring deleterious mutations in the coding sequence may respond to these deleterious mutations with rapid substitution rates.},
}

Animals
*Evolution, Molecular
*Exons/genetics
*Phylogeny
*Primates/genetics
*Mutation/genetics
Humans
*L-Gulonolactone Oxidase/genetics
*Chromosome Inversion/genetics
Pseudogenes/genetics
Conserved Sequence/genetics

@article {pmid38658463,
year = {2024},
author = {Yousfi, FZE and Haroun, AE and Nebhani, C and Belayachi, J and Askander, O and Fahime, EE and Fares, H and Ennibi, K and Abouqal, R and Razine, R and Bouhouche, A},
title = {Prevalence of the protective OAS1 rs10774671-G allele against severe COVID-19 in Moroccans: implications for a North African Neanderthal connection.},
journal = {Archives of virology},
volume = {169},
number = {5},
pages = {109},
pmid = {38658463},
issn = {1432-8798},
mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *2',5'-Oligoadenylate Synthetase/genetics ; Africa, Northern ; Alleles ; *COVID-19/genetics/virology/epidemiology ; Gene Frequency ; Genetic Predisposition to Disease ; Genotype ; Haplotypes ; North African People ; *Polymorphism, Single Nucleotide ; Prevalence ; },
abstract = {The clinical presentation of COVID-19 shows high variability among individuals, which is partly due to genetic factors. The OAS1/2/3 cluster has been found to be strongly associated with COVID-19 severity. We examined this locus in the Moroccan population for the occurrence of the critical variant rs10774671 and its respective haplotype blocks. The frequency of single-nucleotide polymorphisms (SNPs) in the cluster of OAS immunity genes in 157 unrelated individuals of Moroccan origin was determined using an in-house exome database. OAS1 exon 6 of 71 SARS-CoV-2-positive individuals with asymptomatic/mild disease and 74 with moderate/severe disease was sequenced by the Sanger method. The genotypic, allelic, and haplotype frequencies of three SNPs were compared between these two groups. Finally, males in our COVID-19 series were genotyped for the Berber-specific marker E-M81. The prevalence of the OAS1 rs10774671-G allele in present-day Moroccans was found to be 40.4%, which is similar to that found in Europeans. However, it was found equally in both the Neanderthal GGG haplotype and the African GAC haplotype, with a frequency of 20% each. These two haplotypes, and hence the rs10774671-G allele, were significantly associated with protection against severe COVID-19 (p = 0.034, p = 0.041, and p = 0.008, respectively). Surprisingly, in men with the Berber-specific uniparental markers, the African haplotype was absent, while the prevalence of the Neanderthal haplotype was similar to that in Europeans. The protective rs10774671-G allele of OAS1 was found only in the Neanderthal haplotype in Berbers, the indigenous people of North Africa, suggesting that this region may have served as a stepping-stone for the passage of hominids to other continents.},
}

Adult
Aged
Female
Humans
Male
Middle Aged
*2',5'-Oligoadenylate Synthetase/genetics
Africa, Northern
Alleles
*COVID-19/genetics/virology/epidemiology
Gene Frequency
Genetic Predisposition to Disease
Genotype
Haplotypes
North African People
*Polymorphism, Single Nucleotide
Prevalence

@article {pmid38638564,
year = {2024},
author = {Chen, S and Tang, D and Deng, L and Xu, S},
title = {Asian-European differentiation of schizophrenia-associated genes driven by admixture and natural selection.},
journal = {iScience},
volume = {27},
number = {5},
pages = {109560},
pmid = {38638564},
issn = {2589-0042},
abstract = {The European-centered genome-wide association studies of schizophrenia (SCZ) may not be well applied to non-European populations. We analyzed 1,592 reported SCZ-associated genes using the public genome data and found an overall higher Asian-European differentiation on the SCZ-associated variants than at the genome-wide level. Notable examples included 15 missense variants, a regulatory variant SLC5A10-rs1624825, and a damaging variant TSPAN18-rs1001292. Independent local adaptations in recent 25,000 years, after the Asian-European divergence, could have contributed to such genetic differentiation, as were identified at a missense mutation LTN1-rs57646126-A in Asians, and a non-risk allele ZSWIM6-rs72761442-G in Europeans. Altai-Neanderthal-derived alleles may have opposite effects on SCZ susceptibility between ancestries. Furthermore, adaptive introgression was detected on the non-risk haplotype at 1q21.2 in Europeans, while in Asians it was observed on the SCZ risk haplotype at 3p21.31 which is also potentially ultra-violet protective. This study emphasizes the importance of including more representative Asian samples in future SCZ studies.},
}

@article {pmid38612593,
year = {2024},
author = {Ferreira, RC and Rodrigues, CR and Broach, JR and Briones, MRS},
title = {Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612593},
issn = {1422-0067},
support = {20/08943-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; },
mesh = {Humans ; Animals ; *Neanderthals/genetics ; *Genome, Mitochondrial ; Mutation ; *Alzheimer Disease ; Nucleotides ; },
abstract = {The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.},
}

Humans
Animals
*Neanderthals/genetics
*Genome, Mitochondrial
Mutation
*Alzheimer Disease
Nucleotides

@article {pmid38565571,
year = {2024},
author = {Yaworsky, PM and Nielsen, ES and Nielsen, TK},
title = {The Neanderthal niche space of Western Eurasia 145 ka to 30 ka ago.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7788},
pmid = {38565571},
issn = {2045-2322},
support = {9062-00027B//Danmarks Frie Forskningsfond/ ; },
mesh = {Animals ; *Neanderthals ; Fossils ; },
abstract = {Neanderthals occupied Western Eurasia between 350 ka and 40 ka ago, during the climatically volatile Pleistocene. A key issue is to what extent Neanderthal populations expanded into areas of Western Eurasia and what conditions facilitated such range expansions. The range extent of Neanderthals is generally based on the distribution of Neanderthal material, but the land-altering nature of glacial periods has erased much of the already sparse material evidence of Neanderthals, particularly in the northern latitudes. To overcome this obstacle species distribution models can estimate past distributions of Neanderthals, however, most implementations are generally constrained spatially and temporally and may be artificially truncating the Neanderthal niche space. Using dated contexts from Neanderthal sites from across Western Eurasia, millennial-scale paleoclimate reconstructions, and a spatiotemporal species distribution model, we infer the fundamental climatic niche space of Neanderthals and estimate the extent of Neanderthal occupation. We find that (a.) despite the long timeframe, Neanderthals occupy a relatively narrow fundamental climatic niche space, (b.) the estimated projected potential Neanderthal niche space suggests a larger geographic range than the material record suggests, and (c.) that there was a general decline in the size of the projected potential Neanderthal niche from 145 ka ago onward, possibly contributing to their extinction.},
}

Animals
*Neanderthals
Fossils

@article {pmid38558123,
year = {2024},
author = {Aneli, S and Ceccatelli Berti, C and Gilea, AI and Birolo, G and Mutti, G and Pavesi, A and Baruffini, E and Goffrini, P and Capelli, C},
title = {Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae.},
journal = {Human molecular genetics},
volume = {33},
number = {13},
pages = {1152-1163},
doi = {10.1093/hmg/ddae057},
pmid = {38558123},
issn = {1460-2083},
support = {//Departments of Excellence/ ; //Italian Ministry for University and Research (MIUR, 2018-2022 and MUR, 2023-2027)/ ; //Programma Nazionale della Ricerca PNR 2021-2027 e PON "Ricerca e Innovazione" 2014-2020-progetti di ricerca su tematiche "Innovazione" e "Green"/ ; RF-2016-02361241//Italian Ministry of Health/ ; //University of Parma/ ; GGP19287A//Italian Telethon Foundation/ ; },
mesh = {Humans ; *Saccharomyces cerevisiae/genetics ; *Neanderthals/genetics ; Animals ; Genetic Variation ; Mitochondria/genetics/metabolism ; Alleles ; Genetic Introgression ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.},
}

Humans
*Saccharomyces cerevisiae/genetics
*Neanderthals/genetics
Animals
Genetic Variation
Mitochondria/genetics/metabolism
Alleles
Genetic Introgression
Saccharomyces cerevisiae Proteins/genetics/metabolism

@article {pmid38552260,
year = {2024},
author = {Rmoutilová, R and Brůžek, J and Gómez-Olivencia, A and Madelaine, S and Couture-Veschambre, C and Holliday, T and Maureille, B},
title = {Sex estimation of the adult Neandertal Regourdou 1 (Montignac, France): Implications for sexing human fossil remains.},
journal = {Journal of human evolution},
volume = {189},
number = {},
pages = {103470},
doi = {10.1016/j.jhevol.2023.103470},
pmid = {38552260},
issn = {1095-8606},
mesh = {Animals ; Humans ; Male ; *Neanderthals/anatomy & histology ; Fossils ; Genomics ; Paleontology ; *Hominidae ; France ; },
abstract = {Sex is a biological trait fundamental to the study of hominin fossils. Among the many questions that can be addressed are those related to taxonomy, biological variability, sexual dimorphism, paleoobstetrics, funerary selection, and paleodemography. While new methodologies such as paleogenomics or paleoproteomics can be used to determine sex, they have not been systematically applied to Pleistocene human remains due to their destructive nature. Therefore, we estimated sex from the coxal bone of the newly discovered pelvic remains of the Regourdou 1 Neandertal (Southwest France, MIS 5) based on morphological and metric data employing two methods that have been recently revised and shown to be reliable in multiple studies. Both methods calculate posterior probabilities of the estimate. The right coxal bone of Regourdou 1 was partially reconstructed providing additional traits for sex estimation. These methods were cross validated on 14 sufficiently preserved coxal bones of specimens from the Neandertal lineage. Our results show that the Regourdou 1 individual, whose postcranial skeleton is not robust, is a male, and that previous sex attributions of comparative Neandertal specimens are largely in agreement with those obtained here. Our results encourage additional morphological research of fossil hominins in order to develop a set of methods that are applicable, reliable, and reproducible.},
}

Animals
Humans
Male
*Neanderthals/anatomy & histology
Fossils
Genomics
Paleontology
*Hominidae
France

@article {pmid38489387,
year = {2024},
author = {Groh, JS and Coop, G},
title = {The temporal and genomic scale of selection following hybridization.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {12},
pages = {e2309168121},
pmid = {38489387},
issn = {1091-6490},
support = {R35 GM136290/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Genome/genetics ; Genomics ; Hybridization, Genetic ; Nucleic Acid Hybridization ; Haplotypes ; *Neanderthals/genetics ; Selection, Genetic ; },
abstract = {Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on the Discrete Wavelet Transform to study the genomic scale of local ancestry variation and its association with recombination rates and show that these methods capture temporal dynamics of drift and genome-wide selection after hybridization. We apply these methods to published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio) and to inferred Neanderthal introgression in modern humans. Across systems, upward of 20% of variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. Signatures of selection at fine genomic scales suggest selection over longer time scales; however, we suggest that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from contiguous segments of genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available and can help shed light on generalities of the genomic consequences of interspecific hybridization.},
}

Animals
Humans
*Genome/genetics
Genomics
Hybridization, Genetic
Nucleic Acid Hybridization
Haplotypes
*Neanderthals/genetics
Selection, Genetic

@article {pmid38477186,
year = {2024},
author = {Pablos, A and Arsuaga, JL},
title = {Tarsals from the Sima de los Huesos Middle Pleistocene site (Atapuerca, Burgos, Spain).},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {307},
number = {7},
pages = {2635-2664},
doi = {10.1002/ar.25425},
pmid = {38477186},
issn = {1932-8494},
support = {PGC2018-093925-B-C33//MCI/AEI/FEDER, UE/ ; PGC2018-093925-B-C31//MCI/AEI/FEDER, UE/ ; PID2021-122355NB-C31//MCIN/AEI/10.13039/501100011033/FEDER, UE/ ; 949330/ERC_/European Research Council/International ; EMERGIA20_00403//Junta de Andalucía, Spain/ ; //Junta de Castilla y León and Fundación Atapuerca/ ; },
mesh = {Animals ; *Fossils/anatomy & histology ; Spain ; *Hominidae/anatomy & histology ; *Biological Evolution ; Tarsal Bones/anatomy & histology ; Neanderthals/anatomy & histology ; Humans ; Male ; Female ; },
abstract = {Here, we provide a complete, updated, and illustrated inventory, as well as a comprehensive study, of the tarsals (rearfoot) recovered from the Middle Pleistocene site of Sima de los Huesos (SH, Atapuerca, Spain) in comparison to other Homo comparative samples, both extant and fossil. The minimum number of individuals (MNI) estimated from the tarsals has been established as 15, which represents 51.7% of the 29 dental individuals identified within the SH sample. Within the SH hominin foot sample, an exclusive combination of primitive or plesiomorphic and derived or autapomorphic traits can be observed when compared with other Homo individuals/populations. Other characters are shared among SH hominins and Neandertals that might represent shared derived or autapomorphic traits for this evolutionary line, and most are likely related to robusticity (e.g., rectangular-like trochlea of the talus, broad calcanei, broad naviculars, and short lateral cuneiforms). Additionally, we observed some exclusive autapomorphic traits in the SH tarsal sample (e.g., narrow head of the talus and short intermediate cuneiforms). A few exclusive traits in SH tarsal remains are even more robust than in Neandertals (e.g., broad lateral malleolar facet in talus, more projected sustentaculum tali, and broad medial cuneiform). These traits could suggest a slightly higher level of gracilization in the tarsal bones of Neandertals compared to the SH sample that is also supported by other anatomical postcranial skeleton elements. Additionally, some paleobiological inferences are made in relation to body size (stature and body mass) and some associations are proposed within the SH sample. In conclusion, the morphology of the SH tarsi confirms an evolutionary relationship of sister groups between this population and Neandertals, probably representing a morphotype similar to the Neandertal ancestors.},
}

Animals
*Fossils/anatomy & histology
Spain
*Hominidae/anatomy & histology
*Biological Evolution
Tarsal Bones/anatomy & histology
Neanderthals/anatomy & histology
Humans
Male
Female

@article {pmid38461589,
year = {2024},
author = {Najafzadeh, A and Hernaiz-García, M and Benazzi, S and Chen, B and Hublin, JJ and Kullmer, O and Pokhojaev, A and Sarig, R and Sorrentino, R and Vazzana, A and Fiorenza, L},
title = {Finite element analysis of Neanderthal and early Homo sapiens maxillary central incisor.},
journal = {Journal of human evolution},
volume = {189},
number = {},
pages = {103512},
doi = {10.1016/j.jhevol.2024.103512},
pmid = {38461589},
issn = {1095-8606},
mesh = {Humans ; Adolescent ; Animals ; *Neanderthals ; Incisor ; Computer Simulation ; Finite Element Analysis ; Crowns ; Stress, Mechanical ; },
abstract = {Neanderthal anterior teeth are very large and have a distinctive morphology characterized by robust 'shovel-shaped' crowns. These features are frequently seen as adaptive responses in dissipating heavy mechanical loads resulting from masticatory and non-masticatory activities. Although the long-standing debate surrounding this hypothesis has played a central role in paleoanthropology, is still unclear if Neanderthal anterior teeth can resist high mechanical loads or not. A novel way to answer this question is to use a multidisciplinary approach that considers together tooth architecture, dental wear and jaw movements. The aim of this study is to functionally reposition the teeth of Le Moustier 1 (a Neanderthal adolescent) and Qafzeh 9 (an early Homo sapiens adolescent) derived from wear facet mapping, occlusal fingerprint analysis and physical dental restoration methods. The restored dental arches are then used to perform finite element analysis on the left central maxillary incisor during edge-to-edge occlusion. The results show stress distribution differences between Le Moustier 1 and Qafzeh 9, with the former displaying higher tensile stress in enamel around the lingual fossa but lower concentration of stress in the lingual aspect of the root surface. These results seem to suggest that the presence of labial convexity, lingual tubercle and of a large root surface in Le Moustier 1 incisor helps in dissipating mechanical stress. The absence of these dental features in Qafzeh 9 is compensated by the presence of a thicker enamel, which helps in reducing the stress in the tooth crown.},
}

Humans
Adolescent
Animals
*Neanderthals
Incisor
Computer Simulation
Finite Element Analysis
Crowns
Stress, Mechanical

@article {pmid38458749,
year = {2024},
author = {Geier, A and Trost, J and Wang, K and Schmid, C and Krawczyk, M and Schiffels, S},
title = {PNPLA3 fatty liver allele was fixed in Neanderthals and segregates neutrally in humans.},
journal = {Gut},
volume = {73},
number = {6},
pages = {1008-1014},
doi = {10.1136/gutjnl-2023-331594},
pmid = {38458749},
issn = {1468-3288},
support = {851511/ERC_/European Research Council/International ; },
mesh = {Animals ; Humans ; *Acyltransferases/genetics ; *Alleles ; DNA, Ancient/analysis ; *Fatty Liver/genetics ; Gene Frequency ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotype ; *Neanderthals/genetics ; *Phospholipases A2, Calcium-Independent/genetics ; },
abstract = {OBJECTIVE: Fat deposition is modulated by environmental factors and genetic predisposition. Genome-wide association studies identified PNPLA3 p.I148M (rs738409) as a common variant that increases risk of developing liver steatosis. When and how this variant evolved in humans has not been studied to date.

DESIGN: Here we analyse ancient DNA to track the history of this allele throughout human history. In total, 6444 published ancient (modern humans, Neanderthal, Denisovan) and 3943 published present day genomes were used for analysis after extracting genotype calls for PNPLA3 p.I148M. To quantify changes through time, logistic and, by grouping individuals according to geography and age, linear regression analyses were performed.

RESULTS: We find that archaic human individuals (Neanderthal, Denisovan) exclusively carried a fixed PNPLA3 risk allele, whereas allele frequencies in modern human populations range from very low in Africa to >50% in Mesoamerica. Over the last 15 000 years, distributions of ancestral and derived alleles roughly match the present day distribution. Logistic regression analyses did not yield signals of natural selection during the last 10 000 years.

CONCLUSION: Archaic human individuals exclusively carried a fixed PNPLA3 allele associated with fatty liver, whereas allele frequencies in modern human populations are variable even in the oldest samples. Our observation might underscore the advantage of fat storage in cold climate and particularly for Neanderthal under ice age conditions. The absent signals of natural selection during modern human history does not support the thrifty gene hypothesis in case of PNPLA3 p.I148M.},
}

Animals
Humans
*Acyltransferases/genetics
*Alleles
DNA, Ancient/analysis
*Fatty Liver/genetics
Gene Frequency
Genetic Predisposition to Disease
Genome-Wide Association Study
Genotype
*Neanderthals/genetics
*Phospholipases A2, Calcium-Independent/genetics

@article {pmid38454744,
year = {2024},
author = {Pantoja-Pérez, A and Arsuaga, JL},
title = {The Cranium I: Neurocranium.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {307},
number = {7},
pages = {2278-2324},
doi = {10.1002/ar.25413},
pmid = {38454744},
issn = {1932-8494},
support = {PID2021-122355NB-C31//MCIN/AEI/10.13039/501100011033 and "ERDF A way of making Europe"/ ; PGC2018-093925-B-C31//MCIN/AEI/10.13039/501100011033 and "ERDF A way of making Europe"/ ; 949330//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program/ ; //CaixaBank-Fundación Atapuerca/ ; },
mesh = {Animals ; *Skull/anatomy & histology ; *Neanderthals/anatomy & histology ; Male ; Female ; *Fossils ; Humans ; *Biological Evolution ; },
abstract = {The Sima de los Huesos (SH) site has provided a significant collection of hominin remains, including numerous cranial fragments, which have contributed to our understanding of the MP human population. The taxonomic classification of the SH hominins remains a topic of debate, with some studies suggesting a close relationship to Neandertals based on nuclear DNA analysis. The cranial morphology of the SH specimens exhibits a mix of Neandertal-like features and primitive traits observed in earlier Homo populations, providing insights into the evolutionary pattern of the Neanderthal lineage. This study focuses on the neurocranial traits of the SH population and describes three previously undescribed cranial individuals. The SH cranial collection now comprises 20 nearly complete crania, representing approximately two-thirds of the estimated population size. The analysis of the SH population reveals variations in robustness, frontal torus development, sagittal keeling, and occipital torus morphology, which may be related to sexual dimorphism and ontogenetic factors. The suprainiac region exhibits notable ontogenetic changes, while suture obliteration patterns do not strictly correlate with dental age. Metric measurements, particularly cranial breadths, highlight significant intrapopulation variation within the SH sample. Compared with other Middle Pleistocene (MP) hominins, the SH cranial vault displays archaic characteristics but differs from Homo erectus and Neandertals. The SH individuals have relatively short and tall cranial vaults, distinguishing them from other MP fossils. These findings contribute to our understanding of the MP human populations and their evolutionary trajectories.},
}

Animals
*Skull/anatomy & histology
*Neanderthals/anatomy & histology
Male
Female
*Fossils
Humans
*Biological Evolution

@article {pmid38450997,
year = {2024},
author = {Gómez-Olivencia, A and Arsuaga, JL},
title = {The Sima de los Huesos thorax and lumbar spine: Selected traits and state-of-the-art.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {307},
number = {7},
pages = {2465-2490},
doi = {10.1002/ar.25414},
pmid = {38450997},
issn = {1932-8494},
support = {PGC2018-093925-B-C33//Ministerio de Ciencia, Innovación y Universidades/ ; PID2021-122355NB-C31//Ministerio de Ciencia, Innovación y Universidades/ ; RYC-2017-22558//Ramón y Cajal fellowship/ ; //Fundación Atapuerca/ ; //Junta de Castilla y León/ ; },
mesh = {*Lumbar Vertebrae/anatomy & histology ; Animals ; *Fossils/anatomy & histology ; Humans ; *Thoracic Vertebrae/anatomy & histology ; *Neanderthals/anatomy & histology ; *Biological Evolution ; *Thorax/anatomy & histology ; Ribs/anatomy & histology ; Hominidae/anatomy & histology ; },
abstract = {Information on the evolution of the thorax and lumbar spine in the genus Homo is hampered by a limited fossil record due to the inherent fragility of vertebrae and ribs. Neandertals show significant metric and morphological differences in these two anatomical regions, when compared to Homo sapiens. Thus, the important fossil record from the Middle Pleistocene site of Sima de los Huesos (SH) not only offers important information on the evolution of these anatomical regions within the Neandertal lineage but also provides important clues to understand the evolution of these regions at the genus level. We present the current knowledge of the costal skeleton, and the thoracic and lumbar spine anatomy of the hominins found in Sima de los Huesos compared to that of Neandertals and modern humans. The current SH fossil record comprises 738 vertebral specimens representing a minimum of 70 cervical, 95 thoracic and 47 lumbar vertebrae, 652 rib fragments representing a minimum of 118 ribs, and 26 sternal fragments representing 4 sterna. The SH hominins exhibit a morphological pattern in their thorax and lumbar spine more similar to that of Neandertals than to that of H. sapiens, which is consistent with the phylogenetic position of these hominins. However, there are some differences between the SH hominins and Neandertals in these anatomical regions, primarily in the orientation of the lumbar transverse processes and in the robusticity of the second ribs. The presence of some but not all of the suite of Neandertal-derived features is consistent with the pattern found in the cranium and other postcranial regions of this population.},
}

*Lumbar Vertebrae/anatomy & histology
Animals
*Fossils/anatomy & histology
Humans
*Thoracic Vertebrae/anatomy & histology
*Neanderthals/anatomy & histology
*Biological Evolution
*Thorax/anatomy & histology
Ribs/anatomy & histology
Hominidae/anatomy & histology

@article {pmid38420653,
year = {2024},
author = {Hernaiz-García, M and Zanolli, C and Martín-Francés, L and Mazurier, A and Benazzi, S and Sarig, R and Fu, J and Kullmer, O and Fiorenza, L},
title = {Masticatory habits of the adult Neanderthal individual BD 1 from La Chaise-de-Vouthon (France).},
journal = {American journal of biological anthropology},
volume = {184},
number = {1},
pages = {e24926},
doi = {10.1002/ajpa.24926},
pmid = {38420653},
issn = {2692-7691},
support = {//Biomedicine Discovery Scholarship from Monash University/ ; DP190100465//Australian Research Council/ ; },
mesh = {Adult ; Humans ; Animals ; *Neanderthals ; *Tooth ; *Tooth Wear ; France ; Habits ; },
abstract = {OBJECTIVES: The analysis of dental wear provides a useful approach for dietary and cultural habit reconstructions of past human populations. The analysis of macrowear patterns can also be used to better understand the individual chewing behavior and to investigate the biomechanical responses during different biting scenarios. The aim of this study is to evaluate the diet and chewing performance of the adult Neanderthal Bourgeois-Delaunay 1 (BD 1) and to investigate the relationship between wear and cementum deposition under mechanical demands.

MATERIALS AND METHODS: The macrowear pattern of BD 1 was analyzed using the occlusal fingerprint analysis method. We propose a new method for the bilateral measurement of the cementum volume along both buccal and lingual sides of the molar root.

RESULTS: BD 1's anterior dentition is more affected by wear compared to the posterior one. The macrowear pattern suggest a normal chewing behavior and a mixed-diet coming from temperate environments. The teeth on the left side of the mandible display greater levels of wear, as well as the buccal side of the molar crowns. The cementum analysis shows higher buccal volume along the molar roots.

DISCUSSION: BD1 could have been preferably chewing on the left side of the mandible. The exploitation of various food resources suggested by the macrowear analysis is compatible with the environmental reconstructions. Finally, the greater wear on the buccal side of the molar occlusal surface and the greater volume of cementum in that side of the molar roots offers a preliminary understanding about the potential correlation between dental wear and cementum deposition.},
}

Adult
Humans
Animals
*Neanderthals
*Tooth
*Tooth Wear
France
Habits

@article {pmid38405782,
year = {2024},
author = {Kerdoncuff, E and Skov, L and Patterson, N and Zhao, W and Lueng, YY and Schellenberg, GD and Smith, JA and Dey, S and Ganna, A and Dey, AB and Kardia, SLR and Lee, J and Moorjani, P},
title = {50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38405782},
issn = {2692-8205},
support = {R01 AG051125/AG/NIA NIH HHS/United States ; R35 GM142978/GM/NIGMS NIH HHS/United States ; RF1 AG055273/AG/NIA NIH HHS/United States ; },
abstract = {India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India-including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups-providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ~1.5 Gb (or 50%) of the introgressing Neanderthal and ~0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.},
}

@article {pmid38380556,
year = {2024},
author = {Pablos, A and Arsuaga, JL},
title = {Metatarsals and foot phalanges from the Sima de los Huesos Middle Pleistocene site (Atapuerca, Burgos, Spain).},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {307},
number = {7},
pages = {2665-2707},
doi = {10.1002/ar.25412},
pmid = {38380556},
issn = {1932-8494},
support = {PGC2018-093925-B-C33//Ministerio de Ciencia e Innovación/ ; PGC2018-093925-B-C31//Ministerio de Ciencia e Innovación/ ; PID2021-122355NB-C31//MCIN/ ; 949330//H2020 European Research Council/ ; EMERGIA20_00403//EMERGIA/ ; //Junta de Castilla y León/ ; },
mesh = {Animals ; *Fossils/anatomy & histology ; Spain ; *Metatarsal Bones/anatomy & histology ; Humans ; *Hominidae/anatomy & histology/physiology ; Biological Evolution ; Neanderthals/anatomy & histology ; Toe Phalanges/anatomy & histology ; },
abstract = {This study provides a complete, updated and illustrated inventory, as well as a comprehensive study, of the metatarsals and foot phalanges (forefoot) recovered from the Middle Pleistocene site of Sima de los Huesos (SH, Atapuerca, Spain) in comparison to other Homo comparative samples, both extant and fossils. This current updated review has established a minimum number of individuals (MNI) of 17, which represent 58.6% of the 29 dental individuals identified within the SH sample. An exclusive or autoapomorphic combination of traits can be recognized within the SH hominin foot sample. A few traits appear primitive or plesiomorphic when compared with earlier Homo individuals and other recent modern humans. There are other metrical and morphological traits that SH hominins and Neandertals have in common that sometimes represent shared derived traits in this evolutionary line, most of which are probably related to robusticity. Furthermore, some exclusive autoapomorphic traits are observed in the SH sample: a very broad first metatarsal, long and broad hallucal proximal foot phalanges and possibly extremely robust lateral distal foot phalanges compared to those of Neandertals and modern humans. In these last traits, the SH metatarsals and pedal phalanges are even more robust than in Neandertals. They are herein named as "hyper-Neandertal" traits, which could suggest a slight gracilization process in this evolutionary line, at least in the hallux toe. Finally, some paleobiological inferences are made in relation to body size (stature and body mass) and some associations are proposed within the SH sample.},
}

Animals
*Fossils/anatomy & histology
Spain
*Metatarsal Bones/anatomy & histology
Humans
*Hominidae/anatomy & histology/physiology
Biological Evolution
Neanderthals/anatomy & histology
Toe Phalanges/anatomy & histology

@article {pmid38379413,
year = {2024},
author = {Cerrito, P and Nava, A and Radovčić, D and Borić, D and Cerrito, L and Basdeo, T and Ruggiero, G and Frayer, DW and Kao, AP and Bondioli, L and Mancini, L and Bromage, TG},
title = {Correction: 'Dental cementum virtual histology of Neanderthal teeth from Krapina (Croatia, 130-120 kyr): an informed estimate of age, sex and adult stressors' (2022), by Cerrito et al.},
journal = {Journal of the Royal Society, Interface},
volume = {21},
number = {211},
pages = {20240069},
doi = {10.1098/rsif.2024.0069},
pmid = {38379413},
issn = {1742-5662},
}

@article {pmid38377343,
year = {2024},
author = {Liu, S and Luo, H and Zhang, P and Li, Y and Hao, D and Zhang, S and Song, T and Xu, T and He, S},
title = {Adaptive Selection of Cis-regulatory Elements in the Han Chinese.},
journal = {Molecular biology and evolution},
volume = {41},
number = {3},
pages = {},
pmid = {38377343},
issn = {1537-1719},
support = {XDB38040300//Chinese Academy of Sciences/ ; 2021YFF0703701//National Key R&D Program of China/ ; 91940306//National Natural Science Foundation of China/ ; 2019FY100102//MOST, China/ ; 2022M713311//China Postdoctoral Science Foundation/ ; //National Genomics Data Center, China/ ; },
mesh = {Humans ; Animals ; *Diabetes Mellitus, Type 2/genetics ; Selection, Genetic ; Regulatory Sequences, Nucleic Acid ; Promoter Regions, Genetic ; *Neanderthals/genetics ; China ; Enhancer Elements, Genetic ; },
abstract = {Cis-regulatory elements have an important role in human adaptation to the living environment. However, the lag in population genomic cohort studies and epigenomic studies, hinders the research in the adaptive analysis of cis-regulatory elements in human populations. In this study, we collected 4,013 unrelated individuals and performed a comprehensive analysis of adaptive selection of genome-wide cis-regulatory elements in the Han Chinese. In total, 12.34% of genomic regions are under the influence of adaptive selection, where 1.00% of enhancers and 2.06% of promoters are under positive selection, and 0.06% of enhancers and 0.02% of promoters are under balancing selection. Gene ontology enrichment analysis of these cis-regulatory elements under adaptive selection reveals that many positive selections in the Han Chinese occur in pathways involved in cell-cell adhesion processes, and many balancing selections are related to immune processes. Two classes of adaptive cis-regulatory elements related to cell adhesion were in-depth analyzed, one is the adaptive enhancers derived from neanderthal introgression, leads to lower hyaluronidase level in skin, and brings better performance on UV-radiation resistance to the Han Chinese. Another one is the cis-regulatory elements regulating wound healing, and the results suggest the positive selection inhibits coagulation and promotes angiogenesis and wound healing in the Han Chinese. Finally, we found that many pathogenic alleles, such as risky alleles of type 2 diabetes or schizophrenia, remain in the population due to the hitchhiking effect of positive selections. Our findings will help deepen our understanding of the adaptive evolution of genome regulation in the Han Chinese.},
}

Humans
Animals
*Diabetes Mellitus, Type 2/genetics
Selection, Genetic
Regulatory Sequences, Nucleic Acid
Promoter Regions, Genetic
*Neanderthals/genetics
China
Enhancer Elements, Genetic

@article {pmid38367960,
year = {2024},
author = {Voinescu, CD and Mozere, M and Genovese, G and Downie, ML and Gupta, S and Gale, DP and Bockenhauer, D and Kleta, R and Arcos-Burgos, M and Stanescu, HC},
title = {A Neanderthal haplotype introgressed into the human genome confers protection against membranous nephropathy.},
journal = {Kidney international},
volume = {105},
number = {4},
pages = {791-798},
doi = {10.1016/j.kint.2024.01.017},
pmid = {38367960},
issn = {1523-1755},
mesh = {Humans ; Animals ; *Neanderthals/genetics ; Haplotypes ; *Glomerulonephritis, Membranous/genetics ; Genome, Human ; Genome-Wide Association Study ; Receptors, Phospholipase A2/genetics ; },
abstract = {Class 2 HLA and PLA2R1 alleles are exceptionally strong genetic risk factors for membranous nephropathy (MN), leading, through an unknown mechanism, to a targeted autoimmune response. Introgressed archaic haplotypes (introduced from an archaic human genome into the modern human genome) might influence phenotypes through gene dysregulation. Here, we investigated the genomic region surrounding the PLA2R1 gene. We reconstructed the phylogeny of Neanderthal and modern haplotypes in this region and calculated the probability of the observed clustering being the result of introgression or common descent. We imputed variants for the participants in our previous genome-wide association study and we compared the distribution of Neanderthal variants between MN cases and controls. The region associated with the lead MN risk locus in the PLA2R1 gene was confirmed and showed that, within a 507 kb region enriched in introgressed sequence, a stringently defined 105 kb haplotype, intersecting the coding regions for PLA2R1 and ITGB6, is inherited from Neanderthals. Thus, introgressed Neanderthal haplotypes overlapping PLA2R1 are differentially represented in MN cases and controls, with enrichment In controls suggesting a protective effect.},
}

Humans
Animals
*Neanderthals/genetics
Haplotypes
*Glomerulonephritis, Membranous/genetics
Genome, Human
Genome-Wide Association Study
Receptors, Phospholipase A2/genetics

@article {pmid38345759,
year = {2024},
author = {Yaghmouri, M and Izadi, P},
title = {Role of the Neanderthal Genome in Genetic Susceptibility to COVID-19: 3p21.31 Locus in the Spotlight.},
journal = {Biochemical genetics},
volume = {62},
number = {6},
pages = {4239-4263},
pmid = {38345759},
issn = {1573-4927},
mesh = {*Neanderthals/genetics ; Animals ; Humans ; *COVID-19/genetics ; *Genetic Predisposition to Disease ; *SARS-CoV-2 ; *Chromosomes, Human, Pair 3/genetics ; Genome-Wide Association Study ; },
abstract = {Since the outbreak of COVID-19, genome-wide association studies have tried to discover the role of genetic predisposition in the clinical variability of this viral infection. The findings of various investigations have led to several loci for COVID-19 genetic susceptibility. Among candidate regions, the 3p21.31 locus has been in the spotlight among scientists, as it can increase the risk of severe COVID-19 by almost two fold. In addition to its substantial association with COVID-19 severity, this locus is related to some common diseases, such as diabetes, malignancies, and coronary artery disease. This locus also harbors evolutionary traces of Neanderthal genomes, which is believed to be the underlying reason for its association with COVID-19 severity. Additionally, the inheritance of this locus from Neanderthals seems to be under positive selection. This review aims to summarize a collection of evidence on the 3p21.31 locus and its impact on COVID-19 outcomes by focusing on the risk variants originated from the Neanderthal genome. Moreover, we discuss candidate genes at this locus and the possible mechanisms by which they influence the progression of COVID-19 symptoms. Better insights into human genetic susceptibility to newly emerging diseases such as COVID-19 and its evolutionary origin can provide fundamentals for risk assessment of different populations as well as the development of personalized prevention and treatments based on genomic medicine.},
}

*Neanderthals/genetics
Animals
Humans
*COVID-19/genetics
*Genetic Predisposition to Disease
*SARS-CoV-2
*Chromosomes, Human, Pair 3/genetics
Genome-Wide Association Study

@article {pmid38293167,
year = {2024},
author = {Janivara, R and Hazra, U and Pfennig, A and Harlemon, M and Kim, MS and Eaaswarkhanth, M and Chen, WC and Ogunbiyi, A and Kachambwa, P and Petersen, LN and Jalloh, M and Mensah, JE and Adjei, AA and Adusei, B and Joffe, M and Gueye, SM and Aisuodionoe-Shadrach, OI and Fernandez, PW and Rohan, TE and Andrews, C and Rebbeck, TR and Adebiyi, AO and Agalliu, I and Lachance, J},
title = {Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38293167},
issn = {2692-8205},
support = {R35 GM133727/GM/NIGMS NIH HHS/United States ; U01 CA184374/CA/NCI NIH HHS/United States ; U01 CA257328/CA/NCI NIH HHS/United States ; },
abstract = {Androgenetic alopecia is a highly heritable trait. However, much of our understanding about the genetics of male pattern baldness comes from individuals of European descent. Here, we examined a novel dataset comprising 2,136 men from Ghana, Nigeria, Senegal, and South Africa that were genotyped using a custom array. We first tested how genetic predictions of baldness generalize from Europe to Africa, finding that polygenic scores from European GWAS yielded AUC statistics that ranged from 0.513 to 0.546, indicating that genetic predictions of baldness in African populations performed notably worse than in European populations. Subsequently, we conducted the first African GWAS of androgenetic alopecia, focusing on self-reported baldness patterns at age 45. After correcting for present age, population structure, and study site, we identified 266 moderately significant associations, 51 of which were independent (p-value < 10[-5], r[2] < 0.2). Most baldness associations were autosomal, and the X chromosomes does not appear to have a large impact on baldness in African men. Finally, we examined the evolutionary causes of continental differences in genetic architecture. Although Neanderthal alleles have previously been associated with skin and hair phenotypes, we did not find evidence that European-ascertained baldness hits were enriched for signatures of ancient introgression. Most loci that are associated with androgenetic alopecia are evolving neutrally. However, multiple baldness-associated SNPs near the EDA2R and AR genes have large allele frequency differences between continents. Collectively, our findings illustrate how evolutionary history contributes to the limited portability of genetic predictions across ancestries.},
}

@article {pmid38269094,
year = {2024},
author = {Jambrina-Enríquez, M and Mallol, C and Herrera Herrera, AV and Gonzalez-Urquijo, J and Lazuen, T},
title = {Microstratigraphic, lipid biomarker and stable isotope study of a middle Palaeolithic combustion feature from Axlor, Spain.},
journal = {iScience},
volume = {27},
number = {1},
pages = {108755},
pmid = {38269094},
issn = {2589-0042},
abstract = {Archaeological research has increasingly focused on studying combustion features as valuable sources of information regarding past technological and cultural aspects. The use of microstratigraphic and biomolecular techniques enables the identification of combustion residues and substrate components, and infer about past fire-related activities and the environments. Our study conducted on a combustion feature (Level N, ∼100 Ka) at the Axlor cave, a Middle Paleolithic site in northern Iberia, exemplifies the interdisciplinary approach to combustion features. Micromorphological features revealed depositional activities associated with occupations such as hearth rake-out and trampling. Through molecular (n-alkanes, n-alcohols, and n-fatty acids) and isotopic analysis (δ[13]C16:0 and δ[13]C18:0), we infer the good preservation of organic matter, the contributions of non-ruminant fats, and the dead-wood gathering strategies by Neanderthal groups. By combining microstratigraphic and biomolecular approaches, our study significantly contributes to the advancement of our current understanding of Neanderthal pyrotechnology.},
}

@article {pmid38262226,
year = {2024},
author = {Bailey, SE and Davies, TW and Imbrasas, MD and Lazuen, T and Hublin, JJ and González-Urquijo, J},
title = {New Neanderthal remains from Axlor cave (Dima, Biscay, northern Iberian Peninsula).},
journal = {Journal of human evolution},
volume = {187},
number = {},
pages = {103483},
doi = {10.1016/j.jhevol.2023.103483},
pmid = {38262226},
issn = {1095-8606},
mesh = {Animals ; *Neanderthals ; Europe ; Fossils ; Caves ; Archaeology ; },
}

Animals
*Neanderthals
Europe
Fossils
Caves
Archaeology

@article {pmid38213708,
year = {2023},
author = {Borodko, DD and Zhenilo, SV and Sharko, FS},
title = {Search for differentially methylated regions in ancient and modern genomes.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {27},
number = {7},
pages = {820-828},
doi = {10.18699/VJGB-23-95},
pmid = {38213708},
issn = {2500-0462},
abstract = {Currently, active research is focused on investigating the mechanisms that regulate the development of various pathologies and their evolutionary dynamics. Epigenetic mechanisms, such as DNA methylation, play a significant role in evolutionary processes, as their changes have a faster impact on the phenotype compared to mutagenesis. In this study, we attempted to develop an algorithm for identifying differentially methylated regions associated with metabolic syndrome, which have undergone methylation changes in humans during the transition from a hunter-gatherer to a sedentary lifestyle. The application of existing whole-genome bisulfite sequencing methods is limited for ancient samples due to their low quality and fragmentation, and the approach to obtaining DNA methylation profiles differs significantly between ancient hunter-gatherer samples and modern tissues. In this study, we validated DamMet, an algorithm for reconstructing ancient methylomes. Application of DamMet to Neanderthal and Denisovan genomes showed a moderate level of correlation with previously published methylation profiles and demonstrated an underestimation of methylation levels in the reconstructed profiles by an average of 15-20 %. Additionally, we developed a new Python-based algorithm that allows for the comparison of methylomes in ancient and modern samples, despite the absence of methylation profiles in modern bone tissue within the context of obesity. This analysis involves a two-step data processing approach, where the first step involves the identification and filtration of tissue-specific methylation regions, and the second step focuses on the direct search for differentially methylated regions in specific areas associated with the researcher's target condition. By applying this algorithm to test data, we identified 38 differentially methylated regions associated with obesity, the majority of which were located in promoter regions. The pipeline demonstrated sufficient efficiency in detecting these regions. These results confirm the feasibility of reconstructing DNA methylation profiles in ancient samples and comparing them with modern methylomes. Furthermore, possibilities for further methodological development and the implementation of a new step for studying differentially methylated positions associated with evolutionary processes are discussed.},
}