@article {pmid38020913,
year = {2023},
author = {Agata, A and Ohtsuka, S and Noji, R and Gotoh, H and Ono, K and Nomura, T},
title = {A Neanderthal/Denisovan GLI3 variant contributes to anatomical variations in mice.},
journal = {Frontiers in cell and developmental biology},
volume = {11},
number = {},
pages = {1247361},
doi = {10.3389/fcell.2023.1247361},
pmid = {38020913},
issn = {2296-634X},
abstract = {Changes in genomic structures underlie phenotypic diversification in organisms. Amino acid-changing mutations affect pleiotropic functions of proteins, although little is known about how mutated proteins are adapted in existing developmental programs. Here we investigate the biological effects of a variant of the GLI3 transcription factor (GLI3[R1537C]) carried in Neanderthals and Denisovans, which are extinct hominins close to modern humans. R1537C does not compromise protein stability or GLI3 activator-dependent transcriptional activities. In contrast, R1537C affects the regulation of downstream target genes associated with developmental processes. Furthermore, genome-edited mice carrying the Neanderthal/Denisovan GLI3 mutation exhibited various alterations in skeletal morphology. Our data suggest that an extinct hominin-type GLI3 contributes to species-specific anatomical variations, which were tolerated by relaxed constraint in developmental programs during human evolution.},
}

@article {pmid38012927,
year = {2023},
author = {Lee, OY and Wu, HHT and Besra, GS and Minnikin, DE and Jaeger, HY and Maixner, F and Zink, A and Gasparik, M and Pap, I and Bereczki, Z and Pálfi, G},
title = {Sensitive lipid biomarker detection for tuberculosis in late Neanderthal skeletons from Subalyuk Cave, Hungary.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {143S},
number = {},
pages = {102420},
doi = {10.1016/j.tube.2023.102420},
pmid = {38012927},
issn = {1873-281X},
abstract = {Skeletal remains of two Neanderthal individuals, a 25-35 year-old woman and a 3-4 year-old child, were discovered in a Subalyuk Cave in North-Eastern Hungary. Radiocarbon dating of the female and child remains revealed an age of 39,732-39,076 and 36,117-35,387 cal BP, respectively. Paleopathological studies of these Neanderthal remains revealed probable evidence of skeletal mycobacterial infection, including in the sacrum of the adult specimen and the endocranial surface of the child's skull. Application of PCR amplification to the juvenile cranium and a vertebra gave a positive result (IS6110) for tuberculosis, backed up by spoligotyping. Lipid biomarker analyses of the same two specimens revealed definitive signals for C32 mycoserosates, a very characteristic component of the Mycobacterium tuberculosis complex (MTBC). A vertebra from the adult provided weak evidence for mycocerosate biomarkers. The correlation of probable skeletal lesions with characteristic amplified DNA fragments and a proven lipid biomarker points to the presence of tuberculosis in these Neanderthals. In particular, the closely similar biomarker profiles, for two distinct juvenile cranial and vertebral bones, strengthen this diagnosis.},
}

@article {pmid38012926,
year = {2023},
author = {Pálfi, G and Molnár, E and Bereczki, Z and Coqueugniot, H and Dutour, O and Tillier, AM and Rosendahl, W and Sklánitz, A and Mester, Z and Gasparik, M and Maixner, F and Zink, A and Minnikin, DE and Pap, I},
title = {Re-examination of the Subalyuk Neanderthal remains uncovers signs of probable TB infection (Subalyuk Cave, Hungary).},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {143S},
number = {},
pages = {102419},
doi = {10.1016/j.tube.2023.102419},
pmid = {38012926},
issn = {1873-281X},
abstract = {In 1932, skeletal remains of two Neanderthal individuals, a young adult female and a 3-4-year-old child, were discovered in Subalyuk Cave in Northern Hungary [1,2]. Results of the anthropological examination were published some years after this important discovery. Methodological progress encouraged re-examination of the material during the last few years. Radiocarbon dating revealed a chronological age of 39,732-39,076 cal. BP for the adult female and 36,117-35,387 cal. BP for the child [3]. Morphological paleopathological studies of these Neanderthal remains uncovered distinct evidence of skeletal infections. Alterations of the adult individual's sacrum suggest probable early-stage sacroiliitis, while several vertebral bodies indicate superficial osseous remodelling of infectious origin. Traces of pathological lesions were observed on the endocranial surface of the child's skull, reflecting a reaction of meningeal tissues, a consequence of a probable TB-related meningeal infectious process. Results of recent paleomicrobiological examinations - lipid biomarker and aDNA studies - support the morphological diagnosis of probable TB infections [4].},
}

@article {pmid37862773,
year = {2023},
author = {López-Rey, JM and García-Martínez, D and Martelli, S and Beyer, B and Palancar, CA and Torres-Sánchez, I and García-Río, F and Bastir, M},
title = {Estimation of the upper diaphragm in KNM-WT 15000 (Homo erectus s.l.) and Kebara 2 (Homo neanderthalensis) using a Homo sapiens model.},
journal = {Journal of human evolution},
volume = {185},
number = {},
pages = {103442},
doi = {10.1016/j.jhevol.2023.103442},
pmid = {37862773},
issn = {1095-8606},
mesh = {Animals ; Humans ; *Neanderthals ; Diaphragm ; *Hominidae ; Biological Evolution ; Thorax ; Fossils ; },
}

Animals
Humans
*Neanderthals
Diaphragm
*Hominidae
Biological Evolution
Thorax
Fossils

@article {pmid37992125,
year = {2023},
author = {Di Santo, LN and Quilodran, CS and Currat, M},
title = {Temporal variation in introgressed segments' length statistics computed from a limited number of ancient genomes sheds light on past admixture pulses.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad252},
pmid = {37992125},
issn = {1537-1719},
abstract = {Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remains a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a two-population system and described temporal neutral introgression patterns under a single- and two-pulse admixture model. We computed six summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within-genomes, as well as genome-wide introgression proportions and related measures. The first two statistics could confidently be used to infer inter-lineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.},
}

@article {pmid37989099,
year = {2023},
author = {Ragsdale, AP},
title = {Human evolution: Neanderthal footprints in African genomes.},
journal = {Current biology : CB},
volume = {33},
number = {22},
pages = {R1197-R1200},
doi = {10.1016/j.cub.2023.10.005},
pmid = {37989099},
issn = {1879-0445},
abstract = {Human and Neanderthal populations met and mixed on multiple occasions over evolutionary time, resulting in the exchange of genetic material. New genomic analyses of diverse African populations reveal a history of bidirectional gene flow and selection acting on introgressed alleles.},
}

@article {pmid37977419,
year = {2023},
author = {Urnikyte, A and Masiulyte, A and Pranckeniene, L and Kučinskas, V},
title = {Disentangling archaic introgression and genomic signatures of selection at human immunity genes.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105528},
doi = {10.1016/j.meegid.2023.105528},
pmid = {37977419},
issn = {1567-7257},
abstract = {Pathogens and infectious diseases have imposed exceptionally strong selective pressure on ancient and modern human genomes and contributed to the current variation in many genes. There is evidence that modern humans acquired immune variants through interbreeding with ancient hominins, but the impact of such variants on human traits is not fully understood. The main objectives of this research were to infer the genetic signatures of positive selection that may be involved in adaptation to infectious diseases and to investigate the function of Neanderthal alleles identified within a set of 50 Lithuanian genomes. Introgressed regions were identified using the machine learning tool ArchIE. Recent positive selection signatures were analysed using iHS. We detected high-scoring signals of positive selection at innate immunity genes (EMB, PARP8, HLAC, and CDSN) and evaluated their interactions with the structural proteins of pathogens. Interactions with human immunodeficiency virus (HIV) 1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. Overall, genomic regions introgressed from Neanderthals were shown to be enriched in genes related to immunity, keratinocyte differentiation, and sensory perception.},
}

@article {pmid37925533,
year = {2023},
author = {Raja, A and Kuiper, JJW},
title = {Evolutionary immuno-genetics of endoplasmic reticulum aminopeptidase II (ERAP2).},
journal = {Genes and immunity},
volume = {},
number = {},
pages = {},
pmid = {37925533},
issn = {1476-5470},
support = {954992//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; },
abstract = {Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a proteolytic enzyme involved in adaptive immunity. The ERAP2 gene is highly polymorphic and encodes haplotypes that confer resistance against lethal infectious diseases, but also increase the risk for autoimmune disorders. Identifying how ERAP2 influences susceptibility to these traits requires an understanding of the selective pressures that shaped and maintained allelic variation throughout human evolution. Our review discusses the genetic regulation of haplotypes and diversity in naturally occurring ERAP2 allotypes in the global population. We outline how these ERAP2 haplotypes evolved during human history and highlight the presence of Neanderthal DNA sequences in ERAP2 of modern humans. Recent evidence suggests that human adaptation during the last ~10,000 years and historic pandemics left a significant mark on the ERAP2 gene that determines susceptibility to infectious and inflammatory diseases today.},
}

@article {pmid37851812,
year = {2023},
author = {Quilodrán, CS and Rio, J and Tsoupas, A and Currat, M},
title = {Past human expansions shaped the spatial pattern of Neanderthal ancestry.},
journal = {Science advances},
volume = {9},
number = {42},
pages = {eadg9817},
doi = {10.1126/sciadv.adg9817},
pmid = {37851812},
issn = {2375-2548},
abstract = {The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.},
}

@article {pmid37846608,
year = {2023},
author = {Chen, Y and Yu, XY and Xu, SJ and Shi, XQ and Zhang, XX and Sun, C},
title = {An indel introduced by Neanderthal introgression, rs3835124:ATTTATT > ATT, might contribute to prostate cancer risk by regulating PDK1 expression.},
journal = {Annals of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1111/ahg.12533},
pmid = {37846608},
issn = {1469-1809},
support = {//National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities/ ; },
abstract = {INTRODUCTION: Prostate cancer is one of the most common cancer types in males and rs12621278:A > G has been suggested to be associated with this disease by previous genome-wide association studies. One thousand genomes project data analysis indicated that rs12621278:A > G is within two long-core haplotypes. However, the origin, causal variant(s), and molecular function of these haplotypes were remaining unclear.

MATERIALS AND METHODS: Population genetics analysis and functional genomics work was performed for this locus.

RESULTS: Phylogeny analysis verified that the rare haplotype is derived from Neanderthal introgression. Genome annotation suggested that three genetic variants in the core haplotypes, rs116108611:G > A, rs139972066:AAAAAAAA > AAAAAAAAA, and rs3835124:ATTTATT > ATT, are located in functional regions. Luciferase assay indicated that rs139972066:AAAAAAAA > AAAAAAAAA and rs116108611:G > A are not able to alter ITGA6 (integrin alpha 6) and ITGA6 antisense RNA 1 expression, respectively. In contrast, rs3835124:ATTTATT > ATT can significantly influence PDK1 (pyruvate dehydrogenase kinase 1) expression, which was verified by expression quantitative trait locus analysis. This genetic variant can alter transcription factor cut like homeobox 1 interaction efficiency. The introgressed haplotype was observed to be subject to positive selection in East Asian populations. The molecular function of the haplotype suggested that Neanderthal should be with lower PDK1 expression and further different energy homeostasis from modern human.

CONCLUSION: This study provided new insight into the contribution of Neanderthal introgression to human phenotypes.},
}

@article {pmid37837965,
year = {2023},
author = {Harris, DN and Platt, A and Hansen, MEB and Fan, S and McQuillan, MA and Nyambo, T and Mpoloka, SW and Mokone, GG and Belay, G and Fokunang, C and Njamnshi, AK and Tishkoff, SA},
title = {Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.09.066},
pmid = {37837965},
issn = {1879-0445},
abstract = {Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia ∼250 kya, and subsequent admixture with Neanderthals, resulting in ∼6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups-a hallmark of incipient speciation.},
}

@article {pmid37828055,
year = {2023},
author = {Russo, G and Milks, A and Leder, D and Koddenberg, T and Starkovich, BM and Duval, M and Zhao, JX and Darga, R and Rosendahl, W and Terberger, T},
title = {First direct evidence of lion hunting and the early use of a lion pelt by Neanderthals.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {16405},
pmid = {37828055},
issn = {2045-2322},
support = {76202-762/17//Niedersächsisches Ministerium für Wissenschaft und Kultur/ ; 76202-762/17//Niedersächsisches Ministerium für Wissenschaft und Kultur/ ; 76202-762/17//Niedersächsisches Ministerium für Wissenschaft und Kultur/ ; 76202-762/17//Niedersächsisches Ministerium für Wissenschaft und Kultur/ ; RYC2018-025221//Ramón y Cajal Spanish fallowiship/ ; RYC2018-025221//Ramón y Cajal Spanish fallowiship/ ; },
abstract = {During the Upper Paleolithic, lions become an important theme in Paleolithic art and are more frequent in anthropogenic faunal assemblages. However, the relationship between hominins and lions in earlier periods is poorly known and primarily interpreted as interspecies competition. Here we present new evidence for Neanderthal-cave lion interactions during the Middle Paleolithic. We report new evidence of hunting lesions on the 48,000 old cave lion skeleton found at Siegsdorf (Germany) that attest to the earliest direct instance of a large predator kill in human history. A comparative analysis of a partial puncture to a rib suggests that the fatal stab was delivered with a wooden thrusting spear. We also present the discovery of distal lion phalanges at least 190,000 old from Einhornhöhle (Germany), representing the earliest example of the use of cave lion skin by Neanderthals in Central Europe. Our study provides novel evidence on a new dimension of Neanderthal behavioral complexity.},
}

@article {pmid37819902,
year = {2023},
author = {Angelucci, DE and Nabais, M and Zilhão, J},
title = {Formation processes, fire use, and patterns of human occupation across the Middle Palaeolithic (MIS 5a-5b) of Gruta da Oliveira (Almonda karst system, Torres Novas, Portugal).},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0292075},
doi = {10.1371/journal.pone.0292075},
pmid = {37819902},
issn = {1932-6203},
abstract = {Gruta da Oliveira features a c. 13 m-thick infilling that includes a c. 6.5 m-thick archaeological deposit (the "Middle Palaeolithic sequence" complex), which Bayesian modelling of available dating results places in MIS 5a (layers 7-14) and MIS 5b (layers 15-25), c. 71,000-93,000 years ago. The accumulation primarily consists of sediment washed in from the slope through gravitational processes and surface dynamics. The coarse fraction derives from weathering of the cave's limestone bedrock. Tectonic activity and structural instability caused the erosional retreat of the scarp face, explaining the large, roof-collapsed rock masses found through the stratification. The changes in deposition and diagenesis observed across the archaeological sequence are minor and primarily controlled by local factors and the impact of humans and other biological agents. Pulses of stadial accumulation-reflected in the composition of the assemblages of hunted ungulates, mostly open-country and rocky terrain taxa (rhino, horse, ibex)-alternate with interstadial hiatuses-during which carbonate crusts and flowstone formed. Humans were active at the cave throughout, but occupation was intermittent, which allowed for limited usage by carnivores when people visited less frequently. During the accumulation of layers 15-25 (c. 85,000-93,000 years ago), the carnivore guild was dominated by wolf and lion, while brown bear and lynx predominate in layers 7-14 (c. 71,000-78,000 years ago). In the excavated areas, conditions for residential use were optimal during the accumulation of layers 20-22 (c. 90,000-92,000 years ago) and 14 (c. 76,000-78,000 years ago), which yielded dense, hearth-focused scatters of stone tools and burnt bones. The latter are ubiquitous, adding to the growing body of evidence that Middle Palaeolithic Neandertals used fire in regular, consistent manner. The patterns of site usage revealed at Gruta da Oliveira are no different from those observed 50,000 years later in comparable early Upper Palaeolithic and Solutrean cave sites of central Portugal.},
}

@article {pmid37816865,
year = {2023},
author = {Faux, P and Ding, L and Ramirez-Aristeguieta, LM and Chacón-Duque, JC and Comini, M and Mendoza-Revilla, J and Fuentes-Guajardo, M and Jaramillo, C and Arias, W and Hurtado, M and Villegas, V and Granja, V and Barquera, R and Everardo-Martínez, P and Quinto-Sánchez, M and Gómez-Valdés, J and Villamil-Ramírez, H and Silva de Cerqueira, CC and Hünemeier, T and Ramallo, V and Gonzalez-José, R and Schüler-Faccini, L and Bortolini, MC and Acuña-Alonzo, V and Canizales-Quinteros, S and Poletti, G and Gallo, C and Rothhammer, F and Rojas, W and Schmid, AB and Adhikari, K and Bennett, DL and Ruiz-Linares, A},
title = {Neanderthal introgression in SCN9A impacts mechanical pain sensitivity.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {958},
pmid = {37816865},
issn = {2399-3642},
abstract = {The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.},
}

@article {pmid37808839,
year = {2023},
author = {Villanea, FA and Peede, D and Kaufman, EJ and Añorve-Garibay, V and Witt, KE and Villa-Islas, V and Zeloni, R and Marnetto, D and Moorjani, P and Jay, F and Valdmanis, PN and Ávila-Arcos, MC and Huerta-Sánchez, E},
title = {The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.09.25.559202},
pmid = {37808839},
abstract = {All humans carry a small fraction of archaic ancestry across the genome, the legacy of gene flow from Neanderthals, Denisovans, and other hominids into the ancestors of modern humans. While the effects of Neanderthal ancestry on human fitness and health have been explored more thoroughly, there are fewer examples of adaptive introgression of Denisovan variants. Here, we study the gene MUC19 , for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions, from lubrication to immunity. We find the diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed Latin American individuals among global population, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans. We find that some Neanderthals--Vindija and Chagyrskaya--carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into human populations through Neanderthal introgression rather than Denisovan introgression. Finally, we find that the Denisovan-like MUC19 haplotype carries a higher copy number of a 30 base-pair variable number tandem repeat relative to the Human-like haplotype, and that copy numbers of this repeat are exceedingly high in American populations. Our results suggest that the Denisovan-like MUC19 haplotype served as the raw genetic material for positive selection as American populations adapted to novel environments during their movement from Beringia into North and then South America.},
}

@article {pmid37794824,
year = {2023},
author = {Carretero, JM and Rodríguez, L and García-González, R and Arsuaga, JL},
title = {Main morphological characteristics and sexual dimorphism of hominin adult femora from the Sima de los Huesos Middle Pleistocene site (Sierra de Atapuerca, Spain).},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25331},
pmid = {37794824},
issn = {1932-8494},
support = {PID2021-122355NB-C31//Ministerio de Ciencia, Innovación y Universidades/ ; //MCIN/AEI// ; //Junta de Castilla y León/ ; //Fundación Atapuerca/ ; },
abstract = {The excellent fossil record from Sima de los Huesos (SH) includes three well-known complete adult femora and several partial specimens that have not yet been published in detail. This fossil record provides an opportunity to analyze the morphology of European pre-Neandertal adult femur and its variation with different evolution patterns. Currently, there are a minimum of five adult individuals (males or females). In this study, we compiled previously published basic anatomical and biometric characteristics of SH adult femora, emphasizing the most relevant features compared to other recent and fossil hominins. The SH femora exhibited a primitive morphological pattern common to all non-Homo sapiens femora, as well as most of the Neandertal traits. Therefore, the complete Upper Pleistocene Neandertal pattern was well-established in Middle Pleistocene ancestors long before the proper Neandertals appeared. Additionally, we highlight that the SH and Neandertal femora share some morphological traits and proportions with modern humans that hold sexual significance in our species, regardless of size. Keeping this in mind, we discussed the sex determination of the complete SH specimens and re-evaluated sex allocation in two of them.},
}

@article {pmid37792425,
year = {2023},
author = {Rodríguez, L and García-González, R and Arsuaga, JL and Carretero, JM},
title = {Exploring the morphology of adult tibia and fibula from Sima de los Huesos site in sierra de Atapuerca, Burgos, Spain.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25336},
pmid = {37792425},
issn = {1932-8494},
support = {//MCIN/AEI/10.13039/501100011033/FEDER, UE grant number PID2021-122355NB-C31/ ; },
abstract = {The analysis of the locomotor anatomy of Late Pleistocene Homo has largely focused on changes in proximal femur and pelvic morphologies, with much attention centered on the emergence of modern humans. Although much of the focus has been on changes in the proximal femur, some research has also been conducted on tibiae and, to a lesser extent, fibulae. With this in mind, we present one of the largest samples of the same population of human tibiae and fibulae from the Middle Pleistocene to determine their main characteristic traits and establish similarities and differences, primarily with those of Neanderthals and modern humans, but also with other Middle Pleistocene specimens in the fossil record. Through this study, we established that the Middle Pleistocene population from the Sima de los Huesos (Atapuerca, Burgos, Spain) had lower leg long bones similar to those of Neanderthals, although there were some important differences, such as bone length, which this fossil individuals resembled those of modern humans and not to Neanderthals. This fact is related to the crural index and leg length, even though we do not have any true association between femora and tibiae yet, it has implications for establishing locomotor efficiency and climate adaptation.},
}

@article {pmid37790518,
year = {2023},
author = {Giacomini, K and Yee, SW and Ferrández-Peral, L and Alentorn, P and Fontsere, C and Ceylan, M and Koleske, M and Handin, N and Artegoitia, V and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, C and Capra, J and Artursson, P and Newman, J and Marques-Bonet, T},
title = {Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-3263845/v1},
pmid = {37790518},
abstract = {SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.},
}

@article {pmid37783199,
year = {2023},
author = {Zhang, Y and Li, Z},
title = {Investigating the internal structure of the suprainiac fossa in Xuchang 2.},
journal = {Journal of human evolution},
volume = {184},
number = {},
pages = {103440},
doi = {10.1016/j.jhevol.2023.103440},
pmid = {37783199},
issn = {1095-8606},
}

@article {pmid37747127,
year = {2023},
author = {Hui, J and Balzeau, A},
title = {The diploic venous system in Homo neanderthalensis and fossil Homo sapiens: A study using high-resolution computed tomography.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24843},
pmid = {37747127},
issn = {2692-7691},
support = {ANR-20-CE27-0009//Agence Nationale de la Recherche/ ; //China Scholarship Council/ ; },
abstract = {OBJECTIVES: The diploic venous system has been hypothesized to be related to human brain evolution, though its evolutionary trajectory and physiological functions remain largely unclear. This study examines the characteristics of the diploic venous channels (DCs) in a selection of well-preserved Homo neanderthalensis and Upper Paleolithic Homo sapiens crania, searching for the differences between the two taxa and exploring the associations between brain anatomy and DCs.

MATERIALS AND METHODS: Five H. neanderthalensis and four H. sapiens fossil specimens from Western Europe were analyzed. Based on Micro-CT scanning and 3D reconstruction, the distribution pattern and draining orifices of the DCs were inspected qualitatively. The size of the DCs was quantified by volume calculation, and the degree of complexity was quantified by fractal analyses.

RESULTS: High-resolution data show the details of the DC structures not documented in previous studies. H. neanderthalensis and H. sapiens specimens share substantial similarities in the DCs. The noticeable differences between the two samples manifest in the connecting points surrounding the frontal sinuses, parietal foramina, and asterional area.

DISCUSSION: This study provides a better understanding of the anatomy of the DCs in H. neanderthalensis and H. sapiens. The connection patterns of the DCs have potential utility in distinguishing between the two taxa and in the phylogenetic and taxonomic discussion of the Neandertal-like specimens with controversial taxonomic status.},
}

@article {pmid37738342,
year = {2023},
author = {Vidal-Cordasco, M and Terlato, G and Ocio, D and Marín-Arroyo, AB},
title = {Neanderthal coexistence with Homo sapiens in Europe was affected by herbivore carrying capacity.},
journal = {Science advances},
volume = {9},
number = {38},
pages = {eadi4099},
doi = {10.1126/sciadv.adi4099},
pmid = {37738342},
issn = {2375-2548},
abstract = {It has been proposed that climate change and the arrival of modern humans in Europe affected the disappearance of Neanderthals due to their impact on trophic resources; however, it has remained challenging to quantify the effect of these factors. By using Bayesian age models to derive the chronology of the European Middle to Upper Paleolithic transition, followed by a dynamic vegetation model that provides the Net Primary Productivity, and a macroecological model to compute herbivore abundance, we show that in continental regions where the ecosystem productivity was low or unstable, Neanderthals disappeared before or just after the arrival of Homo sapiens. In contrast, regions with high and stable productivity witnessed a prolonged coexistence between both species. The temporal overlap between Neanderthals and H. sapiens is significantly correlated with the carrying capacity of small- and medium-sized herbivores. These results suggest that herbivore abundance released the trophic pressure of the secondary consumers guild, which affected the coexistence likelihood between both human species.},
}

@article {pmid37737280,
year = {2023},
author = {Fajardo, S and Kozowyk, PRB and Langejans, GHJ},
title = {Measuring ancient technological complexity and its cognitive implications using Petri nets.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14961},
pmid = {37737280},
issn = {2045-2322},
support = {804151//European Union's Horizon 2020/ ; 804151//European Union's Horizon 2020/ ; 804151//European Union's Horizon 2020/ ; },
abstract = {We implement a method from computer sciences to address a challenge in Paleolithic archaeology: how to infer cognition differences from material culture. Archaeological material culture is linked to cognition, and more complex ancient technologies are assumed to have required complex cognition. We present an application of Petri net analysis to compare Neanderthal tar production technologies and tie the results to cognitive requirements. We applied three complexity metrics, each relying on their own unique definitions of complexity, to the modeled production processes. Based on the results, we propose that Neanderthal technical cognition may have been analogous to that of contemporary modern humans. This method also enables us to distinguish the high-order cognitive functions combining traits like planning, inhibitory control, and learning that were likely required by different ancient technological processes. The Petri net approach can contribute to our understanding of technology and cognitive evolution as it can be used on different materials and technologies, across time and species.},
}

@article {pmid37731612,
year = {2023},
author = {Breno, M and Noris, M and Rubis, N and Parvanova, AI and Martinetti, D and Gamba, S and Liguori, L and Mele, C and Piras, R and Orisio, S and Valoti, E and Alberti, M and Diadei, O and Bresin, E and Rigoldi, M and Prandini, S and Gamba, T and Stucchi, N and Carrara, F and Daina, E and Benigni, A and Remuzzi, G and , },
title = {A GWAS in the pandemic epicenter highlights the severe COVID-19 risk locus introgressed by Neanderthals.},
journal = {iScience},
volume = {26},
number = {10},
pages = {107629},
pmid = {37731612},
issn = {2589-0042},
abstract = {Large GWAS indicated that genetic factors influence the response to SARS-CoV-2. However, sex, age, concomitant diseases, differences in ancestry, and uneven exposure to the virus impacted the interpretation of data. We aimed to perform a GWAS of COVID-19 outcome in a homogeneous population who experienced a high exposure to the virus and with a known infection status. We recruited inhabitants of Bergamo province-that in spring 2020 was the epicenter of the SARS-Cov-2 pandemic in Europe-via an online questionnaire followed by personal interviews. Cases and controls were matched by age, sex and risk factors. We genotyped 1195 individuals and replicated the association at the 3p21.31 locus with severity, but with a stronger effect size that further increased in gravely ill patients. Transcriptome-wide association study highlighted eQTLs for LZTFL1 and CCR9. We also identified 17 loci not previously reported, suggestive for an association with either COVID-19 severity or susceptibility.},
}

@article {pmid37713634,
year = {2023},
author = {Ge, X and Lu, Y and Chen, S and Gao, Y and Ma, L and Liu, L and Liu, J and Ma, X and Kang, L and Xu, S},
title = {Genetic origins and adaptive evolution of the Deng people on the Tibetan Plateau.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad205},
pmid = {37713634},
issn = {1537-1719},
abstract = {The Tibetan Plateau is populated by diverse ethnic groups, but most of them are under-represented in genomics studies compared with the Tibetans. Here, to gain further insight into the genetic diversity and evolutionary history of the people living in the Tibetan Plateau, we sequenced 54 whole genomes of the Deng people with high coverage (30-60×) and analyzed the data together with that of Tibetans and Sherpas, as well as 968 ancient Asian genomes and available archaic and modern human data. We identified 17.74 million novel single-nucleotide variants from the newly sequenced genomes, although the Deng people showed reduced genomic diversity and a relatively small effective population size. Compared with the other Tibetan highlander groups which are highly admixed, the Deng people are dominated by a sole ancestry that could be traced to some ancient northern East Asian populations. The divergence between Deng and Tibetan people (∼4,700-7,200 years) was more recent than that between highlanders and the Han Chinese (HAN) (Deng-HAN: ∼9,000-14,000 years, TIB-HAN: 7,200-10,000 years). Adaptive genetic variants (AGVs) identified in the Deng are only partially shared with those previously reported in the Tibetans like HLA-DQB1; while others like KLHL12, were not reported in Tibetans. In contrast, the top candidate genes harboring AGVs as previously identified in Tibetans, like EPAS1 and EGLN1, do not show strong positive selection signals in Deng. Interestingly, Deng also showed a different archaic introgression scenario from that observed in the Tibetans. Our results suggest that convergent adaptation might be prevalent on the Tibetan Plateau.},
}

@article {pmid37679507,
year = {2023},
author = {Kozowyk, PRB and Baron, LI and Langejans, GHJ},
title = {Identifying Palaeolithic birch tar production techniques: challenges from an experimental biomolecular approach.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14727},
pmid = {37679507},
issn = {2045-2322},
abstract = {The intentional production of birch bark tar by European Neanderthals as early as 190,000 years ago plays an important role in discussions about the technological and behavioural complexity of Pleistocene hominins. However, research is hampered because it is currently unknown how Neanderthals were producing birch tar. There are several different techniques that could have been employed, but these differ in their apparent production complexity, time and resource efficiency. Identifying production processes in the archaeological record is therefore paramount for furthering research on the technical behavioural repertoire. Organic biomarkers, identified with Gas Chromatograph-Mass Spectrometry (GC-MS), have been used to identify possible production processes during the Neolithic. Here we test whether these biomarkers can also distinguish Palaeolithic (aceramic) tar production methods. We produced tar using five different methods and analysed their biomolecular composition with GC-MS. Our results show that the biomarkers used to distinguish Neolithic tar production strategies using ceramic technology cannot be reliably used to identify tar production processes using aceramic Palaeolithic techniques. More experimentation is required to produce a larger reference library of different tars for future comparisons. To achieve this, complete GC-MS datasets must also be made publicly available, as we have done with our data.},
}

@article {pmid37679497,
year = {2023},
author = {Kozowyk, PRB and Fajardo, S and Langejans, GHJ},
title = {Scaling Palaeolithic tar production processes exponentially increases behavioural complexity.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14709},
pmid = {37679497},
issn = {2045-2322},
support = {804151//Horizon 2020 Framework Programme/ ; },
abstract = {Technological processes, reconstructed from the archaeological record, are used to study the evolution of behaviour and cognition of Neanderthals and early modern humans. In comparisons, technologies that are more complex infer more complex behaviour and cognition. The manufacture of birch bark tar adhesives is regarded as particularly telling and often features in debates about Neanderthal cognition. One method of tar production, the 'condensation technique', demonstrates a pathway for Neanderthals to have discovered birch bark tar. However, to improve on the relatively low yield, and to turn tar into a perennial innovation, this method likely needed to be scaled up. Yet, it is currently unknown how scaling Palaeolithic technological processes influences their complexity. We used Petri net models and the Extended Cyclomatic Metric to measure system complexity of birch tar production with a single and three concurrent condensation assemblies. Our results show that changing the number of concurrent tar production assemblies substantially increases the measured complexity. This has potential implications on the behavioural and cognitive capacities required by Neanderthals, such as an increase in cooperation or inhibition control.},
}

@article {pmid37676865,
year = {2023},
author = {Flegontov, P and Işıldak, U and Maier, R and Yüncü, E and Changmai, P and Reich, D},
title = {Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes.},
journal = {PLoS genetics},
volume = {19},
number = {9},
pages = {e1010931},
doi = {10.1371/journal.pgen.1010931},
pmid = {37676865},
issn = {1553-7404},
abstract = {f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.},
}

@article {pmid37675658,
year = {2023},
author = {Mester, Z and Coqueugniot, H and Tillier, AM and Rosendahl, W and Friedrich, R and Zink, A and Maixner, F and Dutour, O and Bereczki, Z and Gasparik, M and Pap, I and Pálfi, G},
title = {First direct dating of the Late Neanderthal remains from Subalyuk Cave in Northern Hungary.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {},
number = {},
pages = {},
doi = {10.1127/anthranz/2023/1716},
pmid = {37675658},
issn = {0003-5548},
abstract = {The Subalyuk hominin remains were uncovered in 1932 in a cave of the same name in the Bükk Mountains, near the village of Cserépfalu in Borsod-Abaúj-Zemplén County, Northern Hungary. The remains represent two individuals, an adult and a young child who have been described in a few publications since their discovery, providing substantial anthropological data and general assessments of their Neanderthal affiliation. They were associated with Late Mousterian industry. Thus, the Bükk Mountains gain importance in the discussion concerning the contribution of East Central European sites to the debate on the peopling history of Europe during the Late Middle to Early Upper Palaeolithic transition. In this paper, we summarize the archaeological and chronological context of the two individuals, and publish the first direct dating results that place them among the Last Neanderthals of Central Europe.},
}

@article {pmid37660151,
year = {2023},
author = {Glunčić, M and Vlahović, I and Rosandić, M and Paar, V},
title = {Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14420},
pmid = {37660151},
issn = {2045-2322},
support = {KK.01.1.1.01.0004//Competitiveness and Cohesion Operational Programme - European Regional Development Fund/ ; IP-2019-04-2757//Hrvatska Zaklada za Znanost/ ; },
abstract = {It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.},
}

@article {pmid37659139,
year = {2023},
author = {Fiorenza, L and Habashi, W and Moggi-Cecchi, J and Benazzi, S and Sarig, R},
title = {Relationship between interproximal and occlusal wear in Australopithecus africanus and Neanderthal molars.},
journal = {Journal of human evolution},
volume = {183},
number = {},
pages = {103423},
doi = {10.1016/j.jhevol.2023.103423},
pmid = {37659139},
issn = {1095-8606},
}

@article {pmid37578977,
year = {2023},
author = {Chevy, ET and Huerta-Sánchez, E and Ramachandran, S},
title = {Integrating sex-bias into studies of archaic introgression on chromosome X.},
journal = {PLoS genetics},
volume = {19},
number = {8},
pages = {e1010399},
pmid = {37578977},
issn = {1553-7404},
support = {R01 GM118652/GM/NIGMS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; R35 GM139628/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Male ; *Hominidae/genetics ; Genome ; X Chromosome/genetics ; Asian People ; Genome, Human ; *Neanderthals/genetics ; },
abstract = {Evidence of interbreeding between archaic hominins and humans comes from methods that infer the locations of segments of archaic haplotypes, or 'archaic coverage' using the genomes of people living today. As more estimates of archaic coverage have emerged, it has become clear that most of this coverage is found on the autosomes- very little is retained on chromosome X. Here, we summarize published estimates of archaic coverage on autosomes and chromosome X from extant human samples. We find on average 7 times more archaic coverage on autosomes than chromosome X, and identify broad continental patterns in this ratio: greatest in European samples, and least in South Asian samples. We also perform extensive simulation studies to investigate how the amount of archaic coverage, lengths of coverage, and rates of purging of archaic coverage are affected by sex-bias caused by an unequal sex ratio within the archaic introgressors. Our results generally confirm that, with increasing male sex-bias, less archaic coverage is retained on chromosome X. Ours is the first study to explicitly model such sex-bias and its potential role in creating the dearth of archaic coverage on chromosome X.},
}

Animals
Humans
Male
*Hominidae/genetics
Genome
X Chromosome/genetics
Asian People
Genome, Human
*Neanderthals/genetics

@article {pmid37609337,
year = {2023},
author = {Yee, SW and Ferrández-Peral, L and Alentorn, 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 Capra, JA and Artursson, P and Newman, JW and Marques-Bonet, T and Giacomini, KM},
title = {Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.08.08.552553},
pmid = {37609337},
abstract = {SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.},
}

@article {pmid37588361,
year = {2020},
author = {Sánchez Goñi, MF},
title = {Regional impacts of climate change and its relevance to human evolution.},
journal = {Evolutionary human sciences},
volume = {2},
number = {},
pages = {e55},
pmid = {37588361},
issn = {2513-843X},
abstract = {The traditional concept of long and gradual, glacial-interglacial climate changes during the Quaternary has been challenged since the 1980s. High temporal resolution analysis of marine, terrestrial and ice geological archives has identified rapid, millennial- to centennial-scale, and large-amplitude climatic cycles throughout the last few million years. These changes were global but have had contrasting regional impacts on the terrestrial and marine ecosystems, with in some cases strong changes in the high latitudes of both hemispheres but muted changes elsewhere. Such a regionalization has produced environmental barriers and corridors that have probably triggered niche contractions/expansions of hominin populations living in Eurasia and Africa. This article reviews the long- and short-timescale ecosystem changes that have punctuated the last few million years, paying particular attention to the environments of the last 650,000 years, which have witnessed key events in the evolution of our lineage in Africa and Eurasia. This review highlights, for the first time, a contemporaneity between the split between Denisovan and Neanderthals, at ~650-400 ka, and the strong Eurasian ice-sheet expansion down to the Black Sea. This ice expansion could form an ice barrier between Europe and Asia that may have triggered the genetic drift between these two populations.},
}

@article {pmid37574541,
year = {2023},
author = {Piccardi, M and Gentiluomo, M and Bertoncini, S and Pezzilli, R and Erőss, B and Bunduc, S and Uzunoglu, FG and Talar-Wojnarowska, R and Vanagas, T and Sperti, C and Oliverius, M and Aoki, MN and Ermini, S and Hussein, T and Boggi, U and Jamroziak, K and Maiello, E and Morelli, L and Vodickova, L and Di Franco, G and Landi, S and Szentesi, A and Lovecek, M and Puzzono, M and Tavano, F and van Laarhoven, HWM and Zerbi, A and Mohelnikova-Duchonova, B and Stocker, H and Costello, E and Capurso, G and Ginocchi, L and Lawlor, RT and Vanella, G and Bazzocchi, F and Izbicki, JR and Latiano, A and Bueno-de-Mesquita, B and Ponz de Leon Pisani, R and Schöttker, B and Soucek, P and Hegyi, P and Gazouli, M and Hackert, T and Kupcinskas, J and Poskiene, L and Tacelli, M and Roth, S and Carrara, S and Perri, F and Hlavac, V and Theodoropoulos, GE and Busch, OR and Mambrini, A and van Eijck, CHJ and Arcidiacono, P and Scarpa, A and Pasquali, C and Basso, D and Lucchesi, M and Milanetto, AC and Neoptolemos, JP and Cavestro, GM and Janciauskas, D and Chen, X and Chammas, R and Goetz, M and Brenner, H and Archibugi, L and Dannemann, M and Canzian, F and Tofanelli, S and Campa, D},
title = {Exploring the Neandertal legacy of pancreatic ductal adenocarcinoma risk in Eurasians.},
journal = {Biological research},
volume = {56},
number = {1},
pages = {46},
pmid = {37574541},
issn = {0717-6287},
support = {C7690/A26881/CRUK_/Cancer Research UK/United Kingdom ; },
abstract = {BACKGROUND: The genomes of present-day non-Africans are composed of 1-3% of Neandertal-derived DNA as a consequence of admixture events between Neandertals and anatomically modern humans about 50-60 thousand years ago. Neandertal-introgressed single nucleotide polymorphisms (aSNPs) have been associated with modern human disease-related traits, which are risk factors for pancreatic ductal adenocarcinoma (PDAC), such as obesity, type 2 diabetes, and inflammation. In this study, we aimed at investigating the role of aSNPs in PDAC in three Eurasian populations.

RESULTS: The high-coverage Vindija Neandertal genome was used to select aSNPs in non-African populations from 1000 Genomes project phase 3 data. Then, the association between aSNPs and PDAC risk was tested independently in Europeans and East Asians, using existing GWAS data on more than 200 000 individuals. We did not find any significant associations between aSNPs and PDAC in samples of European descent, whereas, in East Asians, we observed that the Chr10p12.1-rs117585753-T allele (MAF = 10%) increased the risk to develop PDAC (OR = 1.35, 95%CI 1.19-1.54, P = 3.59 × 10[-6]), with a P-value close to a threshold that takes into account multiple testing.

CONCLUSIONS: Our results show only a minimal contribution of Neandertal SNPs to PDAC risk.},
}

@article {pmid37561879,
year = {2023},
author = {Ruan, J and Timmermann, A and Raia, P and Yun, KS and Zeller, E and Mondanaro, A and Di Febbraro, M and Lemmon, D and Castiglione, S and Melchionna, M},
title = {Climate shifts orchestrated hominin interbreeding events across Eurasia.},
journal = {Science (New York, N.Y.)},
volume = {381},
number = {6658},
pages = {699-704},
doi = {10.1126/science.add4459},
pmid = {37561879},
issn = {1095-9203},
abstract = {When, where, and how often hominin interbreeding happened is largely unknown. We study the potential for Neanderthal-Denisovan admixture using species distribution models that integrate extensive fossil, archaeological, and genetic data with transient coupled general circulation model simulations of global climate and biomes. Our Pleistocene hindcast of past hominins' habitat suitability reveals pronounced climate-driven zonal shifts in the main overlap region of Denisovans and Neanderthals in central Eurasia. These shifts, which influenced the timing and intensity of potential interbreeding events, can be attributed to the response of climate and vegetation to past variations in atmospheric carbon dioxide and Northern Hemisphere ice-sheet volume. Therefore, glacial-interglacial climate swings likely played an important role in favoring gene flow between archaic humans.},
}

@article {pmid37561595,
year = {2023},
author = {Garralda, MD and Le Cabec, A and Maíllo Fernández, JM and Maureille, B and Gunz, P and Neira, A and Hublin, JJ and Bernaldo de Quirós, F},
title = {Mousterian human fossils from El Castillo cave (Puente Viesgo, Cantabria, Spain).},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10021},
pmid = {37561595},
issn = {2037-0644},
abstract = {El Castillo cave is a well-known site because of its Paleolithic archaeology and parietal rock art. This paper is focused on the human remains found by V. Cabrera in the Mousterian Unit XX assigned to MIS 4 and early MIS 3. The fossils consist of one upper left second premolar (ULP4), one incomplete proximal hand phalanx, and one partial femoral head. The tooth and the phalanx were assigned to adults, whereas the femoral head belonged to an immature individual due to the absence of fusion traces to the metaphyseal surface. The external morphology and metrical characterization of the Castillo-1466 (ULP4) tooth crown was quantified and compared to the variability of other Neanderthal dental remains and a sample of modern human populations. We also quantified its 3D enamel thickness distribution, its roots morphology, as well as the presence of chipping, and their possible relation to masticatory or paramasticatory activities. Castillo-1466 shows crown dimensions compatible with middle-sized Neanderthal teeth, but with a remarkably thicker enamel than other Neanderthal premolars, such as Marillac 13. The femoral head and the hand phalanx fragment are compared to published values for Neanderthals, although both partial fossils lack diagnostic features precluding any clear taxonomic diagnostic. Therefore, their attribution to Neanderthals is assumed based on the dating of the layers in which they were discovered. El Castillo cave Mousterian fossils represent another contribution to the knowledge of the Middle Paleolithic populations of Northern Spain, where different sites along the Cantabrian mountains yielded several human remains assigned to MIS 4 and early MIS 3.},
}

@article {pmid37558883,
year = {2023},
author = {Aquino, Y and Bisiaux, A and Li, Z and O'Neill, M and Mendoza-Revilla, J and Merkling, SH and Kerner, G and Hasan, M and Libri, V and Bondet, V and Smith, N and de Cevins, C and Ménager, M and Luca, F and Pique-Regi, R and Barba-Spaeth, G and Pietropaoli, S and Schwartz, O and Leroux-Roels, G and Lee, CK and Leung, K and Wu, JT and Peiris, M and Bruzzone, R and Abel, L and Casanova, JL and Valkenburg, SA and Duffy, D and Patin, E and Rotival, M and Quintana-Murci, L},
title = {Dissecting human population variation in single-cell responses to SARS-CoV-2.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37558883},
issn = {1476-4687},
abstract = {Humans display substantial interindividual clinical variability after SARS-CoV-2 infection[1-3], the genetic and immunological basis of which has begun to be deciphered[4]. However, the extent and drivers of population differences in immune responses to SARS-CoV-2 remain unclear. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells-from 222 healthy donors of diverse ancestries-that were stimulated with SARS-CoV-2 or influenza A virus. We show that SARS-CoV-2 induces weaker, but more heterogeneous, interferon-stimulated gene activity compared with influenza A virus, and a unique pro-inflammatory signature in myeloid cells. Transcriptional responses to viruses display marked population differences, primarily driven by changes in cell abundance including increased lymphoid differentiation associated with latent cytomegalovirus infection. Expression quantitative trait loci and mediation analyses reveal a broad effect of cell composition on population disparities in immune responses, with genetic variants exerting a strong effect on specific loci. Furthermore, we show that natural selection has increased population differences in immune responses, particularly for variants associated with SARS-CoV-2 response in East Asians, and document the cellular and molecular mechanisms by which Neanderthal introgression has altered immune functions, such as the response of myeloid cells to viruses. Finally, colocalization and transcriptome-wide association analyses reveal an overlap between the genetic basis of immune responses to SARS-CoV-2 and COVID-19 severity, providing insights into the factors contributing to current disparities in COVID-19 risk.},
}

@article {pmid37543983,
year = {2023},
author = {Augoyard, M and Zanolli, C and Santos, F and Oettlé, AC and L'Abbé, EN and Le Luyer, M and Cazenave, M and Colard, T and Hoffman, J and Profico, A and Bayle, P},
title = {Evaluation of age, sex, and ancestry-related variation in cortical bone and dentine volumes in modern humans, and a preliminary assessment of cortical bone-dentine covariation in later Homo.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10019},
pmid = {37543983},
issn = {2037-0644},
abstract = {Cortical bone and dentine share similarities in their embryological origin, development, and genetic background. Few analyses have combined the study of cortical bone and dentine to quantify their covariation relative to endogenous and exogenous factors. However, knowing how these tissues relate in individuals is of great importance to decipher the factors acting on their evolution, and ultimately to understand the mechanisms responsible for the different patterns of tissue proportions shown in hominins. The aims of this study are to examine age-, sex-, and ancestry-related variation in cortical bone and dentine volumes, and to preliminary assess the possible covariation between these tissues in modern humans and in five composite Neandertals. The modern analytical sample includes 12 immature individuals from France and 49 adults from France and South Africa. Three-dimensional tissue proportions were assessed from microtomographic records of radii and permanent maxillary canines. Results suggest ontogenic differences and a strong sexual dimorphism in cortical bone and dentine developments. The developmental pattern of dentine also seems to vary according to individual's ancestry. We measure a stronger covariation signal between cortical bone and dentine volumes than with any other dental tissue. A more complex covariation pattern is shown when splitting the modern sample by age, sex, and ancestry, as no signal is found in some subsamples while others show a covariation between cortical bone and either crown or radicular dentine. Finally, no difference in cortical bone volume is noticed between the modern young adults and the five young adult composite Neandertals from Marine Isotopic Stages (MIS) 5 and 3. Greater dentine Cortical bone and dentine (co)variation volumes are measured in the MIS 5 chimeric Neandertals whereas a strong interpopulation variation in dentine thickness is noticed in the MIS 3 chimeric Neandertals. Further research on the cortical bonedentine covariation will increase understanding of the impact of endogenous and exogenous factors on the development of the mineralized tissues.},
}

@article {pmid37542146,
year = {2023},
author = {Gicqueau, A and Schuh, A and Henrion, J and Viola, B and Partiot, C and Guillon, M and Golovanova, L and Doronichev, V and Gunz, P and Hublin, JJ and Maureille, B},
title = {Anatomically modern human in the Châtelperronian hominin collection from the Grotte du Renne (Arcy-sur-Cure, Northeast France).},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12682},
pmid = {37542146},
issn = {2045-2322},
mesh = {Animals ; Infant, Newborn ; Humans ; *Hominidae/anatomy & histology ; *Neanderthals ; France ; Europe ; Spain ; Fossils ; },
abstract = {Around 42,000 years ago, anatomically modern humans appeared in Western Europe to the detriment of indigenous Neanderthal groups. It is during this period that new techno-cultural complexes appear, such as the Châtelperronian that extends from northern Spain to the Paris Basin. The Grotte du Renne (Arcy-sur-Cure) is a key site for discussing the biological identity of its makers. This deposit has yielded several Neanderthal human remains in its Châtelperronian levels. However, the last inventory of the paleoanthropological collection attributed to this techno-complex allowed the identification of an ilium belonging to a neonate (AR-63) whose morphology required a thorough analysis to assess its taxonomic attribution. Using geometric morphometrics, we quantified its morphology and compared it to that of 2 Neanderthals and 32 recent individuals deceased during the perinatal period to explore their morphological variation. Our results indicate a morphological distinction between the ilia of Neanderthals and anatomically modern neonates. Although AR-63 is slightly outside recent variability, it clearly differs from the Neanderthals. We propose that this is due to its belonging to an early modern human lineage whose morphology differs slightly from present-day humans. We also explore different hypotheses about the presence of this anatomically modern neonate ilium among Neanderthal remains.},
}

Animals
Infant, Newborn
Humans
*Hominidae/anatomy & histology
*Neanderthals
France
Europe
Spain
Fossils

@article {pmid37528143,
year = {2023},
author = {Badino, F and Pini, R and Ravazzi, C and Chytrý, M and Bertuletti, P and Bortolini, E and Dudová, L and Peresani, M and Romandini, M and Benazzi, S},
title = {High-resolution ecosystem changes pacing the millennial climate variability at the Middle to Upper Palaeolithic transition in NE-Italy.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12478},
pmid = {37528143},
issn = {2045-2322},
mesh = {Humans ; Animals ; *Ecosystem ; *Neanderthals ; Forests ; Trees ; Italy ; },
abstract = {Observation of high-resolution terrestrial palaeoecological series can decipher relationships between past climatic transitions, their effects on ecosystems and wildfire cyclicity. Here we present a new radiocarbon dated record from Lake Fimon (NE-Italy) covering the 60-27 ka interval. Palynological, charcoal fragments and sediment lithology analysis were carried out at centennial to sub-centennial resolutions. Identification of the best modern analogues for MIS 3 ecosystems further enabled to thoroughly reconstruct structural changes in the vegetation through time. This series also represents an "off-site" reference record for chronologically well-constrained Palaeolithic sites documenting Neanderthal and Homo sapiens occupations within the same region. Neanderthals lived in a mosaic of grasslands and woodlands, composed of a mixture of boreal and broad-leaved temperate trees analogous to those of the modern Central-Eastern Europe, the Southern Urals and central-southern Siberia. Dry and other grassland types expanded steadily from 44 to 43 ka and peaked between 42 and 39 ka, i.e., about the same time when Sapiens reached this region. This vegetation, which finds very few reliable modern analogues in the adopted Eurasian calibration set, led to the expansion of ecosystems able to sustain large herds of herbivores. During 39-27 ka, the landscape was covered by steppe, desert-steppe and open dry boreal forests similar to those of the modern Altai-Sayan region. Both Neanderthal and Sapiens lived in contexts of expanded fire-prone ecosystems modulated by the high-frequency climatic cycles of MIS 3.},
}

Humans
Animals
*Ecosystem
*Neanderthals
Forests
Trees
Italy

@article {pmid37516110,
year = {2023},
author = {Maasch, JRMA and Torres, MDT and Melo, MCR and de la Fuente-Nunez, C},
title = {Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2023.07.001},
pmid = {37516110},
issn = {1934-6069},
abstract = {Molecular de-extinction could offer avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted within extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observed in vitro for modern and archaic protein fragments identified with panCleave. Lead peptides showed resistance to proteolysis and exhibited variable membrane permeabilization. Additionally, representative modern and archaic protein fragments showed anti-infective efficacy against A. baumannii in both a skin abscess infection model and a preclinical murine thigh infection model. These results suggest that machine-learning-based encrypted peptide prospection can identify stable, nontoxic peptide antibiotics. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery.},
}

@article {pmid37507506,
year = {2023},
author = {Sidik, S},
title = {AI search of Neanderthal proteins resurrects 'extinct' antibiotics.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37507506},
issn = {1476-4687},
}

@article {pmid37500909,
year = {2023},
author = {Pawar, H and Rymbekova, A and Cuadros-Espinoza, S and Huang, X and de Manuel, M and van der Valk, T and Lobon, I and Alvarez-Estape, M and Haber, M and Dolgova, O and Han, S and Esteller-Cucala, P and Juan, D and Ayub, Q and Bautista, R and Kelley, JL and Cornejo, OE and Lao, O and Andrés, AM and Guschanski, K and Ssebide, B and Cranfield, M and Tyler-Smith, C and Xue, Y and Prado-Martinez, J and Marques-Bonet, T and Kuhlwilm, M},
title = {Ghost admixture in eastern gorillas.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {37500909},
issn = {2397-334X},
support = {098051/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.},
}

@article {pmid37496118,
year = {2023},
author = {Muotri, AR},
title = {Brain Model Technology and Its Implications.},
journal = {Cambridge quarterly of healthcare ethics : CQ : the international journal of healthcare ethics committees},
volume = {},
number = {},
pages = {1-5},
doi = {10.1017/S096318012300018X},
pmid = {37496118},
issn = {1469-2147},
abstract = {The complexity of the human brain creates a spectrum of sophisticated behavioral repertoires, such as language, tool use, self-awareness, symbolic thought, cultural learning, and consciousness. Understanding how the human brain achieves that has been a longstanding challenge for neuroscientists and may bring insights into the evolution of human cognition and disease states. Human pluripotent stem cells could differentiate into specialized cell types and tissues in vitro. From this pluripotent state, it is possible to generate models of the human brain, such as brain organoids. The recent observation that brain organoids can spontaneously develop complex neural network activity in a dish can help one understand how neural network oscillations evolve and vary between normal and disease states. Moreover, this finding can be leveraged to other applications outside medicine, including engineering and artificial intelligence. However, as the brain model technology becomes more complex, it raises a series of ethical and moral dilemmas. This article discusses the status of this technology, some of its current limitations, and a vision of the future.},
}

@article {pmid37493308,
year = {2023},
author = {Bird, EE and Kivell, TL and Dunmore, CJ and Tocheri, MW and Skinner, MM},
title = {Trabecular bone structure of the proximal capitate in extant hominids and fossil hominins with implications for midcarpal joint loading and the dart-thrower's motion.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24824},
pmid = {37493308},
issn = {2692-7691},
support = {336301//FP7 European Research Council Starting Grant/ ; 819960//European Union's Horizon 2020 research and innovation programme/ ; 435-2017-1234//ERC-SSHRC Visiting Scholar Program and SSHRC Insight Grant/ ; //The Max Planck Society/ ; //University of Kent/ ; //The Calleva Foundation/ ; },
abstract = {OBJECTIVES: This research examines whether the distribution of trabecular bone in the proximal capitates of extant hominids, as well as several fossil hominin taxa, is associated with the oblique path of the midcarpal joint known as the dart-thrower's motion (DTM).

MATERIALS AND METHODS: We analyzed proximal capitates from extant (Pongo n = 12; Gorilla n = 11; Pan n = 10; fossil and recent Homo sapiens n = 29) and extinct (Australopithecus sediba n = 2; Homo naledi n = 1; Homo floresiensis n = 2; Neandertals n = 3) hominids using a new canonical holistic morphometric analysis, which quantifies and visualizes the distribution of trabecular bone using relative bone volume as a fraction of total volume (rBV/TV).

RESULTS: Homo sapiens and Neandertals had a continuous band of high rBV/TV that extended across the scaphoid, lunate, and hamate subarticular regions, but other fossil hominins and extant great apes did not. A. sediba expressed a distinct combination of human-like and Pan-like rBV/TV distribution. Both H. floresiensis and H. naledi had high rBV/TV on the ulnar-side of the capitate but low rBV/TV on the radial-side.

CONCLUSION: The proximal capitates of H. sapiens and Neandertals share a distinctive distribution of trabecular bone that suggests that these two species of Homo regularly load(ed) their midcarpal joints along the full extent of the oblique path of the DTM. The observed pattern in A. sediba suggests that human-like stress at the capito-scaphoid articular surface was combined with Pan-like wrist postures, whereas the patterns in H. floresiensis and H. naledi suggest their midcarpal joints were loaded differently from that of H. sapiens and Neandertals.},
}

@article {pmid37452091,
year = {2023},
author = {Yang, C and Zhou, Y and Song, Y and Wu, D and Zeng, Y and Nie, L and Liu, P and Zhang, S and Chen, G and Xu, J and Zhou, H and Zhou, L and Qian, X and Liu, C and Tan, S and Zhou, C and Dai, W and Xu, M and Qi, Y and Wang, X and Guo, L and Fan, G and Wang, A and Deng, Y and Zhang, Y and Jin, J and He, Y and Guo, C and Guo, G and Zhou, Q and Xu, X and Yang, H and Wang, J and Xu, S and Mao, Y and Jin, X and Ruan, J and Zhang, G},
title = {The complete and fully-phased diploid genome of a male Han Chinese.},
journal = {Cell research},
volume = {},
number = {},
pages = {},
pmid = {37452091},
issn = {1748-7838},
abstract = {Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.},
}

@article {pmid37406034,
year = {2023},
author = {Smith, TM and Arora, M and Bharatiya, M and Dirks, W and Austin, C},
title = {Brief Communication: Elemental Models of Primate Nursing and Weaning Revisited.},
journal = {American journal of biological anthropology},
volume = {180},
number = {1},
pages = {216-223},
pmid = {37406034},
issn = {2692-7691},
support = {R00 HD087523/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; Humans ; Weaning ; Barium/analysis ; *Tooth/chemistry ; Strontium/analysis ; Papio ; },
abstract = {OBJECTIVES: Intra-tooth patterns of trace elements barium (Ba) and strontium (Sr) have been used to infer human and nonhuman primate nursing histories, including australopithecine and Neanderthal juveniles. Here we contrast the two elemental models in first molars (M1s) of four wild baboons and explore the assumptions that underlie each.

MATERIALS AND METHODS: Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was employed to create comprehensive calcium-normalized barium and strontium (Ba/Ca, Sr/Ca) maps of M1 enamel and dentine at 35 micron resolution.

RESULTS: Postnatal Ba/Ca values were typically high, peaking ~0.5 years of age and then decreasing throughout M1 crown formation; all four individuals showed minimal Ba/Ca values between ~1.2-1.8 years, consistent with field reports of the cessation of suckling. Enamel Sr/Ca did not support patterns of previous LA-ICP-MS spot sampling as the enamel rarely showed discrete Sr/Ca secretory zonation. Increases in Sr/Ca appeared in coronal dentine beginning ~0.3 years, with varied peak value ages (~0.7-2.7 years) and no evidence of a predicted postweaning decline.

DISCUSSION: Inferences of baboon weaning ages from initial Ba/Ca minima are more congruent with behavioral observations than Sr/Ca maxima; this is consistent with studies of captive macaques of known weaning ages. Elemental variation is more apparent in the coronal dentine than the enamel of these baboons, which may relate to its more rapid mineralization and protection from the oral environment. Inferences of nursing histories from enamel Sr/Ca patterns alone should be reconsidered, and elevated values of Ba/Ca and Sr/Ca in teeth formed after weaning require further study.},
}

Animals
Humans
Weaning
Barium/analysis
*Tooth/chemistry
Strontium/analysis
Papio

@article {pmid37379741,
year = {2023},
author = {Henrion, J and Hublin, JJ and Maureille, B},
title = {New Neanderthal remains from the Châtelperronian-attributed layer X of the Grotte du Renne (Arcy-sur-Cure, France).},
journal = {Journal of human evolution},
volume = {181},
number = {},
pages = {103402},
doi = {10.1016/j.jhevol.2023.103402},
pmid = {37379741},
issn = {1095-8606},
mesh = {Animals ; *Neanderthals ; France ; *Hominidae ; Fossils ; },
}

Animals
*Neanderthals
France
*Hominidae
Fossils

@article {pmid37359819,
year = {2023},
author = {Tozzi, A},
title = {Non-ultrametric phylogenetic trees shed new light on Neanderthal introgression.},
journal = {Organisms, diversity & evolution},
volume = {},
number = {},
pages = {1-9},
pmid = {37359819},
issn = {1439-6092},
abstract = {Ultrametric spaces are widely used to depict evolutionary times in phylogenetic trees since they assume that every population/species is located at the tips of bifurcating branches of the same length. The discrete branching of ultrametric trees permits the measurement of distances between pairs of individuals that are proportional to their divergence time. Here the traditional ultrametric concept of bifurcating and divergent phylogenetic tree is overturned and a new type of non-ultrametric diagram is introduced. The objective of this study is the description of gene flows in branching species/populations in terms of converging trees instead of bifurcating trees. To provide an operational example, the paleoanthropological issue of the date of Neanderthal genome's introgression in non-African humans is examined. Neanderthals and ancient humans are not anymore two species that exchange chunks of DNA, rather become a single, novel cluster of extant hominins that must be considered by itself. The novel converging, non-ultrametric phylogenetic trees permit the calibration of molecular clocks with a twofold benefit. When the date of the branching of two population/species from a common ancestor is known, the novel approach allows to calculate the time of subsequent introgressions. On the contrary, when the date of the introgression between two population/species is known, the novel approach allows to detect the time of their previous branching from a common ancestor.},
}

@article {pmid37354658,
year = {2023},
author = {Condemi, S and Panuel, M and Chaumoitre, K and Belcastro, MG and Pietrobelli, A and Voisin, JL},
title = {A pathological Neandertal thumb phalanx from Moula-Guercy (France).},
journal = {International journal of paleopathology},
volume = {42},
number = {},
pages = {14-17},
doi = {10.1016/j.ijpp.2023.06.002},
pmid = {37354658},
issn = {1879-9825},
abstract = {OBJECTIVE: To discuss a Neandertal pathological adult first pollical proximal phalanx (I2-104) from the Baume de Moula-Guercy (Ardèche, France) and evaluate the possible causes of this pathology.

METHODS: Macroscopic analyses of external features, as well as CT imaging, were used in the analysis RESULTS: The presence of asymmetric eburnation on the distal epiphysis associated with an osteophyte on the palmar surface, as well as the absence of periosteal bone reaction visible on CT images, is consistent with osteoarthritis.

CONCLUSION: Osteoarthritis (OA) can have different origins and the cause is difficult to identify. The pathology of the Moula-Guercy I2-104 phalanx may be due to a genetic predisposition for OA known in Neandertals and associated with short limb bones. The OA could have been aggravated by the age of this individual and by an inflammatory reaction caused by repeated movements and intense vibrations provoked by high-frequency knapping or by other use of the hands SIGNIFICANCE: The I2-104 phalanx is the first Neandertal pollical phalanx known to display OA, although joints of this bone are frequently affected by this pathology in modern humans. Thus, greater insight into the presence and consequences of Neandertal behaviors is offered LIMITATION: It is impossible to give a definitive conclusion on the cause(s) of the OA in this case.

More data is needed concerning OA within Neandertals and its relationship with behavior and genetics.},
}

@article {pmid37345623,
year = {2023},
author = {Rodríguez, L and García-González, R and Arsuaga, JL and Carretero, JM},
title = {Uncovering the adult morphology of the forearm bones from the Sima de los Huesos Site in Atapuerca (Spain), with comments on biomechanical features.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25281},
pmid = {37345623},
issn = {1932-8494},
support = {//Fieldwork at the Atapuerca sites is funded by the Junta de Castilla y León and the Fundación Atapuerca/ ; PID2021-122355NB-C31//MCIN/AEI/10.13039/501100011033/FEDER, UE/ ; },
abstract = {The forearm skeleton is composed of two bones: the radius and the ulna. This is closely related to manipulative movements. The ulna is part of the elbow joint, whereas the radius and ulna together with the scaphoid and lunate bones, form the wrist joints. Thus, morphofunctional analysis of the adult Sima de los Huesos (SH) forearm bones, provides clues about manipulative activities in one Pleistocene population. From 1976 to the present, over 7000 human fossils have been recovered from the SH site. The radial sample comprised 98 labeled fragments, of which 49 belonged to adult individuals, representing at least 7 individuals. The ulnar sample included 31 labeled adult fossils representing at least nine individuals. In this study, we describe the SH radii and ulnae and analyze their functional implications for manipulative and forearm movements. We confirmed that the SH radii are long and curved, with variations in robusticity and radial tuberosity orientation. The SH ulnae are characterized by an anteriorly oriented trochlear notch, a massive olecranon process, an obliquely oriented radial notch, a blunt and short supinator crest, a gracile and curved diaphysis, and a round and anteriorly oriented pronator crests. In general, they exhibit Neanderthal morphology. The SH collection provides a unique opportunity to conduct morphological analyses of these bones in the Middle Pleistocene population.},
}

@article {pmid37343032,
year = {2023},
author = {Marquet, JC and Freiesleben, TH and Thomsen, KJ and Murray, AS and Calligaro, M and Macaire, JJ and Robert, E and Lorblanchet, M and Aubry, T and Bayle, G and Bréhéret, JG and Camus, H and Chareille, P and Egels, Y and Guillaud, É and Guérin, G and Gautret, P and Liard, M and O'Farrell, M and Peyrouse, JB and Thamó-Bozsó, E and Verdin, P and Wojtczak, D and Oberlin, C and Jaubert, J},
title = {The earliest unambiguous Neanderthal engravings on cave walls: La Roche-Cotard, Loire Valley, France.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0286568},
pmid = {37343032},
issn = {1932-6203},
mesh = {Humans ; Animals ; *Neanderthals ; Engraving and Engravings ; Caves ; France ; Europe ; Fossils ; Archaeology ; },
abstract = {Here we report on Neanderthal engravings on a cave wall at La Roche-Cotard (LRC) in central France, made more than 57±3 thousand years ago. Following human occupation, the cave was completely sealed by cold-period sediments, which prevented access until its discovery in the 19th century and first excavation in the early 20th century. The timing of the closure of the cave is based on 50 optically stimulated luminescence ages derived from sediment collected inside and from around the cave. The anthropogenic origin of the spatially-structured, non-figurative marks found within the cave is confirmed using taphonomic, traceological and experimental evidence. Cave closure occurred significantly before the regional arrival of H. sapiens, and all artefacts from within the cave are typical Mousterian lithics; in Western Europe these are uniquely attributed to H. neanderthalensis. We conclude that the LRC engravings are unambiguous examples of Neanderthal abstract design.},
}

Humans
Animals
*Neanderthals
Engraving and Engravings
Caves
France
Europe
Fossils
Archaeology

@article {pmid37342325,
year = {2023},
author = {Mocci, S and Littera, R and Chessa, L and Campagna, M and Melis, M and Ottelio, CM and Piras, IS and Lai, S and Firinu, D and Tranquilli, S and Mascia, A and Vacca, M and Schirru, D and Lecca, LI and Rassu, S and Cannas, F and Sanna, C and Carta, MG and Sedda, F and Giuressi, E and Cipri, S and Miglianti, M and Perra, A and Giglio, S},
title = {A review of the main genetic factors influencing the course of COVID-19 in Sardinia: the role of human leukocyte antigen-G.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1138559},
pmid = {37342325},
issn = {1664-3224},
mesh = {Humans ; *HLA-G Antigens/genetics ; Gene Frequency ; 3' Untranslated Regions/genetics ; *COVID-19/genetics ; SARS-CoV-2/genetics ; },
abstract = {INTRODUCTION: A large number of risk and protective factors have been identified during the SARS-CoV-2 pandemic which may influence the outcome of COVID-19. Among these, recent studies have explored the role of HLA-G molecules and their immunomodulatory effects in COVID-19, but there are very few reports exploring the genetic basis of these manifestations. The present study aims to investigate how host genetic factors, including HLA-G gene polymorphisms and sHLA-G, can affect SARS-CoV-2 infection.

MATERIALS AND METHODS: We compared the immune-genetic and phenotypic characteristics between COVID-19 patients (n = 381) with varying degrees of severity of the disease and 420 healthy controls from Sardinia (Italy).

RESULTS: HLA-G locus analysis showed that the extended haplotype HLA-G*01:01:01:01/UTR-1 was more prevalent in both COVID-19 patients and controls. In particular, this extended haplotype was more common among patients with mild symptoms than those with severe symptoms [22.7% vs 15.7%, OR = 0.634 (95% CI 0.440 - 0.913); P = 0.016]. Furthermore, the most significant HLA-G 3'UTR polymorphism (rs371194629) shows that the HLA-G 3'UTR Del/Del genotype frequency decreases gradually from 27.6% in paucisymptomatic patients to 15.9% in patients with severe symptoms (X[2 ]= 7.095, P = 0.029), reaching the lowest frequency (7.0%) in ICU patients (X[2 ]= 11.257, P = 0.004). However, no significant differences were observed for the soluble HLA-G levels in patients and controls. Finally, we showed that SARS-CoV-2 infection in the Sardinian population is also influenced by other genetic factors such as β-thalassemia trait (rs11549407C>T in the HBB gene), KIR2DS2/HLA-C C1+ group combination and the HLA-B*58:01, C*07:01, DRB1*03:01 haplotype which exert a protective effect [P = 0.005, P = 0.001 and P = 0.026 respectively]. Conversely, the Neanderthal LZTFL1 gene variant (rs35044562A>G) shows a detrimental consequence on the disease course [P = 0.001]. However, by using a logistic regression model, HLA-G 3'UTR Del/Del genotype was independent from the other significant variables [ORM = 0.4 (95% CI 0.2 - 0.7), PM = 6.5 x 10[-4]].

CONCLUSION: Our results reveal novel genetic variants which could potentially serve as biomarkers for disease prognosis and treatment, highlighting the importance of considering genetic factors in the management of COVID-19 patients.},
}

Humans
*HLA-G Antigens/genetics
Gene Frequency
3' Untranslated Regions/genetics
*COVID-19/genetics
SARS-CoV-2/genetics

@article {pmid37337589,
year = {2023},
author = {Groh, J and Coop, G},
title = {The temporal and genomic scale of selection following hybridization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37337589},
abstract = {Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the dynamics underlying these patterns within hybrid populations have been lacking. Here, we develop methods based on the Wavelet Transform to understand the spatial genomic scale of local ancestry variation and its association with recombination rates. We present theory and use simulations to show how wavelet-based decompositions of ancestry variance along the genome and the correlation between ancestry and recombination reflect the joint effects of recombination, genetic drift, and genome-wide selection against introgressed alleles. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of local ancestry variation at varying spatial genomic scales through time. Using wavelet approaches to identify the genomic scale of variance in ancestry and its correlates, we show that these methods can detect temporally localized effects of drift and selection. We apply these methods to previously published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio), and to inferred Neanderthal introgression in modern humans. Across systems, we find that upwards of 20% of the 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. We also see signals of selection at fine genomic scales and much longer time scales. However, we show that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from 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.},
}

@article {pmid37337097,
year = {2023},
author = {Baquedano, E and Arsuaga, JL and Pérez-González, A and Laplana, C and Márquez, B and Huguet, R and Gómez-Soler, S and Villaescusa, L and Galindo-Pellicena, MÁ and Rodríguez, L and García-González, R and Ortega, MC and Martín-Perea, DM and Ortega, AI and Hernández-Vivanco, L and Ruiz-Liso, G and Gómez-Hernanz, J and Alonso-Martín, JI and Abrunhosa, A and Moclán, A and Casado, AI and Vegara-Riquelme, M and Álvarez-Fernández, A and Domínguez-García, ÁC and Álvarez-Lao, DJ and García, N and Sevilla, P and Blain, HA and Ruiz-Zapata, B and Gil-García, MJ and Álvarez-Vena, A and Sanz, T and Quam, R and Higham, T},
title = {Author Correction: A symbolic Neanderthal accumulation of large herbivore crania.},
journal = {Nature human behaviour},
volume = {7},
number = {7},
pages = {1228},
doi = {10.1038/s41562-023-01650-5},
pmid = {37337097},
issn = {2397-3374},
}

@article {pmid37315093,
year = {2023},
author = {Ågren, R and Patil, S and Zhou, X and , and Sahlholm, K and Pääbo, S and Zeberg, H},
title = {Major Genetic Risk Factors for Dupuytren's Disease Are Inherited From Neandertals.},
journal = {Molecular biology and evolution},
volume = {40},
number = {6},
pages = {},
pmid = {37315093},
issn = {1537-1719},
mesh = {Animals ; Humans ; Male ; Alleles ; *Dupuytren Contracture/genetics ; *Neanderthals/genetics ; Risk Factors ; },
abstract = {Dupuytren's disease is characterized by fingers becoming permanently bent in a flexed position. Whereas people of African ancestry are rarely afflicted by Dupuytren's disease, up to ∼30% of men over 60 years suffer from this condition in northern Europe. Here, we meta-analyze 3 biobanks comprising 7,871 cases and 645,880 controls and find 61 genome-wide significant variants associated with Dupuytren's disease. We show that 3 of the 61 loci harbor alleles of Neandertal origin, including the second and third most strongly associated ones (P = 6.4 × 10-132 and P = 9.2 × 10-69, respectively). For the most strongly associated Neandertal variant, we identify EPDR1 as the causal gene. Dupuytren's disease is an example of how admixture with Neandertals has shaped regional differences in disease prevalence.},
}

Animals
Humans
Male
Alleles
*Dupuytren Contracture/genetics
*Neanderthals/genetics
Risk Factors

@article {pmid37315040,
year = {2023},
author = {Baumann, M and Plisson, H and Maury, S and Renou, S and Coqueugniot, H and Vanderesse, N and Kolobova, K and Shnaider, S and Rots, V and Guérin, G and Rendu, W},
title = {On the Quina side: A Neanderthal bone industry at Chez-Pinaud site, France.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0284081},
pmid = {37315040},
issn = {1932-6203},
mesh = {Animals ; *Neanderthals ; Acclimatization ; Artifacts ; France ; Industry ; *Reindeer ; },
abstract = {Did Neanderthal produce a bone industry? The recent discovery of a large bone tool assemblage at the Neanderthal site of Chagyrskaya (Altai, Siberia, Russia) and the increasing discoveries of isolated finds of bone tools in various Mousterian sites across Eurasia stimulate the debate. Assuming that the isolate finds may be the tip of the iceberg and that the Siberian occurrence did not result from a local adaptation of easternmost Neanderthals, we looked for evidence of a similar industry in the Western side of their spread area. We assessed the bone tool potential of the Quina bone-bed level currently under excavation at chez Pinaud site (Jonzac, Charente-Maritime, France) and found as many bone tools as flint ones: not only the well-known retouchers but also beveled tools, retouched artifacts and a smooth-ended rib. Their diversity opens a window on a range of activities not expected in a butchering site and not documented by the flint tools, all involved in the carcass processing. The re-use of 20% of the bone blanks, which are mainly from large ungulates among faunal remains largely dominated by reindeer, raises the question of blank procurement and management. From the Altai to the Atlantic shore, through a multitude of sites where only a few objects have been reported so far, evidence of a Neanderthal bone industry is emerging which provides new insights on Middle Paleolithic subsistence strategies.},
}

Animals
*Neanderthals
Acclimatization
Artifacts
France
Industry
*Reindeer

@article {pmid37308599,
year = {2023},
author = {Curtis, D and Amos, W},
title = {The human genome harbours widespread exclusive yin yang haplotypes.},
journal = {European journal of human genetics : EJHG},
volume = {},
number = {},
pages = {},
pmid = {37308599},
issn = {1476-5438},
abstract = {There have been reports of examples of exclusive yin yang haplotypes, differing at every locus, but there has been no systematic search for them. Unphased whole genome sequence data for 2504 unrelated 1000 Genomes subjects was searched for chains of SNPs having global minor allele frequency (MAF) > =0.1 made up of at least 20 SNPs in complete linkage disequilibrium with each other and with no pair being separated by more than 9 other SNPs. The global distribution of these haplotypes was investigated, along with their ancestral origins and associations with genes and phenotypes. A number of previously unrecognised repeats were noted, flagged by all or most subjects being called as heterozygotes, and these were discarded. There were 5114 exclusive yin yang haplotypes each consisting of on average 34.8 SNPs, each spanning on average 15.7 kb and cumulatively covering 80 Mb. Although for some haplotypes the MAF varied markedly between populations the average global fixation index was similar to that for SNPs elsewhere in the genome and there was no evidence of enrichment for genes or gene ontologies. For all but 92 haplotypes there were partial forms present in the chimpanzee and/or Neanderthal genome, indicating that they had been formed in a gradual process but that intermediate haplotypes were now absent from modern humans. Exclusive yin yang haplotypes cover over 2% of the human genome. The mechanisms accounting for their formation and preservation are unclear. They may serve as useful markers of the dispersal of chromosomal regions through human history.},
}

@article {pmid37304756,
year = {2023},
author = {Kou, SH and Li, J and Tam, B and Lei, H and Zhao, B and Xiao, F and Wang, SM},
title = {TP53 germline pathogenic variants in modern humans were likely originated during recent human history.},
journal = {NAR cancer},
volume = {5},
number = {3},
pages = {zcad025},
pmid = {37304756},
issn = {2632-8674},
abstract = {TP53 is crucial for maintaining genome stability and preventing oncogenesis. Germline pathogenic variation in TP53 damages its function, causing genome instability and increased cancer risk. Despite extensive study in TP53, the evolutionary origin of the human TP53 germline pathogenic variants remains largely unclear. In this study, we applied phylogenetic and archaeological approaches to identify the evolutionary origin of TP53 germline pathogenic variants in modern humans. In the phylogenic analysis, we searched 406 human TP53 germline pathogenic variants in 99 vertebrates distributed in eight clades of Primate, Euarchontoglires, Laurasiatheria, Afrotheria, Mammal, Aves, Sarcopterygii and Fish, but we observed no direct evidence for the cross-species conservation as the origin; in the archaeological analysis, we searched the variants in 5031 ancient human genomes dated between 45045 and 100 years before present, and identified 45 pathogenic variants in 62 ancient humans dated mostly within the last 8000 years; we also identified 6 pathogenic variants in 3 Neanderthals dated 44000 to 38515 years before present and 1 Denisovan dated 158 550 years before present. Our study reveals that TP53 germline pathogenic variants in modern humans were likely originated in recent human history and partially inherited from the extinct Neanderthals and Denisovans.},
}

@article {pmid37269363,
year = {2023},
author = {Garcia-Heras, J},
title = {The 2022 Nobel Prize in Physiology or Medicine.},
journal = {Journal of the Association of Genetic Technologists},
volume = {49},
number = {2},
pages = {56-67},
pmid = {37269363},
issn = {1523-7834},
abstract = {The Nobel Assembly at the Karolinska Institute awarded the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany). This award acknowledged his discoveries about the genomes of extinct hominins (Neandertal man and the Denisovans), the molecular genetic insights of human origin and evolutionary history, and the understanding of phylogenetic relationships between archaic hominins and modern humans. The scientific advances included detection of Neandertal and Denisovan DNA carried by modern humans due to past admixture events, which in turn stimulated active research about the functional and phenotypic significance of such archaic ancestry on non-disease and disease phenotypic features in modern populations. In addition, comparative genomic studies started to delineate the genes and genetic regulation mechanisms that distinguish modern-day humans from the archaic hominins and our immediate ancestors, the anatomically modern humans. These breakthroughs allowed a more thorough understanding of ancestral and modern human population genetics, and propelled the take-off of human paleogenomics as a new scientific discipline in its own right.},
}

@article {pmid37250589,
year = {2023},
author = {Demidenko, YE and Škrdla, P},
title = {Lincombian-Ranisian-Jerzmanowician Industry and South Moravian Sites: a Homo sapiens Late Initial Upper Paleolithic with Bohunician Industrial Generic Roots in Europe.},
journal = {Journal of paleolithic archaeology},
volume = {6},
number = {1},
pages = {17},
pmid = {37250589},
issn = {2520-8217},
abstract = {This article re-examines the Lincombian-Ranisian-Jerzmanowician (LRJ) industry, a well-known Early Upper Paleolithic complex in northern Europe. It is widely thought that the LRJ was produced by late Neanderthals and that its industrial roots are in late Middle Paleolithic industries with bifacial leaf points in north-western Europe. On the basis of evidence from four recently excavated open-air sites in southern Moravia (Czech Republic) (Líšeň/Podolí I, Želešice III/Želešice-Hoynerhügel, Líšeň I/Líšeň-Čtvrtě, and Tvarožná X/Tvarožná, "Za školou"), combined with findings from two cave sites in Bohemia (Nad Kačákem Cave) and southern Moravia (Pekárna Cave) and critical re-examination of the LRJ sites and materials from other areas, we propose that the LRJ should actually be considered a late Initial Upper Paleolithic industry. Its initial dates are just before Heinrich Event 4 (HE-4) and the Campanian Ignimbrite (CI) super-eruption, c. 42-40 ka cal BP. We further propose that LRJ assemblages were produced by Homo sapiens, and that its roots are in the Bohunician industry. The LRJ originated as a result of a gradual technological transition, centering on the development of Levallois points into Jerzmanowice-type blade-points. It is also suggested that the LRJ industry first appeared in Moravia, in central Europe, and spread along with its makers (Homo sapiens) across the northern latitudes of central and western Europe. Accordingly, the IUP "Bohunician package" did not disappear in Europe but gave rise to another IUP industry successfully adapted for the then steppe-tundra belts in northern Europe.},
}

@article {pmid37248239,
year = {2023},
author = {Petersen, J and Englmaier, L and Artemov, AV and Poverennaya, I and Mahmoud, R and Bouderlique, T and Tesarova, M and Deviatiiarov, R and Szilvásy-Szabó, A and Akkuratov, EE and Pajuelo Reguera, D and Zeberg, H and Kaucka, M and Kastriti, ME and Krivanek, J and Radaszkiewicz, T and Gömöryová, K and Knauth, S and Potesil, D and Zdrahal, Z and Ganji, RS and Grabowski, A and Buhl, ME and Zikmund, T and Kavkova, M and Axelson, H and Lindgren, D and Kramann, R and Kuppe, C and Erdélyi, F and Máté, Z and Szabó, G and Koehne, T and Harkany, T and Fried, K and Kaiser, J and Boor, P and Fekete, C and Rozman, J and Kasparek, P and Prochazka, J and Sedlacek, R and Bryja, V and Gusev, O and Adameyko, I},
title = {A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3092},
pmid = {37248239},
issn = {2041-1723},
mesh = {Animals ; Humans ; Body Weight ; *Energy Metabolism/genetics ; Ferritins/genetics ; *Genome-Wide Association Study ; Kidney ; Neanderthals ; },
abstract = {In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow of FAME from Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure in Fame knockout animals, corresponding to genome-wide association studies linking FAME with higher body mass index in humans. Gene expression and subcellular localization analyses reveal that FAME is a membrane-bound protein enriched in the kidneys. Although the gene knockout results in structurally normal kidneys, we detect higher albumin in urine and lowered ferritin in the blood. Through experimental validation, we confirm interactions between FAME and ferritin and show co-localization in vesicular and plasma membranes.},
}

Animals
Humans
Body Weight
*Energy Metabolism/genetics
Ferritins/genetics
*Genome-Wide Association Study
Kidney
Neanderthals

@article {pmid37246494,
year = {2023},
author = {Boneta Jiménez, I and Cardoso, JL and Pérez-García, A},
title = {The turtles from the middle Paleolithic site of Gruta Nova da Columbeira (Bombarral, Portugal): Update through an archaeozoological perspective.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25229},
pmid = {37246494},
issn = {1932-8494},
support = {PID2019-111210GB-I00//Ministerio de Ciencia e Innovación/ ; },
abstract = {Twenty-five years after the preliminary systematic study of the turtle remains (Agrionemys [=Testudo] hermanni and Emys or Mauremys) recovered from Gruta Nova da Columbeira site (Bombarral, Portugal), the results of its review from systematic and archaeozoological perspectives are presented here. Tortoise remains studies from pre-Upper Paleolithic sites worldwide have provided relevant data confirming its role as a dietary supply for hominid populations and informing about their ability to adapt to local environmental resources. The Iberian Peninsula record in general, and specifically, that from Portugal, have yielded substantial evidence to this highly debated topic. In this sense, turtle remains recovered in Gruta Nova da Columbeira site, discovered in the 1960s and the main ensemble chronologically ascribed to the MIS-5 (87.1 ± 6.3 ka BP), offer new information to this debate. Its detailed restudy, has allowed us the identification, justification, and figuration of remains attributed to two Iberian turtle taxa, Chersine hermanni and Emys orbicularis. Therefore, this update on the data concerning the turtle record from Gruta Nova da Columbeira provides new justified taxonomic evidence regarding the Iberian turtle taxa distribution during the Upper Pleistocene. The previously suggested hypothesis about the tortoise human consumption on the site is here evaluated through the development of an archaeozoological and taphonomical analysis, as well as considering the potential documentation of anthropic alterations (e.g., burning, cutmarks, percussion marks). In this sense, this hypothesis is confirmed. In addition, the presence of carnivore activity evidence indicates the engagement of other agents in the deposit formation.},
}

@article {pmid37228449,
year = {2023},
author = {Schmidt, P and Koch, TJ and Blessing, MA and Karakostis, FA and Harvati, K and Dresely, V and Charrié-Duhaut, A},
title = {Production method of the Königsaue birch tar documents cumulative culture in Neanderthals.},
journal = {Archaeological and anthropological sciences},
volume = {15},
number = {6},
pages = {84},
pmid = {37228449},
issn = {1866-9557},
abstract = {UNLABELLED: Birch tar is the oldest synthetic substance made by early humans. The earliest such artefacts are associated with Neanderthals. According to traditional interpretations, their study allows understanding Neanderthal tool behaviours, skills and cultural evolution. However, recent work has found that birch tar can also be produced with simple processes, or even result from fortuitous accidents. Even though these findings suggest that birch tar per se is not a proxy for cognition, they do not shed light on the process by which Neanderthals produced it, and, therefore, cannot evaluate the implications of that behaviour. Here, we address the question of how tar was made by Neanderthals. Through a comparative chemical analysis of the two exceptional birch tar pieces from Königsaue (Germany) and a large reference birch tar collection made with Stone Age techniques, we found that Neanderthals did not use the simplest method to make tar. Rather, they distilled tar in an intentionally created underground environment that restricted oxygen flow and remained invisible during the process. This degree of complexity is unlikely to have been invented spontaneously. Our results suggest that Neanderthals invented or developed this process based on previous simpler methods and constitute one of the clearest indicators of cumulative cultural evolution in the European Middle Palaeolithic.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12520-023-01789-2.},
}

@article {pmid37220274,
year = {2023},
author = {Tobler, R and Souilmi, Y and Huber, CD and Bean, N and Turney, CSM and Grey, ST and Cooper, A},
title = {The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {22},
pages = {e2213061120},
pmid = {37220274},
issn = {1091-6490},
mesh = {Humans ; Animals ; Africa ; *Neanderthals ; Acclimatization ; Arabia ; Selection, Genetic ; },
abstract = {The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.},
}

Humans
Animals
Africa
*Neanderthals
Acclimatization
Arabia
Selection, Genetic

@article {pmid37202264,
year = {2023},
author = {Klein, K and Weniger, GC and Ludwig, P and Stepanek, C and Zhang, X and Wegener, C and Shao, Y},
title = {Assessing climatic impact on transition from Neanderthal to anatomically modern human population on Iberian Peninsula: a macroscopic perspective.},
journal = {Science bulletin},
volume = {68},
number = {11},
pages = {1176-1186},
doi = {10.1016/j.scib.2023.04.025},
pmid = {37202264},
issn = {2095-9281},
mesh = {Humans ; Animals ; *Neanderthals ; Fossils ; Europe ; Europe, Eastern ; Archaeology ; Anti-Mullerian Hormone ; },
abstract = {The Iberian Peninsula is of particular interest for the research on the Neanderthal (NEA) to anatomically modern human (AMH) population transition. The AMHs arrived in Iberia last from Eastern Europe and thus any possible contacts between the two populations occurred here later than elsewhere. The transition process took place in the earlier part of the Marine Isotope Stage 3 (∼60-27 cal ka BP) as repeated and profound climate changes challenged the population stability. To investigate how climate change and population interactions influenced the transition, we combine climate data with archaeological-site data to reconstruct the Human Existence Potential, a measure of the probability of human existence, for both the NEA and AMH populations in the Greenland Interstadial 11-10 (GI11-10) and Stadial 10-9/Heinrich event 4 (GS10-9/HE4) times. It is found that during GS10-9/HE4, large parts of the peninsula became unsuitable for NEA human existence and the NEA settlement areas contracted to isolated coastal hot spots. As a consequence, the NEA networks became highly unstable, triggering the final collapse of the population. The AMHs arrived in Iberia in GI10 but were confined to patches in the northern most strip of the peninsula. They were soon facing the much colder climate of GS10-9/HE4, which prevented their further expansion or even caused a contraction of their settlement areas. Thus, due to the constellation of climate change and the dispersal of the two populations into different regions of the peninsula, it is unlikely that the NEAs and AMHs coexisted in extensive areas and the AMHs had a significant influence on the demography of the NEAs.},
}

Humans
Animals
*Neanderthals
Fossils
Europe
Europe, Eastern
Archaeology
Anti-Mullerian Hormone

@article {pmid37196358,
year = {2023},
author = {Cobat, A and Zhang, Q and Covid Human Genetic Effort, and Abel, L and Casanova, JL and Fellay, J},
title = {Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants.},
journal = {Annual review of biomedical data science},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biodatasci-020222-021705},
pmid = {37196358},
issn = {2574-3414},
abstract = {SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is silent or benign in most infected individuals, but causes hypoxemic COVID-19 pneumonia in about 10% of cases. We review studies of the human genetics of life-threatening COVID-19 pneumonia, focusing on both rare and common variants. Large-scale genome-wide association studies have identified more than 20 common loci robustly associated with COVID-19 pneumonia with modest effect sizes, some implicating genes expressed in the lungs or leukocytes. The most robust association, on chromosome 3, concerns a haplotype inherited from Neanderthals. Sequencing studies focusing on rare variants with a strong effect have been particularly successful, identifying inborn errors of type I interferon (IFN) immunity in 1-5% of unvaccinated patients with critical pneumonia, and their autoimmune phenocopy, autoantibodies against type I IFN, in another 15-20% of cases. Our growing understanding of the impact of human genetic variation on immunity to SARS-CoV-2 is enabling health systems to improve protection for individuals and populations. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 6 is August 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid37192163,
year = {2023},
author = {Rong, S and Neil, CR and Welch, A and Duan, C and Maguire, S and Meremikwu, IC and Meyerson, M and Evans, BJ and Fairbrother, WG},
title = {Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {21},
pages = {e2218308120},
pmid = {37192163},
issn = {1091-6490},
support = {R01 GM127472/GM/NIGMS NIH HHS/United States ; },
mesh = {Male ; Animals ; Humans ; *Neanderthals/genetics ; Semen ; *Hominidae/genetics ; Alleles ; Gene Expression Regulation ; Genome, Human ; },
abstract = {Humans coexisted and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here, we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,169 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 962 exonic splicing mutations that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than that in Neanderthals. Adaptively introgressed variants were enriched for moderate-effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a unique tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a unique Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide unique insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.},
}

Male
Animals
Humans
*Neanderthals/genetics
Semen
*Hominidae/genetics
Alleles
Gene Expression Regulation
Genome, Human

@article {pmid37156940,
year = {2023},
author = {Li, Q and Chen, J and Faux, P and Delgado, ME and Bonfante, B and Fuentes-Guajardo, M and Mendoza-Revilla, J and Chacón-Duque, JC and Hurtado, M and Villegas, V and Granja, V and Jaramillo, C and Arias, W and Barquera, R and Everardo-Martínez, P and Sánchez-Quinto, M and Gómez-Valdés, J and Villamil-Ramírez, H and Silva de Cerqueira, CC and Hünemeier, T and Ramallo, V and Wu, S and Du, S and Giardina, A and Paria, SS and Khokan, MR and Gonzalez-José, R and Schüler-Faccini, L and Bortolini, MC and Acuña-Alonzo, V and Canizales-Quinteros, S and Gallo, C and Poletti, G and Rojas, W and Rothhammer, F and Navarro, N and Wang, S and Adhikari, K and Ruiz-Linares, A},
title = {Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {481},
pmid = {37156940},
issn = {2399-3642},
support = {R01 DE027023/DE/NIDCR NIH HHS/United States ; U01 DE020078/DE/NIDCR NIH HHS/United States ; R01 DE016148/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Neanderthals/genetics ; Genome-Wide Association Study ; Nose ; Cell Differentiation ; },
abstract = {We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10[-8]) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.},
}

Humans
Animals
Mice
*Neanderthals/genetics
Genome-Wide Association Study
Nose
Cell Differentiation

@article {pmid37155903,
year = {2023},
author = {Linscott, B and Pike, AWG and Angelucci, DE and Cooper, MJ and Milton, JS and Matias, H and Zilhão, J},
title = {Reconstructing Middle and Upper Paleolithic human mobility in Portuguese Estremadura through laser ablation strontium isotope analysis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {20},
pages = {e2204501120},
pmid = {37155903},
issn = {1091-6490},
mesh = {Animals ; Humans ; Portugal ; *Hominidae ; *Tooth/chemistry ; Strontium Isotopes/analysis ; *Neanderthals ; *Laser Therapy ; Strontium/analysis ; },
abstract = {Understanding mobility and landscape use is important in reconstructing subsistence behavior, range, and group size, and it may contribute to our understanding of phenomena such as the dynamics of biological and cultural interactions between distinct populations of Upper Pleistocene humans. However, studies using traditional strontium isotope analysis are generally limited to identifying locations of childhood residence or nonlocal individuals and lack the sampling resolution to detect movement over short timescales. Here, using an optimized methodology, we present highly spatially resolved [87]Sr/[86]Sr measurements made by laser ablation multicollector inductively coupled plasma mass spectrometry along the growth axis of the enamel of two marine isotope stage 5b, Middle Paleolithic Neanderthal teeth (Gruta da Oliveira), a Tardiglacial, Late Magdalenian human tooth (Galeria da Cisterna), and associated contemporaneous fauna from the Almonda karst system, Torres Novas, Portugal. Strontium isotope mapping of the region shows extreme variation in [87]Sr/[86]Sr, with values ranging from 0.7080 to 0.7160 over a distance of c. 50 km, allowing short-distance (and arguably short-duration) movement to be detected. We find that the early Middle Paleolithic individuals roamed across a subsistence territory of approximately 600 km[2], while the Late Magdalenian individual parsimoniously fits a pattern of limited, probably seasonal movement along the right bank of the 20-km-long Almonda River valley, between mouth and spring, exploiting a smaller territory of approximately 300 km[2]. We argue that the differences in territory size are due to an increase in population density during the Late Upper Paleolithic.},
}

Animals
Humans
Portugal
*Hominidae
*Tooth/chemistry
Strontium Isotopes/analysis
*Neanderthals
*Laser Therapy
Strontium/analysis

@article {pmid37142741,
year = {2023},
author = {Brand, CM and Colbran, LL and Capra, JA},
title = {Resurrecting the alternative splicing landscape of archaic hominins using machine learning.},
journal = {Nature ecology & evolution},
volume = {7},
number = {6},
pages = {939-953},
pmid = {37142741},
issn = {2397-334X},
support = {R35 GM127087/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Hominidae/genetics ; *Neanderthals/genetics ; Alternative Splicing ; Genome, Human ; Population Density ; },
abstract = {Alternative splicing contributes to adaptation and divergence in many species. However, it has not been possible to directly compare splicing between modern and archaic hominins. Here, we unmask the recent evolution of this previously unobservable regulatory mechanism by applying SpliceAI, a machine-learning algorithm that identifies splice-altering variants (SAVs), to high-coverage genomes from three Neanderthals and a Denisovan. We discover 5,950 putative archaic SAVs, of which 2,186 are archaic-specific and 3,607 also occur in modern humans via introgression (244) or shared ancestry (3,520). Archaic-specific SAVs are enriched in genes that contribute to traits potentially relevant to hominin phenotypic divergence, such as the epidermis, respiration and spinal rigidity. Compared to shared SAVs, archaic-specific SAVs occur in sites under weaker selection and are more common in genes with tissue-specific expression. Further underscoring the importance of negative selection on SAVs, Neanderthal lineages with low effective population sizes are enriched for SAVs compared to Denisovan and shared SAVs. Finally, we find that nearly all introgressed SAVs in humans were shared across the three Neanderthals, suggesting that older SAVs were more tolerated in human genomes. Our results reveal the splicing landscape of archaic hominins and identify potential contributions of splicing to phenotypic differences among hominins.},
}

Animals
Humans
*Hominidae/genetics
*Neanderthals/genetics
Alternative Splicing
Genome, Human
Population Density

@article {pmid37142740,
year = {2023},
author = {Rotival, M},
title = {Archaic hominin traits through the splicing lens.},
journal = {Nature ecology & evolution},
volume = {7},
number = {6},
pages = {800-801},
pmid = {37142740},
issn = {2397-334X},
mesh = {Animals ; *Hominidae ; *Neanderthals ; Biological Evolution ; Phenotype ; },
}

Animals
*Hominidae
*Neanderthals
Biological Evolution
Phenotype

@article {pmid37141315,
year = {2023},
author = {Klapper, M and Hübner, A and Ibrahim, A and Wasmuth, I and Borry, M and Haensch, VG and Zhang, S and Al-Jammal, WK and Suma, H and Fellows Yates, JA and Frangenberg, J and Velsko, IM and Chowdhury, S and Herbst, R and Bratovanov, EV and Dahse, HM and Horch, T and Hertweck, C and González Morales, MR and Straus, LG and Vilotijevic, I and Warinner, C and Stallforth, P},
title = {Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6645},
pages = {619-624},
doi = {10.1126/science.adf5300},
pmid = {37141315},
issn = {1095-9203},
mesh = {Animals ; Humans ; *Biological Products/metabolism ; *Genome, Bacterial ; *Hominidae/genetics ; Metagenome ; *Neanderthals/genetics ; *Furans/metabolism ; DNA, Ancient ; },
abstract = {Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. We investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans ranging from 100,000 years ago to the present and reconstructed 459 bacterial metagenome-assembled genomes. We identified a biosynthetic gene cluster shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites that we name "paleofurans." This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.},
}

Animals
Humans
*Biological Products/metabolism
*Genome, Bacterial
*Hominidae/genetics
Metagenome
*Neanderthals/genetics
*Furans/metabolism
DNA, Ancient

@article {pmid37134082,
year = {2023},
author = {Slimak, L},
title = {The three waves: Rethinking the structure of the first Upper Paleolithic in Western Eurasia.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0277444},
pmid = {37134082},
issn = {1932-6203},
mesh = {Animals ; Humans ; *Hominidae ; Europe ; Archaeology ; France ; *Neanderthals ; Fossils ; },
abstract = {The Neronian is a lithic tradition recognized in the Middle Rhône Valley of Mediterranean France now directly linked to Homo sapiens and securely dated to 54,000 years ago (ka), pushing back the arrival of modern humans in Europe by 10 ka. This incursion of modern humans into Neandertal territory and the relationships evoked between the Neronian and the Levantine Initial Upper Paleolithic (IUP) question the validity of concepts that define the first H. sapiens migrations and the very nature of the first Upper Paleolithic in western Eurasia. Direct comparative analyses between lithic technology from Grotte Mandrin and East Mediterranean archeological sequences, especially Ksar Akil, suggest that the three key phases of the earliest Levantine Upper Paleolithic have very precise technical and chronological counterparts in Western Europe, recognized from the Rhône Valley to Franco-Cantabria. These trans-Mediterranean technical connections suggest three distinct waves of H. sapiens expansion into Europe between 55-42 ka. These elements support an original thesis on the origin, structure, and evolution of the first moments of the Upper Paleolithic in Europe tracing parallel archaeological changes in the East Mediterranean region and Europe.},
}

Animals
Humans
*Hominidae
Europe
Archaeology
France
*Neanderthals
Fossils

@article {pmid37114314,
year = {2022},
author = {Benítez-Burraco, A and Torres-Ruiz, R and Gelabert, P and Lalueza-Fox, C and Rodríguez-Perales, S and García-Bellido, P},
title = {Human-specific changes in two functional enhancers of FOXP2.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {68},
number = {11},
pages = {16-19},
doi = {10.14715/cmb/2022.68.11.3},
pmid = {37114314},
issn = {1165-158X},
mesh = {Humans ; *Forkhead Transcription Factors/genetics/metabolism ; },
abstract = {FOXP2 is a gene involved in language development and function. Neanderthals and humans share the same coding region of the gene, although the formers are thought to have exhibited less sophisticated language abilities. In this paper, we report on several human-specific changes in two functional enhancers of FOXP2. Two of these variants are located within the binding sites for the transcription factors POLR2A and SMARCC1, respectively. Interestingly, SMARCC1 is involved in brain development and vitamin D metabolism. We hypothesize that the human specific change in this position might have resulted in a different regulation pattern of FOXP2 expression in our species compared to extinct hominins, with a potential impact on our language abilities.},
}

Humans
*Forkhead Transcription Factors/genetics/metabolism

@article {pmid37103242,
year = {2023},
author = {Witt, KE and Funk, A and Añorve-Garibay, V and Fang, LL and Huerta-Sánchez, E},
title = {The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations.},
journal = {Genome biology and evolution},
volume = {15},
number = {5},
pages = {},
pmid = {37103242},
issn = {1759-6653},
support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; EHS 1R35GM128946-01/NH/NIH HHS/United States ; },
mesh = {Animals ; Humans ; DNA ; Genome, Human ; *Hominidae/genetics ; *Neanderthals/genetics ; },
abstract = {Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, which have shaped genetic ancestry in modern humans. For example, populations in the Americas are often mosaics of different ancestries due to recent admixture events as part of European colonization. Admixed individuals also often have introgressed DNA from Neanderthals and Denisovans that may have come from multiple ancestral populations, which may affect how archaic ancestry is distributed across an admixed genome. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual's archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight increase of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.},
}

Animals
Humans
DNA
Genome, Human
*Hominidae/genetics
*Neanderthals/genetics

@article {pmid37100851,
year = {2023},
author = {Ríos, L and Sleeper, MM and Danforth, MD and Murphy, HW and Kutinsky, I and Rosas, A and Bastir, M and Gómez-Cambronero, J and Sanjurjo, R and Campens, L and Rider, O and Pastor, F},
title = {The aorta in humans and African great apes, and cardiac output and metabolic levels in human evolution.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {6841},
pmid = {37100851},
issn = {2045-2322},
mesh = {Adult ; Animals ; Humans ; *Hominidae/physiology ; Gorilla gorilla ; Pan troglodytes ; *Neanderthals ; Aorta ; Cardiac Output ; Biological Evolution ; },
abstract = {Humans have a larger energy budget than great apes, allowing the combination of the metabolically expensive traits that define our life history. This budget is ultimately related to the cardiac output, the product of the blood pumped from the ventricle and the number of heart beats per minute, a measure of the blood available for the whole organism physiological activity. To show the relationship between cardiac output and energy expenditure in hominid evolution, we study a surrogate measure of cardiac output, the aortic root diameter, in humans and great apes. When compared to gorillas and chimpanzees, humans present an increased body mass adjusted aortic root diameter. We also use data from the literature to show that over the human lifespan, cardiac output and total energy expenditure follow almost identical trajectories, with a marked increase during the period of brain growth, and a plateau during most of the adult life. The limited variation of adjusted cardiac output with sex, age and physical activity supports the compensation model of energy expenditure in humans. Finally, we present a first study of cardiac output in the skeleton through the study of the aortic impression in the vertebral bodies of the spine. It is absent in great apes, and present in humans and Neanderthals, large-brained hominins with an extended life cycle. An increased adjusted cardiac output, underlying higher total energy expenditure, would have been a key process in human evolution.},
}

Adult
Animals
Humans
*Hominidae/physiology
Gorilla gorilla
Pan troglodytes
*Neanderthals
Aorta
Cardiac Output
Biological Evolution

@article {pmid37091460,
year = {2023},
author = {Sinaei, R and Pezeshki, S and Sinaei, R},
title = {What Kept Back on the Mirror of COVID-19-Related Acute Transverse Myelitis? A Genetic Background!.},
journal = {Iranian journal of child neurology},
volume = {17},
number = {2},
pages = {143-147},
pmid = {37091460},
issn = {1735-4668},
abstract = {COVID-19-associated acute transverse myelitis (ATM) cases have been reported worldwide. Nevertheless, Iran, Italy, and the USA are the most affected countries, witnessing the possibility that genetic factors might be associated with this susceptibility. The genetic variants of the coronavirus-2 entry mechanisms and host innate immune response-related genes like interferons, interleukins, Toll-like receptors, human leukocyte antigens, blood groups, and some risk loci may be accountable. This study describes the compatibility of the geographical distribution between ATM and the Neanderthal core haplotype that confers risk for severe COVID-19 and some possible culprit genes.},
}

@article {pmid37070424,
year = {2023},
author = {Gómez-Olivencia, A and Arsuaga, JL},
title = {The Sima de los Huesos cervical spine.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25224},
pmid = {37070424},
issn = {1932-8494},
support = {//Fundación Atapuerca/ ; //Junta de Castilla y León/ ; PGC2018-093925-B-C33, MCI/AEI/FEDER, UE//Ministerio de Ciencia e Innovación/ ; PID2021-122355NB-C31, MCIN/AEI/10.13039/5011000110, UE//Ministerio de Ciencia e Innovación/ ; RYC-2017-22558//Ramón y Cajal fellowship/ ; },
abstract = {Information regarding the evolution of the neck in genus Homo is hampered owing to a limited fossil record. Neandertals display significant metric and/or morphological differences in all the cervical vertebrae, 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 about the evolution of this anatomical region within the Neandertal lineage, but also provides important clues to understand the evolution of this region at the genus level. We present the current knowledge of the anatomy of the cervical spine of the hominins found in SH compared to that of Neandertals and modern humans, and, when possible, to Homo erectus and Homo antecessor. The current SH fossil record comprises 172 cervical specimens (after refittings) belonging to a minimum of 11 atlases, 13 axes, and 52 subaxial cervical vertebrae. The SH hominins exhibit a morphological pattern in their cervical spine more similar to that of Neandertals than 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 this anatomical region, primarily in the length and robusticity, and to a lesser extent in the orientation of the spinous processes of the lowermost cervical vertebrae. We hypothesize that these differences in the lowermost subaxial cervical vertebrae could be related to the increase in the brain size and/or changes in the morphology of the skull that occurred in the Neandertal lineage.},
}

@article {pmid37053172,
year = {2023},
author = {Doronicheva, EV and Golovanova, LV and Doronichev, VB and Kurbanov, RN},
title = {Archaeological evidence for two culture diverse Neanderthal populations in the North Caucasus and contacts between them.},
journal = {PloS one},
volume = {18},
number = {4},
pages = {e0284093},
pmid = {37053172},
issn = {1932-6203},
mesh = {Animals ; *Neanderthals ; Fossils ; *Hominidae ; Europe ; Europe, Eastern ; Archaeology ; },
abstract = {Neanderthals were widespread during the Middle Palaeolithic (MP) across Europe and Asia, including the Caucasus Mountains. Occupying the border between eastern Europe and West Asia, the Caucasus is important region regarding the Neanderthal occupation of Eurasia. On current radiometric estimates, the MP is represented in the Caucasus between about 260-210 ka and about 40 ka. Archaeological record indicates that several culture diverse MP hominin populations inhabited the Caucasus, but the region complex population history during this period remains poorly understood. In this paper, we identify for the first time the archaeological evidence indicating contacts between two culture diverse MP Neanderthal populations in the North Caucasus and discuss the nature of these contacts. Basing on the lithic assemblages that we excavated at Mezmaiskaya cave in the north-western Caucasus (Kuban River basin) and Saradj-Chuko grotto in the north-central Caucasus (Terek River basin), dating from MIS 5 to MIS 3, and comparative data from other MP sites in the Caucasus, we identify two large cultural regions that existed during the late MP in the North Caucasus. The distinctive toolkits and stone knapping technologies indicate that the MP assemblages from Mezmaiskaya cave and other sites in the west of North Caucasus represent a Caucasian variant of the Eastern Micoquian industry that was wide spread in central and eastern Europe, while the assemblages from Saradj-Chuko Grotto and other sites in the east of North Caucasus closely resemble the Zagros Mousterian industry that was wide spread in the Armenian Highlands, Lesser Caucasus and Zagros Mountains. The archaeological evidence implies that two culture diverse populations of Neanderthals settled the North Caucasus during the Late Pleistocene from two various source regions: from the Armenian Highlands and Lesser Caucasus along the Caspian Sea coast, and from Russian plain along the Sea of Azov coast.},
}

Animals
*Neanderthals
Fossils
*Hominidae
Europe
Europe, Eastern
Archaeology

@article {pmid37035790,
year = {2023},
author = {Chung, S and Son, JW},
title = {How Well Do We Understand Autistic Savant Artists: A Review of Various Hypotheses and Research Findings to Date.},
journal = {Soa--ch'ongsonyon chongsin uihak = Journal of child & adolescent psychiatry},
volume = {34},
number = {2},
pages = {93-111},
pmid = {37035790},
issn = {1225-729X},
abstract = {The authors investigated the artistic characteristics of autistic savant artists, hypotheses on the proximate and ultimate causes of their emergence, recent psychological and other studies about them, and psychological and neuroaesthetic studies about non-savant autistic individuals. The artistic features of autistic savant artists were significantly similar to those of outsider artists. Furthermore, the authors investigated the explanatory power of the paradoxical functional facilitation theory, the superior visual perception hypothesis, the "Hmmmmm" hypothesis, and the Neanderthal theory of autism regarding the emergence of autistic savant artists. In addition, we investigated whether an increase in savant characteristics was related to a decrease in the ability for social communication. The authors suggested that in studies on the aesthetic experience of non-savant autistic individuals, their aesthetic experience ability is never lower than that of neurotypical individuals and that some non-savant autistic individuals may potentially have artistic talent. Finally, the authors reviewed the effectiveness of the "autism savant spectrum syndromic disorder" proposed by some researchers. More scientific and systematic studies on autistic savant artists from a multidisciplinary perspective are warranted.},
}

@article {pmid37016656,
year = {2023},
author = {Turner, MD},
title = {Possible Causes of Hypertrophic Osteoarthropathy in the La Ferrassie 1 Neanderthal.},
journal = {Cureus},
volume = {15},
number = {3},
pages = {e35721},
pmid = {37016656},
issn = {2168-8184},
abstract = {For over a century, researchers have been perplexed by the unique osteological findings on La Ferrassie 1 (LF1), one of the most complete Neanderthal remains ever found. In 1997, Fennel and Trinkaus proposed that LF1 suffered from hypertrophic osteoarthropathy (HOA), likely secondary to chronic thoracic infection or pulmonary malignancy. This disease process can have many etiologies, and no study has fully explored the possible origin of LF1's HOA. Ultimately, it is most likely that LF1's HOA etiology arose from one of the many infectious diseases that prehistoric Neanderthals were exposed to, specifically a chronic pulmonary RNA virus.},
}

@article {pmid37010952,
year = {2023},
author = {Richards, GD and Jabbour, RS and Guipert, G and Defleur, A},
title = {Neanderthal child's maxilla from Baume Moula-Guercy (Soyons, Ardèche, France).},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25218},
pmid = {37010952},
issn = {1932-8494},
support = {03-Activity-059//University of the Pacific/ ; //Saint Mary's College of California/ ; },
abstract = {This article provides an ontogenetically-based comparative description of the Guercy 3 partial child's maxilla with Rdm[2] -RM[1] and unerupted RI[2] -RP[4] from Baume Moula-Guercy (MIS 5e) and examines its affinities to European and Middle Eastern Middle-to-Late Pleistocene (≈MIS 14-MIS 1) Homo. Description of the Guercy 3 maxilla and dentition (7.0 year ± 0.9 month) is based on observations of original fossils, casts, CT scans, literature descriptions, and virtual reconstructions. Our ontogenetic sample comprises 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), Upper (MIS 3-2), and Late Upper Paleolithic (≈MIS 1), and recent H. sapiens. Standard techniques were employed for measurements and developmental age determinations.The Guercy 3 maxilla lacks changes found in Late Neanderthals, including the positioning of the root of the zygomatic process, infraorbital and nasal plates, premaxilla, buccal and labial alveolus, maxillary sinus, nasal cavity, and verticality of anterior tooth implantation. The morphology of the Guercy 3 maxilla more closely approximates that of Sima de los Huesos Preneanderthals, while the dentition more closely approximates the Early-Late Neanderthal condition. Maxillary remains of children and juveniles between MIS 14-MIS 5e are rare, and the available sample is fragmentary and distorted. Although fragmentary, the Guercy 3 maxilla is undistorted and provides new insights into the evolution of the midface in Neanderthals.},
}

@article {pmid37001690,
year = {2023},
author = {Pomeroy, E},
title = {Review: The different adaptive trajectories in Neanderthals and Homo sapiens and their implications for contemporary human physiological variation.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {280},
number = {},
pages = {111420},
doi = {10.1016/j.cbpa.2023.111420},
pmid = {37001690},
issn = {1531-4332},
mesh = {Humans ; Animals ; *Neanderthals/anatomy & histology/physiology ; Acclimatization ; Climate ; Adaptation, Physiological ; Cold Climate ; Fossils ; },
abstract = {Neanderthals are our one of our closest evolutionary cousins, but while they evolved in Eurasia, we (anatomically modern humans, AMH) originated in Africa. This contrasting evolutionary history has led to morphological and genetic distinctions between our species. Neanderthals are characterised by a relatively stocky build, high body mass, proportionally wide bodies and shorter limbs, a bell-shaped ribcage with a wide pelvis, and a long, low cranial vault compared with AMH. Classic readings of Neanderthal morphology link many of these traits to cold climate adaptations, however these interpretations have been questioned and alternative hypotheses including behavioural factors, dietary adaptations, locomotor specialisations, evolutionary history and neutral evolutionary processes have been invoked. Compared with AMH, Neanderthals may have been adapted for strength and power rather than endurance and may have consumed a diet high in animal products. However, reviewing these hypotheses highlights a number of limitations in our understanding of contemporary human physiology and metabolism, including the relationship between climate and morphology in AMH and Neanderthals, physiological limits on protein consumption, and the relationship between gut morphology and diet. As various relevant factors are clearly linked (e.g. diet, behaviour, metabolism, morphology, activity), ultimately a more integrated approach may be needed to fully understand Neanderthal biology. Variation among contemporary AMHs may offer, with caveats, a useful model for understanding the evolution of both Neanderthal and modern human characteristics, which in turn may further deepen our understanding of variability within and between contemporary humans. Neanderthals; Anatomically modern humans; morphology; climate adaptation; power adaptations; metabolism; diet; physiology; endurance running.},
}

Humans
Animals
*Neanderthals/anatomy & histology/physiology
Acclimatization
Climate
Adaptation, Physiological
Cold Climate
Fossils

@article {pmid36998196,
year = {2023},
author = {Quam, R and Martínez, I and Rak, Y and Hylander, B and Pantoja, A and Lorenzo, C and Conde-Valverde, M and Keeling, B and Ortega Martínez, MC and Arsuaga, JL},
title = {The Neandertal nature of the Atapuerca Sima de los Huesos mandibles.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25190},
pmid = {36998196},
issn = {1932-8494},
support = {PID2021-122355NB-C31MCIN/AEI/10.13039/501100011033/FEDER,UE,//Ministerio de Ciencia e Innovación of the Government of Spain/ ; },
abstract = {The recovery of additional mandibular fossils from the Atapuerca Sima de los Huesos (SH) site provides new insights into the evolutionary significance of this sample. In particular, morphological descriptions of the new adult specimens are provided, along with standardized metric data and phylogenetically relevant morphological features for the expanded adult sample. The new and more complete specimens extend the known range of variation in the Atapuerca (SH) mandibles in some metric and morphological details. In other aspects, the addition of new specimens has made it possible to confirm previous observations based on more limited evidence. Pairwise comparisons of individual metric variables revealed the only significant difference between the Atapuerca (SH) hominins and Neandertals was a more vertical symphysis in the latter. Similarly, principal components analysis of size-adjusted variables showed a strong similarity between the Atapuerca (SH) hominins and Neandertals. Morphologically, the Atapuerca (SH) mandibles show nearly the full complement of Neandertal-derived features. Nevertheless, the Neandertals differ from the Atapuerca (SH) mandibles in showing a high frequency of the H/O mandibular foramen, a truncated, thinned and inverted gonial margin, a high placement of the mylohyoid line at the level of the M3, a more vertical symphysis and somewhat more pronounced expression of the chin structures. Size-related morphological variation in the SH hominins includes larger retromolar spaces, more posterior placement of the lateral corpus structures, and stronger markings associated with the muscles of mastication in larger specimens. However, phylogenetically relevant features in the SH sample are fairly stable and do not vary with the overall size of the mandible. Direct comparison of the enlarged mandibular sample from Atapuerca (SH) with the Mauer mandible, the type specimen of H. heidelbergensis, reveals important differences from the SH hominins, and there is no morphological counterpart of Mauer within the SH sample, suggesting the SH fossils should not be assigned to this taxon. The Atapuerca (SH) mandibles show a greater number of derived Neandertal features, particularly those related to midfacial prognathism and in the configuration of the superior ramus, than other European middle Pleistocene specimens. This suggests that more than one evolutionary lineage co-existed in the middle Pleistocene, and, broadly speaking, it appears possible to separate the European middle Pleistocene mandibular remains into two distinct groupings. One group shows a suite of derived Neandertal features and includes specimens from the sites of Atapuerca (SH), Payre, l'Aubesier and Ehringsdorf. The other group includes specimens that generally lack derived Neandertal features and includes the mandibles from the sites of Mauer, Mala Balanica, Montmaurin and (probably) Visogliano. The two published Arago mandibles differ strongly from one another, with Arago 2 probably belonging to this former group, and Neandertal affinities being more difficult to identify in Arago 13. Outside of the SH sample, derived Neandertal features in the mandible only become more common during the second half of the middle Pleistocene. Acceptance of a cladogenetic pattern of evolution during the European middle Pleistocene has the potential to reconcile the predictions of the accretion model and the two phases model for the appearance of Neandertal morphology. The precise taxonomic classification of the SH hominins must contemplate features from the dentition, cranium, mandible and postcranial skeleton, all of which are preserved at the SH site. Nevertheless, the origin of the Neandertal clade may be tied to a speciation event reflected in the appearance of a suite of derived Neandertal features in the face, dentition and mandible, all of which are present in the Atapuerca (SH) hominins. This same suite of features also provides a useful anatomical basis to include other European middle Pleistocene mandibles and crania within the Neandertal clade.},
}

@article {pmid36980999,
year = {2023},
author = {Toncheva, D and Marinova, M and Chobanov, T and Serbezov, D},
title = {Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36980999},
issn = {2073-4425},
mesh = {Animals ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Rare Diseases/genetics ; *Hominidae/genetics ; Genome, Human ; DNA ; },
abstract = {Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.},
}

Animals
Humans
Infant, Newborn
*Neanderthals/genetics
Rare Diseases/genetics
*Hominidae/genetics
Genome, Human
DNA

@article {pmid36979362,
year = {2023},
author = {Xiao, F and Li, J and Lagniton, PNP and Kou, SH and Lei, H and Tam, B and Wang, SM},
title = {Evolutionary Origin of MUTYH Germline Pathogenic Variations in Modern Humans.},
journal = {Biomolecules},
volume = {13},
number = {3},
pages = {},
pmid = {36979362},
issn = {2218-273X},
mesh = {Animals ; Humans ; *Adenomatous Polyposis Coli/genetics/pathology ; *Colorectal Neoplasms/genetics ; Genetic Predisposition to Disease ; Germ Cells ; Germ-Line Mutation ; Mutation ; *Neanderthals/genetics ; Oxidative Stress ; },
abstract = {MUTYH plays an essential role in preventing oxidation-caused DNA damage. Pathogenic germline variations in MUTYH damage its function, causing intestinal polyposis and colorectal cancer. Determination of the evolutionary origin of the variation is essential to understanding the etiological relationship between MUTYH variation and cancer development. In this study, we analyzed the origins of pathogenic germline variants in human MUTYH. Using a phylogenic approach, we searched MUTYH pathogenic variants in modern humans in the MUTYH of 99 vertebrates across eight clades. We did not find pathogenic variants shared between modern humans and the non-human vertebrates following the evolutionary tree, ruling out the possibility of cross-species conservation as the origin of human pathogenic variants in MUTYH. We then searched the variants in the MUTYH of 5031 ancient humans and extinct Neanderthals and Denisovans. We identified 24 pathogenic variants in 42 ancient humans dated between 30,570 and 480 years before present (BP), and three pathogenic variants in Neanderthals dated between 65,000 and 38,310 years BP. Data from our study revealed that human MUTYH pathogenic variants mostly arose in recent human history and partially originated from Neanderthals.},
}

Animals
Humans
*Adenomatous Polyposis Coli/genetics/pathology
*Colorectal Neoplasms/genetics
Genetic Predisposition to Disease
Germ Cells
Germ-Line Mutation
Mutation
*Neanderthals/genetics
Oxidative Stress

@article {pmid36966596,
year = {2023},
author = {Zhang, Y and Li, Z},
title = {Three-dimensional geometric morphometric study of the Xuchang 2 cranium.},
journal = {Journal of human evolution},
volume = {178},
number = {},
pages = {103347},
doi = {10.1016/j.jhevol.2023.103347},
pmid = {36966596},
issn = {1095-8606},
mesh = {Animals ; Humans ; *Neanderthals/anatomy & histology ; Biological Evolution ; Fossils ; Skull/anatomy & histology ; *Hominidae/anatomy & histology ; },
abstract = {Results of traditional metric and nonmetric assessments suggest that the Xuchang hominin shares features with Neanderthals. To comprehensively compare the nuchal morphology of XC 2 to those of the genus Homo, we conduct a three-dimensional geometric morphometric study with 35 cranial landmarks and surface semilandmarks of XC 2, Homo erectus, Middle Pleistocene humans, Neanderthals, and early and recent modern humans. Results reveal that the centroid size of XC 2 is larger than that of early and recent modern humans and can only be compared to that of Middle Pleistocene humans and H. erectus. Early and recent modern humans share a nuchal morphology distinct from archaic hominins (Ngandong H. erectus, Middle Pleistocene humans, and Neanderthals), except for SM 3, Sangiran 17, and Asian and African H. erectus. Although Ngandong specimens differ from the other H. erectus, it is unclear whether this represents a temporal or spatial trend in the process of evolution of this species. The nuchal morphological resemblance between Middle Pleistocene humans and Neanderthals may be attributed to similar cranial architecture and cerebellar shape. The great nuchal morphological variation shared by recent modern humans may indicate a particular developmental pattern. In conclusion, the nuchal morphology of different human groups is highly variable and may be caused by different factors including brain globularization and developmental plasticity. XC 2 shares similar nuchal morphology with Middle Pleistocene humans and Neanderthals, but these results are insufficient to fully resolve the taxonomic status of XC 2.},
}

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

@article {pmid36964200,
year = {2023},
author = {Profico, A and Buzi, C and Di Vincenzo, F and Boggioni, M and Borsato, A and Boschian, G and Marchi, D and Micheli, M and Cecchi, JM and Samadelli, M and Tafuri, MA and Arsuaga, JL and Manzi, G},
title = {Virtual excavation and analysis of the early Neanderthal cranium from Altamura (Italy).},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {316},
pmid = {36964200},
issn = {2399-3642},
mesh = {Animals ; *Neanderthals ; *Hominidae/anatomy & histology ; Skull/anatomy & histology ; Fossils ; Italy ; },
abstract = {Complete Neanderthal skeletons are almost unique findings. A very well-preserved specimen of this kind was discovered in 1993 in the deepest recesses of a karstic system near the town of Altamura in Southern Italy. We present here a detailed description of the cranium, after we virtually extracted it from the surrounding stalagmites and stalactites. The morphology of the Altamura cranium fits within the Neanderthal variability, though it retains features occurring in more archaic European samples. Some of these features were never observed in Homo neanderthalensis, i.e. in fossil specimens dated between 300 and 40 ka. Considering the U-Th age we previously obtained (>130 ka), the morphology of Altamura suggests that the archaic traits it retains may have been originated by geographic isolation of the early Neanderthal populations from Southern Italy.},
}

Animals
*Neanderthals
*Hominidae/anatomy & histology
Skull/anatomy & histology
Fossils
Italy

@article {pmid36950386,
year = {2023},
author = {Skov, L and Coll Macià, M and Lucotte, EA and Cavassim, MIA and Castellano, D and Schierup, MH and Munch, K},
title = {Extraordinary selection on the human X chromosome associated with archaic admixture.},
journal = {Cell genomics},
volume = {3},
number = {3},
pages = {100274},
pmid = {36950386},
issn = {2666-979X},
abstract = {The X chromosome in non-African humans shows less diversity and less Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male X chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies in non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection in partial selective sweeps. Moreover, the swept haplotypes are entirely devoid of archaic ancestry as opposed to the non-swept haplotypes in the same genomic regions. The ancient Ust'-Ishim male dated at 45,000 before the present (BP) also carries the swept haplotypes, implying that selection on the haplotypes must have occurred between 45,000 and 55,000 years ago. Finally, we find that the chromosomal positions of sweeps overlap previously reported hotspots of selective sweeps in great ape evolution, suggesting a mechanism of selection unique to X chromosomes.},
}

@article {pmid36939312,
year = {2023},
author = {Wei, X and Robles, CR and Pazokitoroudi, A and Ganna, A and Gusev, A and Durvasula, A and Gazal, S and Loh, PR and Reich, D and Sankararaman, S},
title = {The lingering effects of Neanderthal introgression on human complex traits.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {36939312},
issn = {2050-084X},
support = {R35 GM125055/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R35GM125055/NH/NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Neanderthals/genetics ; Multifactorial Inheritance ; *Hominidae/genetics ; Gene Frequency ; Genetics, Population ; Genome, Human ; },
abstract = {The genetic variants introduced into the ancestors of modern humans from interbreeding with Neanderthals have been suggested to contribute an unexpected extent to complex human traits. However, testing this hypothesis has been challenging due to the idiosyncratic population genetic properties of introgressed variants. We developed rigorous methods to assess the contribution of introgressed Neanderthal variants to heritable trait variation and applied these methods to analyze 235,592 introgressed Neanderthal variants and 96 distinct phenotypes measured in about 300,000 unrelated white British individuals in the UK Biobank. Introgressed Neanderthal variants make a significant contribution to trait variation (explaining 0.12% of trait variation on average). However, the contribution of introgressed variants tends to be significantly depleted relative to modern human variants matched for allele frequency and linkage disequilibrium (about 59% depletion on average), consistent with purifying selection on introgressed variants. Different from previous studies (McArthur et al., 2021), we find no evidence for elevated heritability across the phenotypes examined. We identified 348 independent significant associations of introgressed Neanderthal variants with 64 phenotypes. Previous work (Skov et al., 2020) has suggested that a majority of such associations are likely driven by statistical association with nearby modern human variants that are the true causal variants. Applying a customized fine-mapping led us to identify 112 regions across 47 phenotypes containing 4303 unique genetic variants where introgressed variants are highly likely to have a phenotypic effect. Examination of these variants reveals their substantial impact on genes that are important for the immune system, development, and metabolism.},
}

Animals
Humans
*Neanderthals/genetics
Multifactorial Inheritance
*Hominidae/genetics
Gene Frequency
Genetics, Population
Genome, Human

@article {pmid36932194,
year = {2023},
author = {Avni, HL and Shvalb, N and Pokhojaev, A and Francis, S and Pelleg-Kallevag, R and Roul, V and Hublin, JJ and Rühli, F and May, H},
title = {Evolutionary roots of the risk of hip fracture in humans.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {283},
pmid = {36932194},
issn = {2399-3642},
support = {2019041//United States-Israel Binational Science Foundation (BSF)/ ; },
mesh = {Humans ; *Hip Fractures/etiology/complications ; Femur Neck ; Femur ; *Osteoporosis ; Risk Factors ; },
abstract = {The transition to bipedal locomotion was a fundamental milestone in human evolution. Consequently, the human skeleton underwent substantial morphological adaptations. These adaptations are responsible for many of today's common physical impairments, including hip fractures. This study aims to reveal the morphological changes in the proximal femur, which increase the risk of intracapsular hip fractures in present-day populations. Our sample includes chimpanzees, early hominins, early Homo Neanderthals, as well as prehistoric and recent humans. Using Geometric Morphometric methods, we demonstrate differences in the proximal femur shape between hominids and populations that practiced different lifestyles. We show that the proximal femur morphology is a risk factor for intracapsular hip fracture independent of osteoporosis. Changes in the proximal femur, such as the shortening of the femoral neck and an increased anterolateral expansion of the greater trochanter, are associated with an increased risk for intracapsular hip fractures. We conclude that intracapsular hip fractures are a trade-off for efficient bipedal walking in humans, and their risk is exacerbated by reduced physical activity.},
}

Humans
*Hip Fractures/etiology/complications
Femur Neck
Femur
*Osteoporosis
Risk Factors

@article {pmid36925053,
year = {2023},
author = {Chen, Z and Reynolds, RH and Pardiñas, AF and Gagliano Taliun, SA and van Rheenen, W and Lin, K and Shatunov, A and Gustavsson, EK and Fogh, I and Jones, AR and Robberecht, W and Corcia, P and Chiò, A and Shaw, PJ and Morrison, KE and Veldink, JH and van den Berg, LH and Shaw, CE and Powell, JF and Silani, V and Hardy, JA and Houlden, H and Owen, MJ and Turner, MR and Ryten, M and Al-Chalabi, A},
title = {The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases.},
journal = {Neurobiology of disease},
volume = {180},
number = {},
pages = {106082},
doi = {10.1016/j.nbd.2023.106082},
pmid = {36925053},
issn = {1095-953X},
support = {NIHR202421/DH_/Department of Health/United Kingdom ; MR/L501529/1/MRC_/Medical Research Council/United Kingdom ; MR/R024804/1/MRC_/Medical Research Council/United Kingdom ; MR/N008324/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Humans ; *Neanderthals/genetics ; *Neurodegenerative Diseases/genetics ; *Alzheimer Disease ; *Parkinson Disease ; *Amyotrophic Lateral Sclerosis ; Selection, Genetic ; },
abstract = {Humans are thought to be more susceptible to neurodegeneration than equivalently-aged primates. It is not known whether this vulnerability is specific to anatomically-modern humans or shared with other hominids. The contribution of introgressed Neanderthal DNA to neurodegenerative disorders remains uncertain. It is also unclear how common variants associated with neurodegenerative disease risk are maintained by natural selection in the population despite their deleterious effects. In this study, we aimed to quantify the genome-wide contribution of Neanderthal introgression and positive selection to the heritability of complex neurodegenerative disorders to address these questions. We used stratified-linkage disequilibrium score regression to investigate the relationship between five SNP-based signatures of natural selection, reflecting different timepoints of evolution, and genome-wide associated variants of the three most prevalent neurodegenerative disorders: Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease. We found no evidence for enrichment of positively-selected SNPs in the heritability of Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease, suggesting that common deleterious disease variants are unlikely to be maintained by positive selection. There was no enrichment of Neanderthal introgression in the SNP-heritability of these disorders, suggesting that Neanderthal admixture is unlikely to have contributed to disease risk. These findings provide insight into the origins of neurodegenerative disorders within the evolution of Homo sapiens and addresses a long-standing debate, showing that Neanderthal admixture is unlikely to have contributed to common genetic risk of neurodegeneration in anatomically-modern humans.},
}

Animals
Humans
*Neanderthals/genetics
*Neurodegenerative Diseases/genetics
*Alzheimer Disease
*Parkinson Disease
*Amyotrophic Lateral Sclerosis
Selection, Genetic

@article {pmid36916962,
year = {2023},
author = {Carretero, JM and García-González, R and Rodríguez, L and Arsuaga, JL},
title = {Main anatomical characteristics of the hominin fossil humeri from the Sima de los Huesos Middle Pleistocene site, Sierra de Atapuerca, Burgos, Spain: An update.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25194},
pmid = {36916962},
issn = {1932-8494},
support = {//Fundación Atapuerca/ ; PID2021-122355NB-C31//Ministerio de Ciencia, Innovación y Universidades (Spain)/ ; },
abstract = {Some of the Sima de los Huesos (SH) humeri have been previously studied and described elsewhere. Here we present an updated inventory and a review of the specimens recovered to the present day. The morphological key traits of the adult and subadult specimens are described, discussed, and illustrated. The SH humeri share with Neandertals many traits usually considered to be Neandertal specializations, thus, most of this morphological pattern is not exclusive to them. The variation found within fossil samples stresses the frequential nature of all these traits and in the specific case of the SH humeri, most of the traits considered as phylogenetically relevant are retained by their descendants, the Neandertals. Some traits are plesiomorphic for the entire genus Homo or are present in European hominins since the early Pleistocene. Finally, some other traits display high variability within the SH sample or different hominin samples and are of uncertain phylogenetic value. Altogether, this evidence is consistent with the hypothesis based on the overall cranial and postcranial morphology that the SH hominins are a sister group to the later Neandertals.},
}

@article {pmid36893252,
year = {2023},
author = {Herai, RH and Semendeferi, K and Muotri, AR},
title = {Comment on "Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals".},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6636},
pages = {eadf0602},
doi = {10.1126/science.adf0602},
pmid = {36893252},
issn = {1095-9203},
mesh = {Animals ; Humans ; *Neanderthals/genetics ; *Neocortex/growth & development ; Neurogenesis/genetics ; *Transketolase ; },
abstract = {Pinson et al. (1) concluded that the modern human TKTL1 gene is responsible for an increased number of cortical neurons. We show that the "putative Neanderthal variant" of TKTL1 is present in modern human backgrounds. We dispute their argument that this genetic variant is responsible for brain differences in modern humans as opposed to Neanderthals.},
}

Animals
Humans
*Neanderthals/genetics
*Neocortex/growth & development
Neurogenesis/genetics
*Transketolase

@article {pmid36893240,
year = {2023},
author = {Pinson, A and Maricic, T and Zeberg, H and Pääbo, S and Huttner, WB},
title = {Response to Comment on "Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals".},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6636},
pages = {eadf2212},
doi = {10.1126/science.adf2212},
pmid = {36893240},
issn = {1095-9203},
mesh = {Animals ; Humans ; *Neanderthals/genetics ; *Neocortex/cytology/growth & development ; *Neural Stem Cells ; *Neurogenesis/genetics ; *Transketolase/genetics ; },
abstract = {Herai et al. discuss the known fact that a low percentage of modern humans who lack any overt phenotypes carry the ancestral TKTL1 allele. Our paper demonstrates that the amino acid substitution in TKTL1 increases neural progenitor cells and neurogenesis in the developing brain. It is another question if, and to what extent, this has consequences for the adult brain.},
}

Animals
Humans
*Neanderthals/genetics
*Neocortex/cytology/growth & development
*Neural Stem Cells
*Neurogenesis/genetics
*Transketolase/genetics

@article {pmid36882431,
year = {2023},
author = {Marín-Arroyo, AB and Terlato, G and Vidal-Cordasco, M and Peresani, M},
title = {Subsistence of early anatomically modern humans in Europe as evidenced in the Protoaurignacian occupations of Fumane Cave, Italy.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {3788},
pmid = {36882431},
issn = {2045-2322},
support = {818299/ERC_/European Research Council/International ; },
mesh = {Animals ; Humans ; Adaptation, Psychological ; Caves ; Europe ; Goats ; Italy ; *Rupicapra ; *Neanderthals ; },
abstract = {Documenting the subsistence strategies developed by early modern humans is relevant for understanding the success of their dispersal throughout Eurasia. Today, we know that there was not a single colonization event and that the process was progressive while coping with the MIS3 abrupt climatic oscillations. Modern humans expanded into the continent by adapting to different topographic situations and by exploiting resources in diverse ecological niches. The northern part of Italy is one of the first European regions where early modern humans are documented. Here, we present the subsistence regimen adopted by the Protoaurignacian groups in two different levels in Fumane Cave based on archaeozoological data. New radiocarbon dates confirm an overlap between Uluzzian and Protoaurignacian occupations, around 42 and 41,000 cal BP, and reveal that modern humans occupied the cave from GI10 to GS9, the last level coinciding with the Heinrich Event 4. The data indicate seasonal site occupations during late spring/summer and that prey exploitation was focused mostly on ibex and chamois, killed in nearby areas. The whole faunal assemblage suggests the presence of early modern humans in a cold environment with mostly open landscapes and patchy woodlands. The estimation of net primary productivity (NPP) in Fumane, compared with other contemporaneous Italian sites, reflects how the NPP fluctuations in the Prealpine area, where Fumane is located, affected the biotic resources in contrast to known Mediterranean sites. From a pan-European perspective, the spatiotemporal fluctuation of the NPP versus the subsistence strategies adopted by Protoaurignacian groups in the continent supports rapid Homo sapiens dispersal and resilience in a mosaic of environments that were affected by significant climate changes.},
}

Animals
Humans
Adaptation, Psychological
Caves
Europe
Goats
Italy
*Rupicapra
*Neanderthals

@article {pmid36871458,
year = {2023},
author = {Jones, EL and Carvalho, M},
title = {Ecospaces of the Middle to Upper Paleolithic transition: The archaeofaunal record of the Iberian Peninsula.},
journal = {Journal of human evolution},
volume = {177},
number = {},
pages = {103331},
doi = {10.1016/j.jhevol.2023.103331},
pmid = {36871458},
issn = {1095-8606},
mesh = {Animals ; Humans ; *Neanderthals ; Archaeology ; Fossils ; Mammals ; },
abstract = {The rich archaeofaunal record of Iberia provides a means of exploring potential differences between Neanderthal and anatomically modern human interactions with the environment. In this article, we present an analysis of Iberian archaeofaunas dating between 60 and 30 ka to explore if, how, and why the faunal ecospaces of Neanderthals and anatomically modern humans differed. We test for impacts of chronology (as a proxy for Neanderthal and anatomically modern human exploitation) and environmental regionalization (using bioclimatic regions) on archaeofaunal composition, using a combination of cluster (unweighted pair-group method using arithmetic averages) and nonmetric multidimensional scaling. Our chronological analysis finds no significant compositional difference between Neanderthal and anatomically modern mammalian faunal assemblages; however, bioclimatic regionalization is stronger in anatomically modern human-affiliated assemblages than in Neanderthal ones, a finding that may indicate a difference in site occupation duration or foraging mobility between Neanderthals and anatomically modern humans.},
}

Animals
Humans
*Neanderthals
Archaeology
Fossils
Mammals

@article {pmid36857333,
year = {2023},
author = {Shoaee, MJ and Breeze, PS and Drake, NA and Hashemi, SM and Vahdati Nasab, H and Breitenbach, SFM and Stevens, T and Boivin, N and Petraglia, MD},
title = {Defining paleoclimatic routes and opportunities for hominin dispersals across Iran.},
journal = {PloS one},
volume = {18},
number = {3},
pages = {e0281872},
pmid = {36857333},
issn = {1932-6203},
mesh = {Humans ; Animals ; Iran ; *Hominidae ; *Neanderthals ; Pakistan ; Water ; },
abstract = {Fossil and archaeological evidence indicates that hominin dispersals into Southwest Asia occurred throughout the Pleistocene, including the expansion of Homo sapiens populations out of Africa. While there is evidence for hominin occupations in the Pleistocene in Iran, as evidenced by the presence of Lower to Upper Paleolithic archaeological sites, the extent to which humid periods facilitated population expansions into western Asia has remained unclear. To test the role of humid periods on hominin dispersals here we assess Paleolithic site distributions and paleoenvironmental records across Iran. We developed the first spatially comprehensive, high-resolution paleohydrological model for Iran in order to assess water availability and its influence on hominin dispersals. We highlight environmentally mediated routes which likely played a key role in Late Pleistocene hominin dispersals, including the expansion of H. sapiens and Neanderthals eastwards into Asia. Our combined analyses indicate that, during MIS 5, there were opportunities for hominins to traverse a northern route through the Alborz and Kopet Dagh Mountains and the Dasht-I Kavir desert owing to the presence of activated fresh water sources. We recognize a new southern route along the Zagros Mountains and extending eastwards towards Pakistan and Afghanistan. We find evidence for a potential northern route during MIS 3, which would have permitted hominin movements and species interactions in Southwest Asia. Between humid periods, these interconnections would have waned, isolating populations in the Zagros and Alborz Mountains, where hominins may have continued to have had access to water.},
}

Humans
Animals
Iran
*Hominidae
*Neanderthals
Pakistan
Water

@article {pmid36841571,
year = {2023},
author = {Ganapathee, DS and Gunz, P},
title = {Insights into brain evolution through the genotype-phenotype connection.},
journal = {Progress in brain research},
volume = {275},
number = {},
pages = {73-92},
doi = {10.1016/bs.pbr.2022.12.013},
pmid = {36841571},
issn = {1875-7855},
mesh = {Animals ; Humans ; Biological Evolution ; *Hominidae ; Brain/anatomy & histology ; *Neanderthals/anatomy & histology/genetics ; Primates ; Phenotype ; Genotype ; },
abstract = {It has recently become possible to start exploring how the genotype translates into human brain morphology and behavior by combining detailed genomic and phenotypic data from thousands of present-day people with archaic genomes of extinct humans, and gene expression data. As a starting point into this emerging interdisciplinary domain, we highlight current debates about which aspects of the modern human brain are unique. We review recent developments from (1) comparative primate neuroscience-a fast-growing field offering an invaluable framework for understanding general mechanisms and the evolution of human-specific traits. (2) paleoanthropology-based on evidence from endocranial imprints in fossil skulls, we trace the evolution from the ape-like brain phenotype of early hominins more than 3 million years ago to the unusual globular brain shape of present-day people. (3) Genomics of present-day and extinct humans. The morphological and genetic differences between modern humans and our closest extinct cousins, the Neandertals, offer important clues about the genetic underpinnings of brain morphology and behavior. The functional consequences of these genetic differences can be tested in animal models, and brain organoids.},
}

Animals
Humans
Biological Evolution
*Hominidae
Brain/anatomy & histology
*Neanderthals/anatomy & histology/genetics
Primates
Phenotype
Genotype