@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},
doi = {10.1007/s12520-023-01789-2},
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},
doi = {10.1073/pnas.2213061120},
pmid = {37220274},
issn = {1091-6490},
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.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2023.04.025},
pmid = {37202264},
issn = {2095-9281},
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.},
}

@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},
doi = {10.1073/pnas.2218308120},
pmid = {37192163},
issn = {1091-6490},
support = {R01 GM127472/GM/NIGMS NIH HHS/United States ; },
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.},
}

@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},
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.},
}

@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},
doi = {10.1073/pnas.2204501120},
pmid = {37155903},
issn = {1091-6490},
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.},
}

@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 = {},
number = {},
pages = {},
pmid = {37142741},
issn = {2397-334X},
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.},
}

@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 = {},
number = {},
pages = {eadf5300},
doi = {10.1126/science.adf5300},
pmid = {37141315},
issn = {1095-9203},
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. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites 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.},
}

@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},
doi = {10.1371/journal.pone.0277444},
pmid = {37134082},
issn = {1932-6203},
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.},
}

@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},
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.},
}

@article {pmid37103242,
year = {2023},
author = {Witt, KE and Funk, A and Añorve-Garibay, V and Lopez Fang, L and Huerta-Sanchez, E},
title = {The impact of modern admixture on archaic human ancestry in human populations.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evad066},
pmid = {37103242},
issn = {1759-6653},
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 enrichment 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.},
}

@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},
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.},
}

@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},
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 {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 {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},
doi = {10.1371/journal.pone.0284093},
pmid = {37053172},
issn = {1932-6203},
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.},
}

@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},
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 = {},
number = {},
pages = {111420},
doi = {10.1016/j.cbpa.2023.111420},
pmid = {37001690},
issn = {1531-4332},
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.},
}

@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},
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 = {},
doi = {10.3390/genes14030727},
pmid = {36980999},
issn = {2073-4425},
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.},
}

@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 = {},
doi = {10.3390/biom13030429},
pmid = {36979362},
issn = {2218-273X},
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.},
}

@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},
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.},
}

@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},
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.},
}

@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 = {},
doi = {10.7554/eLife.80757},
pmid = {36939312},
issn = {2050-084X},
support = {GM100233/NH/NIH HHS/United States ; HG006399/NH/NIH HHS/United States ; R35GM125055/NH/NIH HHS/United States ; },
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 relative to that of modern human variants. We 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 have a significant contribution to trait variation consistent with the polygenic architecture of complex phenotypes (contributing 0.12% of heritable variation averaged across phenotypes). 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 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 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. We therefore developed a customized statistical fine-mapping methodology for introgressed variants that led us to identify 112 regions (at a false discovery proportion of 16%) across 47 phenotypes containing 4,303 unique genetic variants where introgressed variants are highly likely to have a phenotypic effect. Examination of these variants reveal their substantial impact on genes that are important for the immune system, development, and metabolism. Our results provide the first rigorous basis for understanding how Neanderthal introgression modulates complex trait variation in present-day humans.},
}

@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},
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.},
}

@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 = {},
number = {},
pages = {106082},
doi = {10.1016/j.nbd.2023.106082},
pmid = {36925053},
issn = {1095-953X},
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.},
}

@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},
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 {pmid36735645,
year = {2023},
author = {Dekker, J and Larson, T and Tzvetkov, J and Harvey, VL and Dowle, A and Hagan, R and Genever, P and Schrader, S and Soressi, M and Hendy, J},
title = {Spatial analysis of the ancient proteome of archeological teeth using mass spectrometry imaging.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {37},
number = {8},
pages = {e9486},
doi = {10.1002/rcm.9486},
pmid = {36735645},
issn = {1097-0231},
abstract = {RATIONALE: Proteins extracted from archaeological bone and teeth are utilised for investigating the phylogeny of extinct and extant species, the biological sex and age of past individuals, as well as ancient health and physiology. However, variable preservation of proteins in archaeological materials represents a major challenge.

METHODS: To better understand the spatial distribution of ancient proteins preserved within teeth, we applied matrix assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for the first time to bioarchaeological samples to visualise the intensity of proteins in archaeological teeth thin sections. We specifically explored the spatial distribution of four proteins (collagen type I, of which the chains alpha-1 and alpha-2, alpha-2-HS-glycoprotein, haemoglobin subunit alpha and myosin light polypeptide 6).

RESULTS: We successfully identified ancient proteins in archaeological teeth thin sections using mass spectrometry imaging. The data are available via ProteomeXchange with identifier PXD038114. However, we observed that peptides did not always follow our hypotheses for their spatial distribution, with distinct differences observed in the spatial distribution of several proteins, and occasionally between peptides of the same protein.

CONCLUSIONS: While it remains unclear what causes these differences in protein intensity distribution within teeth, as revealed by MALDI-MSI in this study, we have demonstrated that MALDI-MSI can be successfully applied to mineralised bioarchaeological tissues to detect ancient peptides. In future applications, this technique could be particularly fruitful not just for understanding the preservation of proteins in a range of archaeological materials, but making informed decisions on sampling strategies and the targeting of key proteins of archaeological and biological interest.},
}

@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},
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.},
}

@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},
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.},
}

@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},
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.},
}

@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},
doi = {10.1371/journal.pone.0281872},
pmid = {36857333},
issn = {1932-6203},
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.},
}

@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},
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.},
}

@article {pmid36833167,
year = {2023},
author = {González-Álvarez, R and Rodríguez-Sánchez, IP and Barrera-Saldaña, HA},
title = {Gene Content and Coding Diversity of the Growth Hormone Loci of Apes.},
journal = {Genes},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/genes14020241},
pmid = {36833167},
issn = {2073-4425},
abstract = {The growth hormone (GH) locus has experienced a dramatic evolution in primates, becoming multigenic and diverse in anthropoids. Despite sequence information from a vast number of primate species, it has remained unclear how the multigene family was favored. We compared the structure and composition of apes' GH loci as a prerequisite to understanding their origin and possible evolutionary role. These thorough analyses of the GH loci of the chimpanzee, gorilla, and orangutan were done by resorting to previously sequenced bacterial artificial chromosomes (BACs) harboring them, as well as to their respective genome projects data available in GenBank. The GH loci of modern man, Neanderthal, gibbon, and wild boar were retrieved from GenBank. Coding regions, regulatory elements, and repetitive sequences were identified and compared among species. The GH loci of all the analyzed species are flanked by the genes CD79B (5') and ICAM-1 (3'). In man, Neanderthal, and chimpanzee, the loci were integrated by five almost indistinguishable genes; however, in the former two, they rendered three different hormones, and in the latter, four different proteins were derived. Gorilla exhibited six genes, gibbon seven, and orangutan four. The sequences of the proximal promoters, enhancers, P-elements, and a locus control region (LCR) were highly conserved. The locus evolution might have implicated duplications of the ancestral pituitary gene (GH-N) and subsequent diversification of the copies, leading to the placental single GH-V gene and the multiple CSH genes.},
}

@article {pmid36825485,
year = {2023},
author = {Conde-Valverde, M and Martínez, I and Quam, R and Arsuaga, JL},
title = {The ear of the Sima de los Huesos hominins (Atapuerca, Spain).},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25181},
pmid = {36825485},
issn = {1932-8494},
abstract = {Previous studies on the morphology of the inner ear (semicircular canals and cochlea) in the Sima de los Huesos hominin sample have provided important results on the evolution of these structures in the Neandertal lineage. Similarly, studies of the anatomy of the external and middle ear cavities of the Sima de los Huesos hominins have also provided important data on the auditory capacities of this European Middle Pleistocene population. The present contribution provides unpublished data on three new middle ear variables from the Sima de los Huesos fossils and compares these data with values from samples of Pan troglodytes, Homo neanderthalensis and Homo sapiens. The results of this analysis are combined with those obtained in previous studies to characterize the anatomy of the outer, middle and inner ear in the Sima de los Huesos fossils, as well as to establish the order of appearance of the features that characterize Neandertal ears. As in other cranial structures, the ear region in the Sima de los Huesos show a mosaic evolutionary pattern that includes primitive traits, others shared exclusively with Neandertals, and others that are specific to the Sima de los Huesos hominins. Neandertals and Sima de los Huesos hominins share two exclusive features of the middle ear that are among the first characteristics of the Neandertal lineage: a long tympanic cavity and a large entrance and exit of the mastoid antrum. Along with these traits, the Sima de los Huesos hominins present two specialized features: large volumes of the tympanic cavity and the mastoid antrum. Finally, the middle ear of the Neandertals is characterized by the presence of small angles between the tympanic axis and the plane of the oval window.},
}

@article {pmid36823244,
year = {2023},
author = {Wang, PY and Yang, Y and Shi, XQ and Chen, Y and Liu, SD and Wang, HY and Peng, T and Shi, Q and Zhang, W and Sun, C},
title = {Distilling functional variations for human UGT2B4 upstream region based on selection signals and implications for phenotypes of Neanderthal and Denisovan.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {3134},
pmid = {36823244},
issn = {2045-2322},
abstract = {Our previous work identified one region upstream human UGT2B4 (UDP glucuronosyltransferase family 2 member B4) which is associated with breast cancer and under balancing selection. However, the distribution, functional variation and molecular mechanism underlying breast cancer and balancing selection remain unclear. In current study, the two haplotypes with deep divergence are described by analyzing 1000 genomes project data and observed to be with high frequencies in all human populations. Through population genetics analysis and genome annotation, the potential functional region is identified and verified by reporter gene assay. Further mutagenesis indicates that the functional mutations are rs66862535 and rs68096061. Both SNPs can alter the interaction efficiency of transcription factor POU2F1 (POU class 2 homeobox 1). Through chromosome conformation capture, it is identified that the enhancer containing these two SNPs can interact with UGT2B4 promoter. Expression quantitative trait loci analysis indicates that UGT2B4 expression is dependent on the genotype of this locus. The common haplotype in human is lost in four genomes of archaic hominins, which suggests that Neanderthal and Denisovan should present relatively lower UGT2B4 expression and further higher steroid hormone level. This study provides new insight into the contribution of ancient population structure to human phenotypes.},
}

@article {pmid36821540,
year = {2023},
author = {Ghasidian, E and Kafash, A and Kehl, M and Yousefi, M and Heydari-Guran, S},
title = {Modelling Neanderthals' dispersal routes from Caucasus towards east.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0281978},
doi = {10.1371/journal.pone.0281978},
pmid = {36821540},
issn = {1932-6203},
abstract = {The study of the cultural materials associated with the Neanderthal physical remains from the sites in the Caucasus, Central Asia and Siberian Altai and adjacent areas documents two distinct techno-complexes of Micoquian and Mousterian. These findings potentially outline two dispersal routes for the Neanderthals out of Europe. Using data on topography and Palaeoclimate, we generated computer-based least-cost-path modelling for the Neanderthal dispersal routes from Caucasus towards the east. In this regard, two dispersal routes have been identified: A northern route from Greater Caucasus associated with Micoquian techno-complex towards Siberian Altai and a southern route from Lesser Caucasus associated with Mousterian towards Siberian Altai via the Southern Caspian Corridor. Based on archaeological, bio- and physio-geographical data, our model hypothesises that during climatic deterioration phases (e.g. MIS 4) the connection between Greater and Lesser Caucasus was limited. This issue perhaps resulted in the separate development and spread of two cultural groups of Micoquian and Mousterian with an input from two different population sources of Neanderthal influxes: eastern and southern Europe refugia for these two northern and southern dispersal routes respectively. Of these two, we focus on the southern dispersal route, for it comprises a 'rapid dispersal route' towards east. The significant location of the Southern Caspian corridor between high mountains of Alborz and the Caspian Sea, provided a special biogeographical zone and a refugium. This exceptional physio-geographic condition brings forward the Southern Caspian corridor as a potential place of admixture of different hominin species including Neanderthals and homo sapiens.},
}

@article {pmid36806751,
year = {2023},
author = {Cazenave, M and Radovčić, D},
title = {The Neanderthal patellae from Krapina (Croatia): A comparative investigation of their endostructural conformation and distinctive features compared to the extant human condition.},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24709},
pmid = {36806751},
issn = {2692-7691},
abstract = {OBJECTIVES: The Neanderthal patella differs from that of extant humans by being thicker anteroposteriorly and by having more symmetric medial and lateral articular facets. However, it is still unclear to what extent these differences affect knee kinesiology. We aim at assessing the endostructural conformation of Neanderthal patellae to reveal functionally related mechanical information comparatively to the extant human condition. In principle, we expect that the Neanderthal patella (i) shows a higher amount of cortical bone and (ii) a trabecular network organization distinct from the extant human condition.

MATERIALS AND METHODS: By using micro-focus X-ray tomography, we characterized the endostructure of six adult patellae from the OIS 5e Neanderthal site of Krapina, Croatia, the largest assemblage of human fossil patellae assessed so far, and compared their pattern to the configuration displayed by a sample of 22 recent humans.

RESULTS AND DISCUSSION: The first expectation is rejected, indicating that the patellar bone might have not followed the trend of generalized gracilization of the human postcranial skeleton occurred through the Upper Pleistocene. The second prediction is at least partially supported. In Krapina the trabecular network differs from the comparative sample by showing a higher medial density and by lacking a proximal reinforcement. Such conformation indicates similar load patterns exerted in Neanderthals and extant humans by the vastus lateralis, but not by the vastus medialis, with implications on the mediolateral stabilization of the knee joint. However, the patterns of structural variation of the patellar network remain to be assessed in other Neanderthal samples.},
}

@article {pmid36796364,
year = {2023},
author = {Corcoran, M and Chernyshev, M and Mandolesi, M and Narang, S and Kaduk, M and Ye, K and Sundling, C and Färnert, A and Kreslavsky, T and Bernhardsson, C and Larena, M and Jakobsson, M and Karlsson Hedestam, GB},
title = {Archaic humans have contributed to large-scale variation in modern human T cell receptor genes.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2023.01.026},
pmid = {36796364},
issn = {1097-4180},
abstract = {Human T cell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors and regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from four human populations-African, East Asian, South Asian, and European-revealed 175 additional TCR variable and junctional alleles. Most of these contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions including a highly divergent TRGV4 variant, which mediated altered butyrophilin-like molecule 3 (BTNL3) ligand reactivity and was frequent in all modern Eurasian population groups. Our results demonstrate remarkable variation in TCR genes in both individuals and populations, providing a strong incentive for including allelic variation in studies of TCR function in human biology.},
}

@article {pmid36791053,
year = {2023},
author = {Talamo, S and Kromer, B and Richards, MP and Wacker, L},
title = {Back to the future: The advantage of studying key events in human evolution using a new high resolution radiocarbon method.},
journal = {PloS one},
volume = {18},
number = {2},
pages = {e0280598},
doi = {10.1371/journal.pone.0280598},
pmid = {36791053},
issn = {1932-6203},
abstract = {Radiocarbon dating is the most widely applied dating method in archaeology, especially in human evolution studies, where it is used to determine the chronology of key events, such as the replacement of Neanderthals by modern humans in Europe. However, the method does not always provide precise and accurate enough ages to understand the important processes of human evolution. Here we review the newest method developments in radiocarbon dating ('Radiocarbon 3.0'), which can lead us to much better chronologies and understanding of the major events in recent human evolution. As an example, we apply these new methods to discuss the dating of the important Palaeolithic site of Bacho Kiro (Bulgaria).},
}

@article {pmid36790758,
year = {2022},
author = {Oxilia, G and Bortolini, E and Marciani, G and Menghi Sartorio, JC and Vazzana, A and Bettuzzi, M and Panetta, D and Arrighi, S and Badino, F and Figus, C and Lugli, F and Romandini, M and Silvestrini, S and Sorrentino, R and Moroni, A and Donadio, C and Morigi, MP and Slon, V and Piperno, M and Talamo, S and Collina, C and Benazzi, S},
title = {Direct evidence that late Neanderthal occupation precedes a technological shift in southwestern Italy.},
journal = {American journal of biological anthropology},
volume = {179},
number = {1},
pages = {18-30},
doi = {10.1002/ajpa.24593},
pmid = {36790758},
issn = {2692-7691},
abstract = {OBJECTIVES: During the middle-to-upper Paleolithic transition (50,000 and 40,000 years ago), interaction between Neanderthals and Homo sapiens varied across Europe. In southern Italy, the association between Homo sapiens fossils and non-Mousterian material culture, as well as the mode and tempo of Neanderthal demise, are still vividly debated. In this research, we focus on the study of two human teeth by using 3D geometric morphometric approaches for a reliable taxonomical attribution as well as obtaining new radiometric dates on the archeological sequence.

MATERIAL AND METHODS: This work presents two lower deciduous molars uncovered at Roccia San Sebastiano (Mondragone-Caserta, Italy), stratigraphically associated with Mousterian (RSS1) and Uluzzian (RSS2) artifacts. To obtain a probabilistic attribution of the two RSS teeth to each reference taxa group composed of Neanderthals and Homo sapiens, we performed and compared the performance of three supervised learning algorithms (flexible discriminant analysis, multiadaptive regression splines, and random forest) on both crown and cervical outlines obtained by virtual morphometric methods.

RESULTS: We show that RSS1, whose Mousterian context appears more recent than 44,800-44,230 cal BP, can be attributed to a Neanderthal, while RSS2, found in an Uluzzian context that we dated to 42,640-42,380 cal BP, is attributed to Homo sapiens.

DISCUSSION: This site yields the most recent direct evidence for a Neanderthal presence in southern Italy and confirms a later shift to upper Paleolithic technology in southwestern Italy compared to the earliest Uluzzian evidence at Grotta del Cavallo (Puglia, Italy).},
}

@article {pmid36778254,
year = {2023},
author = {Velazquez-Arcelay, K and Colbran, LL and McArthur, E and Brand, C and Siemann, J and McMahon, D and Capra, JA},
title = {Neanderthal Introgression Shaped Human Circadian Traits.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.02.03.527061},
pmid = {36778254},
abstract = {INTRODUCTION: When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultra-violet radiation and an increased variation in seasonal dynamics. However, whether these groups differed substantially in circadian biology, and whether archaic introgression adaptively contributed to human chronotypes remains unknown.

RESULTS: Here we traced the evolution of chronotype based on genomes from archaic hominin and present-day humans. First, we inferred differences in circadian gene sequences, splicing, and regulation between archaic hominins and modern humans. We identified 28 circadian genes containing variants likely to alter splicing in archaics (e.g., CLOCK, PER2, RORB, RORC), and 16 circadian genes likely divergently regulated between present-day humans and archaic hominins, including RORA . These differences suggest the potential for introgression to modify circadian gene expression. Testing this hypothesis, we found that introgressed variants are enriched among eQTLs for circadian genes. Supporting the functional relevance of these regulatory effects, we found that many introgressed alleles have strong associations with chronotype. Strikingly, the strongest introgressed effects on chronotype increase morningness, which is consistent with adaptations to high latitude in other species. Finally, we identified 26 circadian loci with evidence of adaptive introgression, including PER2 and MYBBP1A .

CONCLUSIONS: These findings identify differences in circadian gene regulation between modern humans and archaic hominins and support the contribution of introgression via coordinated effects on variation in human chronotype.

SIGNIFICANCE STATEMENT: Interbreeding between modern humans and Neanderthals created the potential for adaptive introgression as humans moved into new environments that had been populated by Neanderthals for hundreds of thousands of years. Here we discover substantial lineage-specific genetic differences in circadian genes and their regulatory elements between humans and Neanderthals. We then show that introgressed archaic alleles are enriched for effects on circadian gene regulation and consistently increase propensity for morningness in modern Europeans. These results substantially expand our understanding of how the genomes of humans and our closest relatives responded to living in environments with different light/dark cycles, and they demonstrate a coordinated contribution of archaic admixture to modern human chronotype in a direction that is consistent with adaptation to higher latitudes.},
}

@article {pmid36776693,
year = {2023},
author = {Hagymási, K},
title = {The Nobel prize in physiology and medicine - 2022.},
journal = {Structural chemistry},
volume = {},
number = {},
pages = {1-4},
pmid = {36776693},
issn = {1040-0400},
abstract = {The Nobel Assembly at Karolinska Institutet awarded the 2022 Nobel Prize in Physiology or Medicine to a Swedish geneticist, Svante Pääbo, for his discoveries concerning the genomes of extinct hominins and human evolution, for the sequencing of the genome of the Neanderthal, the discovery of a previously unknown hominin, Denisova, and the establishment of a new scientific discipline, paleogenomics.},
}

@article {pmid36763080,
year = {2023},
author = {Jagoda, E and Marnetto, D and Senevirathne, G and Gonzalez, V and Baid, K and Montinaro, F and Richard, D and Falzarano, D and LeBlanc, EV and Colpitts, CC and Banerjee, A and Pagani, L and Capellini, TD},
title = {Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.71235},
pmid = {36763080},
issn = {2050-084X},
abstract = {Individuals infected with the SARS-CoV-2 virus present with a wide variety of symptoms ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe response to COVID-19. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear. Here, we assess the variants present on the risk haplotype for their likelihood of driving the genetic predisposition to severe COVID-19 outcomes. We do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. We then perform a locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify four introgressed alleles that are strong functional candidates for driving the association between this locus and severe COVID-19. Using reporter assays in the presence/absence of SARS-CoV-2, we find evidence that these variants respond to viral infection. These variants likely drive the locus' impact on severity by modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5. These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes.},
}

@article {pmid36749731,
year = {2023},
author = {Kozowyk, PRB},
title = {Archaeological Podocarpus tar supports the cognitive complexity of Neanderthals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {7},
pages = {e2221676120},
doi = {10.1073/pnas.2221676120},
pmid = {36749731},
issn = {1091-6490},
}

@article {pmid36741450,
year = {2022},
author = {Sironi, M and Cagliani, R and Biasin, M and Lo Caputo, S and Saulle, I and Forni, D and Real, LM and Pineda, JA and Exposito, A and Saez, ME and Sinangil, F and Forthal, D and Caruz, A and Clerici, M},
title = {No association of a risk variant for severe COVID-19 with HIV protection in three cohorts of highly exposed individuals.},
journal = {PNAS nexus},
volume = {1},
number = {3},
pages = {pgac138},
pmid = {36741450},
issn = {2752-6542},
abstract = {An extended haplotype on chromosome 3 is the major genetic risk factor for severe COVID-19. The risk haplotype, which was inherited from Neanderthals, decreases the expression of several cytokine receptors, including CCR5. Recently, a study based on three general population cohorts indicated that the minor allele of one of the variants in the haplotype (rs17713054) protects against HIV infection. We thus expected this allele to be over-represented in highly exposed individuals who remain uninfected (exposed seronegative individuals, ESN). To perform a meta-analysis, we genotyped rs17713054 in three ESN cohorts of European ancestry exposed to HIV through different routes. No evidence of association was detected in the single cohorts. The meta-analysis also failed to detect any effect of the variant on protection from HIV-1. The same results were obtained in a Cox-regression analysis for the time to seroconversion. An in-vitro infection assay did not detect differences in viral replication as a function of rs17713054 genotype status. We conclude that the rs17713054 minor allele is not associated with the ESN phenotype and does not modulate HIV infection in vitro.},
}

@article {pmid36730401,
year = {2023},
author = {Curry, A},
title = {Neanderthals lived in groups big enough to eat giant elephants.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6631},
pages = {428},
doi = {10.1126/science.adg9448},
pmid = {36730401},
issn = {1095-9203},
abstract = {Meat from the butchered beasts would have fed hundreds.},
}

@article {pmid36724231,
year = {2023},
author = {Gaudzinski-Windheuser, S and Kindler, L and MacDonald, K and Roebroeks, W},
title = {Hunting and processing of straight-tusked elephants 125.000 years ago: Implications for Neanderthal behavior.},
journal = {Science advances},
volume = {9},
number = {5},
pages = {eadd8186},
doi = {10.1126/sciadv.add8186},
pmid = {36724231},
issn = {2375-2548},
abstract = {Straight-tusked elephants (Palaeoloxodon antiquus) were the largest terrestrial mammals of the Pleistocene, present in Eurasian landscapes between 800,000 and 100,000 years ago. The occasional co-occurrence of their skeletal remains with stone tools has generated rich speculation about the nature of interactions between these elephants and Pleistocene humans: Did hominins scavenge on elephants that died a natural death or maybe even hunt some individuals? Our archaeozoological study of the largest P. antiquus assemblage known, excavated from 125,000-year-old lake deposits in Germany, shows that hunting of elephants weighing up to 13 metric tons was part of the cultural repertoire of Last Interglacial Neanderthals there, over >2000 years, many dozens of generations. The intensity and nutritional yields of these well-documented butchering activities, combined with previously reported data from this Neumark-Nord site complex, suggest that Neanderthals were less mobile and operated within social units substantially larger than commonly envisaged.},
}

@article {pmid36719913,
year = {2023},
author = {Ben-Dor, M and Barkai, R},
title = {A limited protein high-fat diet may explain the low δ[66]Zn conundrum in the Neandertal from Gabasa.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {6},
pages = {e2218081120},
doi = {10.1073/pnas.2218081120},
pmid = {36719913},
issn = {1091-6490},
}

@article {pmid36712807,
year = {2022},
author = {Williams, SA and Zeng, I and Paton, GJ and Yelverton, C and Dunham, C and Ostrofsky, KR and Shukman, S and Avilez, MV and Eyre, J and Loewen, T and Prang, TC and Meyer, MR},
title = {Inferring lumbar lordosis in Neandertals and other hominins.},
journal = {PNAS nexus},
volume = {1},
number = {1},
pages = {pgab005},
pmid = {36712807},
issn = {2752-6542},
abstract = {Lumbar lordosis is a key adaptation to bipedal locomotion in the human lineage. Dorsoventral spinal curvatures enable the body's center of mass to be positioned above the hip, knee, and ankle joints, and minimize the muscular effort required for postural control and locomotion. Previous studies have suggested that Neandertals had less lordotic (ventrally convex) lumbar columns than modern humans, which contributed to historical perceptions of postural and locomotor differences between the two groups. Quantifying lower back curvature in extinct hominins is entirely reliant upon bony correlates of overall lordosis, since the latter is significantly influenced by soft tissue structures (e.g. intervertebral discs). Here, we investigate sexual dimorphism, ancestry, and lifestyle effects on lumbar vertebral body wedging and inferior articular facet angulation, two features previously shown to be significantly correlated with overall lordosis in living individuals, in a large sample of modern humans and Neandertals. Our results demonstrate significant differences between postindustrial cadaveric remains and archaeological samples of people that lived preindustrial lifestyles. We suggest these differences are related to activity and other aspects of lifestyle rather than innate population (ancestry) differences. Neandertal bony correlates of lumbar lordosis are significantly different from all human samples except preindustrial males. Therefore, although Neandertals demonstrate more bony kyphotic wedging than most modern humans, we cast doubt on proposed locomotor and postural differences between the two lineages based on inferred lumbar lordosis (or lack thereof), and we recommend future research compare fossils to modern humans from varied populations and not just recent, postindustrial samples.},
}

@article {pmid36711923,
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 can be highly biased and is not addressed by previously suggested SNP ascertainment schemes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.22.525077},
pmid = {36711923},
abstract = {f -statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. These statistics can provide strong evidence for either admixture or cladality, which can be robust to substantial rates of errors or missing data. f -statistics are guaranteed to be unbiased under "SNP ascertainment" (analyzing non-randomly chosen subsets of single nucleotide polymorphisms) only if it relies on a population that is an outgroup for all groups analyzed. However, ascertainment on a true outgroup that is not co-analyzed with other populations is often impractical and uncommon in the literature. In this study focused on practical rather than theoretical aspects of SNP ascertainment, we show that many non-outgroup ascertainment schemes lead to false rejection of true demographic histories, as well as to failure to reject incorrect models. But the bias introduced by common ascertainments such as the 1240K panel is mostly limited to situations when more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans) or non-human outgroups are co-modelled, for example, f 4 -statistics involving one non-African group, two African groups, and one archaic group. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, cannot fix all these problems since for some classes of f -statistics it is not a clean outgroup ascertainment, and in other cases it demonstrates relatively low power to reject incorrect demographic models since it provides a relatively small number of variants common in anatomically modern humans. And due to the paucity of high-coverage archaic genomes, archaic individuals used for ascertainment often act as sole representatives of the respective groups in an analysis, and we show that this approach is highly problematic. By carrying out large numbers of simulations of diverse demographic histories, we find that bias in inferences based on f -statistics introduced by non-outgroup ascertainment can be minimized if the derived allele frequency spectrum in the population used for ascertainment approaches the spectrum that existed at the root of all groups being co-analyzed. Ascertaining on sites with variants common in a diverse group of African individuals provides a good approximation to such a set of SNPs, addressing the great majority of biases and also retaining high statistical power for studying population history. Such a "pan-African" ascertainment, although not completely problem-free, allows unbiased exploration of demographic models for the widest set of archaic and modern human populations, as compared to the other ascertainment schemes we explored.},
}

@article {pmid36711776,
year = {2023},
author = {Witt, KE and Funk, A and Fang, LL and Huerta-Sanchez, E},
title = {The impact of modern admixture on archaic human ancestry in human populations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.16.524232},
pmid = {36711776},
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, as well as introgression between humans and archaic humans, Neanderthals and Denisovans. One example are genomes from populations in the Americas, as these are often mosaics of different ancestries due to recent admixture events as part of European colonization. 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 enrichment 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.},
}

@article {pmid36707713,
year = {2023},
author = {},
title = {Neanderthals stashed dozens of animal skulls in a cave - but why?.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {36707713},
issn = {1476-4687},
}

@article {pmid36593352,
year = {2023},
author = {Montag, A},
title = {[The history of skin color is the history of mankind!].},
journal = {Dermatologie (Heidelberg, Germany)},
volume = {74},
number = {2},
pages = {75-79},
pmid = {36593352},
issn = {2731-7013},
mesh = {Animals ; Humans ; *Hominidae/genetics ; Skin Pigmentation/genetics ; *Neanderthals ; Africa, Eastern ; Hair Color/genetics ; },
abstract = {In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.},
}

Animals
Humans
*Hominidae/genetics
Skin Pigmentation/genetics
*Neanderthals
Africa, Eastern
Hair Color/genetics

@article {pmid36702939,
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 = {A symbolic Neanderthal accumulation of large herbivore crania.},
journal = {Nature human behaviour},
volume = {},
number = {},
pages = {},
pmid = {36702939},
issn = {2397-3374},
abstract = {This work examines the possible behaviour of Neanderthal groups at the Cueva Des-Cubierta (central Spain) via the analysis of the latter's archaeological assemblage. Alongside evidence of Mousterian lithic industry, Level 3 of the cave infill was found to contain an assemblage of mammalian bone remains dominated by the crania of large ungulates, some associated with small hearths. The scarcity of post-cranial elements, teeth, mandibles and maxillae, along with evidence of anthropogenic modification of the crania (cut and percussion marks), indicates that the carcasses of the corresponding animals were initially processed outside the cave, and the crania were later brought inside. A second round of processing then took place, possibly related to the removal of the brain. The continued presence of crania throughout Level 3 indicates that this behaviour was recurrent during this level's formation. This behaviour seems to have no subsistence-related purpose but to be more symbolic in its intent.},
}

@article {pmid36691623,
year = {2023},
author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC},
title = {Genetic and functional odorant receptor variation in the Homo lineage.},
journal = {iScience},
volume = {26},
number = {1},
pages = {105908},
pmid = {36691623},
issn = {2589-0042},
abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.},
}

@article {pmid36681659,
year = {2022},
author = {Zhou, Z and M A Swagemakers, S and S Lourens, M and Suratannon, N and J van der Spek, P and A S H Dalm, V and A Dik, W and IJspeert, H and van Hagen, PM},
title = {Did variants in inborn errors of immunity genes contribute to the extinction of Neanderthals?.},
journal = {Asian Pacific journal of allergy and immunology},
volume = {40},
number = {4},
pages = {422-434},
doi = {10.12932/AP-251022-1489},
pmid = {36681659},
issn = {0125-877X},
abstract = {BACKGROUND: Neanderthals were a species of archaic humans that became extinct around 40,000 years ago. Modern humans have inherited 1-6% of Neanderthal DNA as a result of interbreeding. These inherited Neanderthal genes have paradoxical influences, while some can provide protection to viral infections, some others are associated with autoimmune/auto-inflammatory diseases.

OBJECTIVE: We aim to investigate whether genetic variants with strong detrimental effects on the function of the immune system could have potentially contributed to the extinction of the Neanderthal population.

METHODS: We used the publically available genome information from an Altai Neanderthal and filtered for potentially damaging variants present in genes associated with inborn errors of immunity (IEI) and checked whether these variants were present in the genomes of the Denisovan, Vindija and Chagyrskaya Neanderthals.

RESULTS: We identified 24 homozygous variants and 15 heterozygous variants in IEI-related genes in the Altai Neanderthal. Two homozygous variants in the UNC13D gene and one variant in the MOGS gene were present in all archaic genomes. Defects in the UNC13D gene are known to cause a severe and often fatal disease called hemophagocytic lymphohistiocystosis (HLH). One of these variants p.(N943S) has been reported in patients with HLH. Variants in MOGS are associated with glycosylation defects in the immune system affecting the susceptibility for infections.

CONCLUSIONS: Although the exact functional impact of these three variants needs further elucidation, we speculate that they could have resulted in an increased susceptibility to severe diseases and may have contributed to the extinction of Neanderthals after exposure to specific infections.},
}

@article {pmid36679036,
year = {2023},
author = {Nezami, E and Gallego, PP},
title = {History, Phylogeny, Biodiversity, and New Computer-Based Tools for Efficient Micropropagation and Conservation of Pistachio (Pistacia spp.) Germplasm.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/plants12020323},
pmid = {36679036},
issn = {2223-7747},
abstract = {The word "pstk" [pistag], used in the ancient Persian language, is the linguistic root from which the current name "pistachio", used worldwide, derives. The word pistachio is generally used to designate the plants and fruits of a single species: Pistacia vera L. Both the plant and its fruits have been used by mankind for thousands of years, specifically the consumption of its fruits by Neanderthals has been dated to about 300,000 years ago. Native to southern Central Asia (including northern Afghanistan and northeastern Iran), its domestication and cultivation occurred about 3000 years ago in this region, spreading to the rest of the Mediterranean basin during the Middle Ages and finally being exported to America and Australia at the end of the 19th century. The edible pistachio is an excellent source of unsaturated fatty acids, carbohydrates, proteins, dietary fiber, vitamins, minerals and bioactive phenolic compounds that help promote human health through their antioxidant capacity and biological activities. The distribution and genetic diversity of wild and domesticated pistachios have been declining due to increasing population pressure and climatic changes, which have destroyed natural pistachio habitats, and the monoculture of selected cultivars. As a result, the current world pistachio industry relies mainly on a very small number of commercial cultivars and rootstocks. In this review we discuss and summarize the current status of: etymology, origin, domestication, taxonomy and phylogeny by molecular analysis (RAPID, RFLP, AFLP, SSR, ISSR, IRAP, eSSR), main characteristics and world production, germplasm biodiversity, main cultivars and rootstocks, current conservation strategies of both conventional propagation (seeds, cutting, and grafting), and non-conventional propagation methods (cryopreservation, slow growth storage, synthetic seed techniques and micropropagation) and the application of computational tools (Design of Experiments (DoE) and Machine Learning: Artificial Neural Networks, Fuzzy logic and Genetic Algorithms) to design efficient micropropagation protocols for the genus Pistacia.},
}

@article {pmid36656646,
year = {2023},
author = {García-González, R and Rodríguez, L and Salazar-Fernández, A and Arsuaga, JL and Carretero, JM},
title = {Updated study of adult and subadult pectoral girdle bones from Sima de los Huesos site (Sierra de Atapuerca, Burgos, Spain). Anatomical and age estimation keys.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25158},
pmid = {36656646},
issn = {1932-8494},
abstract = {Here we present an updated inventory and study of pectoral girdle remains recovered from the Sima de los Huesos (SH) site. Here, we describe the key morphological traits of adults and, for the first time, subadult specimens. Because morphological traits can change with age, we also discuss some shortcomings related to age estimation in postcranial fossil specimens. Adult clavicles from the SH are long with a low robusticity index and marked curvatures in the superior view. Among these traits, only extreme clavicular length seems to characterize subadult individuals. Neandertals share all these traits. In the case of the scapula, the SH specimens share a relatively long and narrow glenoid fossa with Neandertals. This trait is also present in subadult individuals. Additionally, most specimens from SH, adults, and subadults showed a dorsal axillary sulcus on the scapular lateral border, a trait also present in most adult and subadult Neandertals. These traits in adult and subadult specimens supports substantial genetic control for many of them in both human species.},
}

@article {pmid36652426,
year = {2023},
author = {Berlioz, E and Capdepon, E and Discamps, E},
title = {A long-term perspective on Neanderthal environment and subsistence: Insights from the dental microwear texture analysis of hunted ungulates at Combe-Grenal (Dordogne, France).},
journal = {PloS one},
volume = {18},
number = {1},
pages = {e0278395},
doi = {10.1371/journal.pone.0278395},
pmid = {36652426},
issn = {1932-6203},
abstract = {Large bovids and cervids constituted major components of the European Middle Palaeolithic faunas and hence a key resource for Neanderthal populations. In paleoenvironmental reconstructions, red deer (Cervus elaphus) occurrence is classically considered as a tree-cover indicator while Bovinae (Bison priscus and Bos primigenius) and reindeer (Rangifer tarandus) occurrences are typically associated with open landscapes. However, insights into the ecology of extant ungulate populations show a more complex reality. Exploring the diet of past ungulates allows to better comprehend the hunting strategies of Palaeolithic populations and to reconstruct the modifications through time of past landscapes. By reflecting what animals have eaten during the last days or weeks of their life, dental microwear textures of herbivores link a population and its environment. Here we analyzed, via Dental Microwear Texture Analysis (DMTA), the diet of 50 Bos/Bison, 202 R. tarandus and 116 C. elaphus preyed upon by the Neanderthals that occupied Combe-Grenal rock-shelter, one of the most important Mousterian archaeo-sequences in southwestern France considering its long stratigraphy, abundance of faunal remains and the variations perceptible in Palaeolithic material culture. Grazers and mixed-feeders are the most represented dietary categories among Combe-Grenal's guild of herbivores, highlighting the availability, along the sequence, of open landscapes. The absence of clear changes in the use of plant resources by hunted ungulates through time, even though palaeoenvironmental changes were well-documented by previous studies along the sequence, is interpreted as resulting from the hunting of non-randomly selected prey by Neanderthals, preferentially in open environments. Thus, these results provide further insight into the hunting strategies of Neanderthals and modify our perception of potential links between subsistence and material culture. Combe-Grenal hunters "stayed in the open" through millennia, and were not forced to switch to hunting tactics and material technology adapted to close encounters in forested environments.},
}

@article {pmid36651963,
year = {2023},
author = {Moreira, F and Arenas, M and Videira, A and Pereira, F},
title = {Evolution of TOP1 and TOP1MT Topoisomerases in Chordata.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {36651963},
issn = {1432-1432},
abstract = {Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates.},
}

@article {pmid36625544,
year = {2023},
author = {Aqil, A and Speidel, L and Pavlidis, P and Gokcumen, O},
title = {Balancing selection on genomic deletion polymorphisms in humans.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.79111},
pmid = {36625544},
issn = {2050-084X},
abstract = {A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing to balancing selection. Nevertheless, genome-wide investigation of ancient and possibly adaptive deletions remains imperative. Here, we demonstrate an excess of polymorphisms in present-day humans that predate the modern human-Neanderthal split (ancient polymorphisms), which cannot be explained solely by selectively neutral scenarios. We analyze the adaptive mechanisms that underlie this excess in deletion polymorphisms. Using a previously published measure of balancing selection, we show that this excess of ancient deletions is largely owing to balancing selection. Based on the absence of signatures of overdominance, we conclude that it is a rare mode of balancing selection among ancient deletions. Instead, more complex scenarios involving spatially and temporally variable selective pressures are likely more common mechanisms. Our results suggest that balancing selection resulted in ancient deletions harboring disproportionately more exonic variants with GWAS associations. We further found that ancient deletions are significantly enriched for traits related to metabolism and immunity. As a by-product of our analysis, we show that deletions are, on average, more deleterious than single-nucleotide variants. We can now argue that not only is a vast majority of common variants shared among human populations, but a considerable portion of biologically relevant variants has been segregating among our ancestors for hundreds of thousands, if not millions, of years.},
}

@article {pmid36617238,
year = {2023},
author = {Zhang, X and Kim, B and Singh, A and Sankararaman, S and Durvasula, A and Lohmueller, KE},
title = {MaLAdapt reveals novel targets of adaptive introgression from Neanderthals and Denisovans in worldwide human populations.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad001},
pmid = {36617238},
issn = {1537-1719},
abstract = {Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Further, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and on a validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data, and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.},
}

@article {pmid36604552,
year = {2023},
author = {Sansalone, G and Profico, A and Wroe, S and Allen, K and Ledogar, J and Ledogar, S and Mitchell, DR and Mondanaro, A and Melchionna, M and Castiglione, S and Serio, C and Raia, P},
title = {Homo sapiens and Neanderthals share high cerebral cortex integration into adulthood.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {36604552},
issn = {2397-334X},
abstract = {There is controversy around the mechanisms that guided the change in brain shape during the evolution of modern humans. It has long been held that different cortical areas evolved independently from each other to develop their unique functional specializations. However, some recent studies suggest that high integration between different cortical areas could facilitate the emergence of equally extreme, highly specialized brain functions. Here, we analyse the evolution of brain shape in primates using three-dimensional geometric morphometrics of endocasts. We aim to determine, firstly, whether modern humans present unique developmental patterns of covariation between brain cortical areas; and secondly, whether hominins experienced unusually high rates of evolution in brain covariation as compared to other primates. On the basis of analyses including modern humans and other extant great apes at different developmental stages, we first demonstrate that, unlike our closest living relatives, Homo sapiens retain high levels of covariation between cortical areas into adulthood. Among the other great apes, high levels of covariation are only found in immature individuals. Secondly, at the macro-evolutionary level, our analysis of 400 endocasts, representing 148 extant primate species and 6 fossil hominins, shows that strong covariation between different areas of the brain in H. sapiens and Homo neanderthalensis evolved under distinctly higher evolutionary rates than in any other primate, suggesting that natural selection favoured a greatly integrated brain in both species. These results hold when extinct species are excluded and allometric effects are accounted for. Our findings demonstrate that high covariation in the brain may have played a critical role in the evolution of unique cognitive capacities and complex behaviours in both modern humans and Neanderthals.},
}

@article {pmid36594678,
year = {2023},
author = {Laudicina, NM and Cartmill, M},
title = {Clavicle length and shoulder breadth in hominoid evolution.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25144},
pmid = {36594678},
issn = {1932-8494},
abstract = {For a given body mass, hominoids have longer clavicles than typical monkeys, reflecting the lateral reorientation of the hominoid glenoid. Relative length of the clavicle varies among hominoids, with orangutans having longer clavicles than expected for body mass and gorillas and chimpanzees having shorter clavicles than expected. Modern humans conform to the general hominoid distribution, but Neandertals and Upper Paleolithic Homo sapiens have longer clavicles than expected for their size and exhibit marked positive allometry in clavicle length. Relative to clavicle length, adult and newborn humans have broader shoulders (biacromial breadths) than comparable apes, because the reduced elevation of the human shoulder swings the acromion laterally downward away from the head. Since broadened shoulders yield an increased risk of maternal and neonatal injury and/or death from shoulder dystocia during birth, we might expect hominins to manifest trends toward reduction in shoulder breadth and clavicle length. They do not, presumably because of countering selection pressures favoring a long clavicle in the adults. The marked sexual dimorphism seen in patterns of clavicular growth and static adult allometry in humans suggests that those selection pressures have disproportionately affected the males.},
}

@article {pmid36576952,
year = {2022},
author = {Peresani, M},
title = {Inspecting human evolution from a cave. Late Neanderthals and early sapiens at Grotta di Fumane: present state and outlook.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10016},
pmid = {36576952},
issn = {2037-0644},
abstract = {Of the many critical phases of human evolution, one of the most investigated is the transition from the Middle to the Upper Palaeolithic with the pivotal bio-cultural substitution of Neanderthals by Homo sapiens in Western Eurasia. The complexity of this over ten thousands years phase raises from the ensemble of evidence ascribed to the diverse adaptations expressed by Neanderthals and the first representatives of our species. In countless archaeological records Neanderthals left clear traces of a cultural variability dotted with innovations in the technology of stone and bone tools, alongside with manifestations in the range of the symbolic sphere. Together with other aspects of daily life, this evidence contributes shedding light on the cognitive aptitudes of those hominins and reassessing gaps in Pleistocene human diversities. Among archaeological contexts, the cave of Fumane in the Monti Lessini (Veneto Pre-Alps, northeastern Italy) is a key site. It is positioned along the potential trajectory of hominins moving into southern Europe from eastern and southeastern regions and includes a finely layered sedimentary sequence with cultural layers ascribed to the Mousterian, Uluzzian, Aurignacian and Gravettian. The ensemble constitutes one of the most complete, detailed and dated continental stratigraphic series from a segment of the late Pleistocene between 50 and 30 ka cal BP in a cave context of Southern Europe. Assessments based on sedimentological and palaeontological record provide indicators for framing Neanderthals in their respective ecological contexts since the late Middle Pleistocene until their demise during MIS3. On-going research is producing data ascribable to the human ecological relations and the interaction with specific natural resources, thus contributing to shed light on the complexity of Neanderthal behavior. Thanks to the high-resolution archaeological record of the earliest appearances of Homo sapiens, Fumane also provides clues to compare life, subsistence, and cultures between these Pleistocene hominins for comprehensive reasonings on our unicity.},
}

@article {pmid36564491,
year = {2022},
author = {Bañuls-Cardona, S and Blasco, R and Rosell, J and Rufà, A and Vallverdú, J and Rivals, F},
title = {New quantitative method for dental wear analysis of small mammals.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {22231},
pmid = {36564491},
issn = {2045-2322},
abstract = {The application of dental wear study to murids has always been ruled out because of their omnivorous diet, which does not leave significant wear on the dentition. Nevertheless, in our work we select Apodemus sylvaticus (wood mouse) as the object of study for several reasons: its seasonal diet, its ability to resist the gastric juices of predators, the fact that it has not undergone major morphological changes since its appearance 3 million years ago, and its widespread distribution throughout much of Europe and part of Africa. The importance of this work lies in the modifications we make to the dental wear methodology for its application to murids. These enable us to obtain quantitative data on the entire tooth surface. The sample chosen was a total of 75 lower first molars from two different archaeological sites: Teixoneres cave and Xaragalls cave. The chronology of the samples chosen ranges from Marine Isotope Stages 5-3. The data obtained reveal that the part of the tooth that shows most wear is the distal part (entoconid). Furthermore, the results provide us with relevant information on the types of accumulations of remains in the caves (short vs. long term), as well as on the seasonality of Neanderthal occupations during the Upper Pleistocene (MIS5-3) of the northeastern Iberian Peninsula.},
}

@article {pmid36560850,
year = {2022},
author = {Yermakovich, D and Pankratov, V and Võsa, U and Yunusbayev, B and , and Dannemann, M},
title = {Long-range regulatory effects of Neandertal DNA in modern humans.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyac188},
pmid = {36560850},
issn = {1943-2631},
abstract = {The admixture between modern humans and Neandertals has resulted in ∼2% of the genomes of present-day non-Africans being composed of Neandertal DNA. Introgressed Neandertal DNA has been demonstrated to significantly affect the transcriptomic landscape in people today and via this molecular mechanism influence phenotype variation as well. However, little is known about how much of that regulatory impact is mediated through long-range regulatory effects that have been shown to explain ∼20% of expression variation. Here we identified 60 transcription factors (TFs) with their top cis-eQTL SNP in GTEx being of Neandertal ancestry and predicted long-range Neandertal DNA-induced regulatory effects by screening for the predicted target genes of those TFs. We show that the TFs form a significantly connected protein-protein interaction network. Among them are JUN and PRDM5, two brain-expressed TFs that have their predicted target genes enriched in regions devoid of Neandertal DNA. Archaic cis-eQTLs for the 60 TFs include multiple candidates for local adaptation, some of which show significant allele frequency increases over the last ∼10,000 years. A large proportion of the cis-eQTL-associated archaic SNPs have additional associations with various immune traits, schizophrenia, blood cell type composition and anthropometric measures. Finally, we demonstrate that our results are consistent with those of Neandertal-DNA-associated empirical trans-eQTLs. Our results suggest that Neandertal DNA significantly influences regulatory networks, that its regulatory reach goes beyond the 40% of genomic sequence that it still covers in present-day non-Africans and that via the investigated mechanism Neandertal DNA influences the phenotypic variation in people today.},
}

@article {pmid36520391,
year = {2023},
author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Geigl, EM and Grange, T},
title = {Analysis of Ancient Microbial DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2605},
number = {},
pages = {103-131},
pmid = {36520391},
issn = {1940-6029},
abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.},
}

@article {pmid36511798,
year = {2022},
author = {Stringer, C},
title = {The development of ideas about a recent African origin for Homo sapiens.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10009},
pmid = {36511798},
issn = {2037-0644},
abstract = {In this contribution I will review the development of ideas about a recent African origin for our species over the last 50 years, starting from the time of my PhD in the early 1970s. I will examine the instructive and quite different interpretations placed on the 1979 discovery of a partial Neanderthal skeleton associated with a Châtelperronian industry at the rock shelter of St-Césaire in France, and then focus on the crucial years from 1987-1989, including the so-called 'Human Revolution' conference of 1987, and my 1988 Science paper with Peter Andrews: 'Genetic and Fossil Evidence for the Origin of Modern Humans'. Following the historical review, I will assess the status of five proposed models for the evolution of derived Homo sapiens: Recent African Origin (RAO); RAO and Hybridisation (RAOH); Assimilation (AM); Multiregional Evolution (MRE); and Braided Stream (BS). I conclude that a recent African origin model with hybridization (RAOH) is the best supported from the fossil and genetic evidence.},
}

@article {pmid36503519,
year = {2022},
author = {Taravella Oill, AM and Buetow, KH and Wilson, MA},
title = {The role of Neanderthal introgression in liver cancer.},
journal = {BMC medical genomics},
volume = {15},
number = {1},
pages = {255},
pmid = {36503519},
issn = {1755-8794},
support = {R35GM124827/GM/NIGMS NIH HHS/United States ; },
abstract = {BACKGROUND: Neanderthal introgressed DNA has been linked to different normal and disease traits including immunity and metabolism-two important functions that are altered in liver cancer. However, there is limited understanding of the relationship between Neanderthal introgression and liver cancer risk. The aim of this study was to investigate the relationship between Neanderthal introgression and liver cancer risk.

METHODS: Using germline and somatic DNA and tumor RNA from liver cancer patients from The Cancer Genome Atlas, along with ancestry-match germline DNA from unaffected individuals from the 1000 Genomes Resource, and allele specific expression data from normal liver tissue from The Genotype-Tissue Expression project we investigated whether Neanderthal introgression impacts cancer etiology. Using a previously generated set of Neanderthal alleles, we identified Neanderthal introgressed haplotypes. We then tested whether somatic mutations are enriched or depleted on Neanderthal introgressed haplotypes compared to modern haplotypes. We also computationally assessed whether somatic mutations have a functional effect or show evidence of regulating expression of Neanderthal haplotypes. Finally, we compared patterns of Neanderthal introgression in liver cancer patients and the general population.

RESULTS: We find Neanderthal introgressed haplotypes exhibit an excess of somatic mutations compared to modern haplotypes. Variant Effect Predictor analysis revealed that most of the somatic mutations on these Neanderthal introgressed haplotypes are not functional. We did observe expression differences of Neanderthal alleles between tumor and normal for four genes that also showed a pattern of enrichment of somatic mutations on Neanderthal haplotypes. However, gene expression was similar between liver cancer patients with modern ancestry and liver cancer patients with Neanderthal ancestry at these genes. Provocatively, when analyzing all genes, we find evidence of Neanderthal introgression regulating expression in tumor from liver cancer patients in two genes, ARK1C4 and OAS1. Finally, we find that most genes do not show a difference in the proportion of Neanderthal introgression between liver cancer patients and the general population.

CONCLUSION: Our results suggest that Neanderthal introgression provides opportunity for somatic mutations to accumulate, and that some Neanderthal introgression may impact liver cancer risk.},
}

@article {pmid36493597,
year = {2022},
author = {Keeling, BA and Quam, R and Martínez, I and Arsuaga, JL and Maroto, J},
title = {Reassessment of the human mandible from Banyoles (Girona, Spain).},
journal = {Journal of human evolution},
volume = {174},
number = {},
pages = {103291},
doi = {10.1016/j.jhevol.2022.103291},
pmid = {36493597},
issn = {1095-8606},
abstract = {Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.},
}

@article {pmid36480515,
year = {2022},
author = {Vespasiani, DM and Jacobs, GS and Cook, LE and Brucato, N and Leavesley, M and Kinipi, C and Ricaut, FX and Cox, MP and Gallego Romero, I},
title = {Denisovan introgression has shaped the immune system of present-day Papuans.},
journal = {PLoS genetics},
volume = {18},
number = {12},
pages = {e1010470},
doi = {10.1371/journal.pgen.1010470},
pmid = {36480515},
issn = {1553-7404},
abstract = {Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.},
}

@article {pmid36471017,
year = {2022},
author = {Saraiva, LR},
title = {The Neanderthal inside us.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {36471017},
issn = {1471-0064},
}

@article {pmid36467077,
year = {2022},
author = {Schäfer, W and Stähler, T and Pinto Espinoza, C and Danquah, W and Knop, JH and Rissiek, B and Haag, F and Koch-Nolte, F},
title = {Origin, distribution, and function of three frequent coding polymorphisms in the gene for the human P2X7 ion channel.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {1033135},
pmid = {36467077},
issn = {1663-9812},
abstract = {P2X7, an ion channel gated by extracellular ATP, is widely expressed on the plasma membrane of immune cells and plays important roles in inflammation and apoptosis. Several single nucleotide polymorphisms have been identified in the human P2RX7 gene. In contrast to other members of the P2X family, non-synonymous polymorphisms in P2X7 are common. Three of these occur at overall frequencies of more than 25% and affect residues in the extracellular "head"-domain of P2X7 (155 Y/H), its "lower body" (270 R/H), and its "tail" in the second transmembrane domain (348 T/A). Comparison of the P2X7 orthologues of human and other great apes indicates that the ancestral allele is Y-R-T (at 155-270-348). Interestingly, each single amino acid variant displays lower ATP-sensitivity than the ancestral allele. The originally published reference sequence of human P2X7, often referred to as "wildtype," differs from the ancestral allele at all three positions, i.e. H-H-A. The 1,000 Genome Project determined the sequences of both alleles of 2,500 human individuals, including roughly 500 persons from each of the five major continental regions. This rich resource shows that the ancestral alleles Y155, R270, and T348 occur in all analyzed human populations, albeit at strikingly different frequencies in various subpopulations (e.g., 25%-59% for Y155, 59%-77% for R270, and 13%-47% for T348). BLAST analyses of ancient human genome sequences uncovered several homozygous carriers of variant P2X7 alleles, possibly reflecting a high degree of inbreeding, e.g., H-R-T for a 50.000 year old Neanderthal, H-R-A for a 24.000 year old Siberian, and Y-R-A for a 7,000 year old mesolithic European. In contrast, most present-day individuals co-express two copies of P2X7 that differ in one or more amino acids at positions 155, 270, and 348. Our results improve the understanding of how P2X7 structure affects its function and suggest the importance of considering P2X7 variants of participants when designing clinical trials targeting P2X7.},
}

@article {pmid36465121,
year = {2022},
author = {Ma, X and Xu, S},
title = {Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105614},
pmid = {36465121},
issn = {2589-0042},
abstract = {Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as SLC19A2, SLC35F3, and SLC35F4, were assumed to be underlying positive selection in East Asians, but the detailed mechanism remains unknown. Here, we analyzed genome data of 3,823 individuals representing 223 global populations and identified the adaptive haplotypes at thiamine genes. Interestingly, the putative adaptive haplotype at SLC35F4 was of Neanderthal ancestry, while that at SLC35F3 was also likely of archaic origins. Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. We argue that pathogens, rather than agriculture developed ∼10,000 years ago in East Asia, were likely the initial driving force of the putative positive selection. Notably, the first American people did not carry the putative adaptive haplotype at SLC35F4.},
}

@article {pmid36455404,
year = {2022},
author = {Velez, AD and Quam, R and Conde-Valverde, M and Martínez, I and Lorenzo, C and Arsuaga, JL},
title = {Geometric morphometric analysis of the bony labyrinth of the Sima de los Huesos hominins.},
journal = {Journal of human evolution},
volume = {174},
number = {},
pages = {103280},
doi = {10.1016/j.jhevol.2022.103280},
pmid = {36455404},
issn = {1095-8606},
abstract = {The bony labyrinth contains phylogenetic information that can be used to determine interspecific differences between fossil hominins. The present study conducted a comparative 3D geometric morphometric analysis on the bony labyrinth of the Middle Pleistocene Sima de los Huesos (SH) hominins. The findings of this study corroborate previous multivariate analyses of the SH hominin bony labyrinth. The analysis of the semicircular canals revealed the SH hominin canal morphologies appear closer to those of the Neandertals than to those of Homo sapiens. This is attributable to a Neandertal-like ovoid anterior canal, and mediolaterally expanded, circular posterior canal. However, the SH hominins lack the increased torsion in the anterior canal and the inferior orientation of the lateral canal seen in Neandertals. The results of the cochlear analysis indicated that, although there is some overlap, there are notable differences between the SH hominins and the Neandertals. In particular, the SH hominin cochlea appears more constricted than in Neandertals in the first and second turns. A principal component analysis of the full bony labyrinth separated most SH hominins from the Neandertals, which largely clustered with modern humans. A covariance ratio analysis found a significant degree of modularity within the bony labyrinth of all three groups, with the SH hominins and Neandertals displaying the highest modularity. This modular signal in the bony labyrinth may be attributable to different selective pressures related to locomotion and audition. Overall, the results of this study confirm previous suggestions that the semicircular canals in the SH hominins are somewhat derived toward Neandertals, while their cochlea is largely primitive within the genus Homo.},
}

@article {pmid36455403,
year = {2022},
author = {Britton, K and Jimenez, EL and Le Corre, M and Pederzani, S and Daujeard, C and Jaouen, K and Vettese, D and Tütken, T and Hublin, JJ and Moncel, MH},
title = {Multi-isotope zooarchaeological investigations at Abri du Maras: The paleoecological and paleoenvironmental context of Neanderthal subsistence strategies in the Rhône Valley during MIS 3.},
journal = {Journal of human evolution},
volume = {174},
number = {},
pages = {103292},
doi = {10.1016/j.jhevol.2022.103292},
pmid = {36455403},
issn = {1095-8606},
abstract = {The exploitation of mid- and large-sized herbivores (ungulates) was central to hominin subsistence across Late Pleistocene Europe. Reconstructing the paleoecology of prey-taxa is key to better understanding procurement strategies, decisions and behaviors, and the isotope analysis of faunal bones and teeth found at archaeological sites represent a powerful means of accessing information about past faunal behaviors. These isotope zooarchaeological approaches also have a near-unique ability to reveal environmental conditions contemporary to the human activities that produced these remains. Here, we present the results of a multi-isotope, multitissue study of ungulate remains from the Middle Paleolithic site of Abri du Maras, southern France, providing new insights into the living landscapes of the Rhône Valley during MIS 3 (level 4.2 = 55 ± 2 to 42 ± 3 ka; level 4.1 = 46 ± 3 to 40 ± 3 ka). Isotope data (carbon, nitrogen) reveal the dietary niches of different ungulate taxa, including the now-extinct giant deer (Megaloceros). Oxygen isotope data are consistent with a mild seasonal climate during level 4.2, where horse (Equus), bison (Bison), and red deer (Cervus elaphus) were exploited year-round. Strontium and sulfur isotope analyses provide new evidence for behavioral plasticity in Late Pleistocene European reindeer (Rangifer) between level 4.2 and level 4.1, indicating a change from the migratory to the sedentary ecotype. In level 4.1, the strong seasonal nature of reindeer exploitation, combined with their nonmigratory behavior, is consistent with a seasonally restricted use of the site by Neanderthals at that time or the preferential hunting of reindeer when in peak physical condition during the autumn.},
}

@article {pmid36423581,
year = {2022},
author = {Mangan, RJ and Alsina, FC and Mosti, F and Sotelo-Fonseca, JE and Snellings, DA and Au, EH and Carvalho, J and Sathyan, L and Johnson, GD and Reddy, TE and Silver, DL and Lowe, CB},
title = {Adaptive sequence divergence forged new neurodevelopmental enhancers in humans.},
journal = {Cell},
volume = {185},
number = {24},
pages = {4587-4603.e23},
doi = {10.1016/j.cell.2022.10.016},
pmid = {36423581},
issn = {1097-4172},
mesh = {Animals ; Humans ; *Hominidae/genetics ; Regulatory Sequences, Nucleic Acid ; *Neanderthals/genetics ; Genome, Human ; Genomics ; },
abstract = {Searches for the genetic underpinnings of uniquely human traits have focused on human-specific divergence in conserved genomic regions, which reflects adaptive modifications of existing functional elements. However, the study of conserved regions excludes functional elements that descended from previously neutral regions. Here, we demonstrate that the fastest-evolved regions of the human genome, which we term "human ancestor quickly evolved regions" (HAQERs), rapidly diverged in an episodic burst of directional positive selection prior to the human-Neanderthal split, before transitioning to constraint within hominins. HAQERs are enriched for bivalent chromatin states, particularly in gastrointestinal and neurodevelopmental tissues, and genetic variants linked to neurodevelopmental disease. We developed a multiplex, single-cell in vivo enhancer assay to discover that rapid sequence divergence in HAQERs generated hominin-unique enhancers in the developing cerebral cortex. We propose that a lack of pleiotropic constraints and elevated mutation rates poised HAQERs for rapid adaptation and subsequent susceptibility to disease.},
}

Animals
Humans
*Hominidae/genetics
Regulatory Sequences, Nucleic Acid
*Neanderthals/genetics
Genome, Human
Genomics

@article {pmid36418334,
year = {2022},
author = {Deschamps, M and Martín-Lerma, I and Linares-Matás, G and Zilhão, J},
title = {Organization of residential space, site function variability, and seasonality of activities among MIS 5 Iberian Neandertals.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {20221},
pmid = {36418334},
issn = {2045-2322},
mesh = {Animals ; *Neanderthals ; Archaeology ; Climate ; Seasons ; Anthropology, Cultural ; },
abstract = {Whether ethnoarcheological models of hunter-gatherer mobility, landscape use, and structuration of the inhabited space are relevant to the archeology of Neandertals and the Middle Paleolithic remains controversial. The thin lenses of hearth-associated stone tools and faunal remains excavated in sub-complex AS5 of Cueva Antón (Murcia, Spain) significantly advance these debates. Dated to 77.8-85.1 ka, these living floors are interstratified in river-accumulated sands and were buried shortly after abandonment by low-energy inundation events, with minimal disturbance and negligible palimpsest formation. Stone tools were made and ergonomically modified to fit tasks; their spatial distributions and use-wear reveal hearth-focused activities and a division of the inhabited space into resting and working areas. Site function varied with season of the year: units III-i/j1 and III-i/j2-3 record winter visits focused on filleting and hide processing, while woodworking predominated in unit III-b/d, which subsumes visits to the site over the course of at least one winter, one spring, and one summer. These snapshots of Neandertal behavior match expectations derived from the ethnographic and Upper Paleolithic records for the lifeways of hunter-gatherers inhabiting temperate regions with a markedly seasonal climate.},
}

Animals
*Neanderthals
Archaeology
Climate
Seasons
Anthropology, Cultural

@article {pmid36394417,
year = {2022},
author = {Wielgus, K and Danielewski, M and Walkowiak, J},
title = {Svante Pääbo, reader of the Neanderthal genome.},
journal = {Acta physiologica (Oxford, England)},
volume = {},
number = {},
pages = {e13902},
doi = {10.1111/apha.13902},
pmid = {36394417},
issn = {1748-1716},
}

@article {pmid36375244,
year = {2022},
author = {Harvati, K and Reyes-Centeno, H},
title = {Evolution of Homo in the Middle and Late Pleistocene.},
journal = {Journal of human evolution},
volume = {173},
number = {},
pages = {103279},
doi = {10.1016/j.jhevol.2022.103279},
pmid = {36375244},
issn = {1095-8606},
mesh = {Animals ; Humans ; *Hominidae ; Phylogeny ; Biological Evolution ; Fossils ; *Neanderthals ; },
abstract = {The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.},
}

Animals
Humans
*Hominidae
Phylogeny
Biological Evolution
Fossils
*Neanderthals

@article {pmid36345622,
year = {2022},
author = {Tveito, K},
title = {From Icelandic family sagas to Neanderthal genes.},
journal = {Tidsskrift for den Norske laegeforening : tidsskrift for praktisk medicin, ny raekke},
volume = {142},
number = {16},
pages = {},
doi = {10.4045/tidsskr.22.0684},
pmid = {36345622},
issn = {0807-7096},
mesh = {Humans ; Animals ; *Neanderthals/genetics ; Iceland ; },
}

Humans
Animals
*Neanderthals/genetics
Iceland

@article {pmid36344982,
year = {2022},
author = {Koller, D and Wendt, FR and Pathak, GA and De Lillo, A and De Angelis, F and Cabrera-Mendoza, B and Tucci, S and Polimanti, R},
title = {Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations.},
journal = {BMC biology},
volume = {20},
number = {1},
pages = {249},
pmid = {36344982},
issn = {1741-7007},
support = {F32 MH122058/MH/NIMH NIH HHS/United States ; R21 DC018098/DC/NIDCD NIH HHS/United States ; R33 DA047527/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Neanderthals/genetics ; Multifactorial Inheritance ; Genome-Wide Association Study ; Genome, Human ; Asians ; },
abstract = {BACKGROUND: Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum. Evidence of how Neanderthal introgression shaped the genetics of human traits and diseases has been extensively studied in populations of European descent, with signatures of admixture reported for instance in genes associated with pigmentation, immunity, and metabolic traits. However, limited information is currently available about the impact of archaic introgression on other ancestry groups. Additionally, to date, no study has been conducted with respect to the impact of Denisovan introgression on the health and disease of modern populations. Here, we compare the way evolutionary pressures shaped the genetics of complex traits in East Asian and European populations, and provide evidence of the impact of Denisovan introgression on the health of East Asian and Central/South Asian populations.

RESULTS: Leveraging genome-wide association statistics from the Biobank Japan and UK Biobank, we assessed whether Denisovan and Neanderthal introgression together with other evolutionary genomic signatures were enriched for the heritability of physiological and pathological conditions in populations of East Asian and European descent. In EAS, Denisovan-introgressed loci were enriched for coronary artery disease heritability (1.69-fold enrichment, p=0.003). No enrichment for archaic introgression was observed in EUR. We also performed a phenome-wide association study of Denisovan and Neanderthal alleles in six ancestry groups available in the UK Biobank. In EAS, the Denisovan-introgressed SNP rs62391664 in the major histocompatibility complex region was associated with albumin/globulin ratio (beta=-0.17, p=3.57×10[-7]). Neanderthal-introgressed alleles were associated with psychiatric and cognitive traits in EAS (e.g., "No Bipolar or Depression"-rs79043717 beta=-1.5, p=1.1×10[-7]), and with blood biomarkers (e.g., alkaline phosphatase-rs11244089 beta=0.1, p=3.69×10[-116]) and red hair color (rs60733936 beta=-0.86, p=4.49×10[-165]) in EUR. In the other ancestry groups, Neanderthal alleles were associated with several traits, also including the use of certain medications (e.g., Central/South East Asia: indapamide - rs732632 beta=-2.38, p=5.22×10[-7]).

CONCLUSIONS: Our study provides novel evidence regarding the impact of archaic introgression on the genetics of complex traits in worldwide populations, highlighting the specific contribution of Denisovan introgression in EAS populations.},
}

Humans
Animals
*Neanderthals/genetics
Multifactorial Inheritance
Genome-Wide Association Study
Genome, Human
Asians

@article {pmid36336759,
year = {2022},
author = {Richards, GD and Jabbour, RS and Guipert, G and Defleur, A},
title = {Endocranial anatomy of the Guercy 1 early Neanderthal from Baume Moula-Guercy (Soyons, Ardèche, France).},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.25118},
pmid = {36336759},
issn = {1932-8494},
abstract = {We provide the first comparative description of the endocranium of the Guercy 1 Early Neanderthal and examine its affinities to Preneanderthals, Neanderthals, and Homo sapiens. The Guercy 1 cranium derives from deposits chronostratigraphically and biostratigraphically dated to the Eemian Interglacial (MIS 5e). For comparative purposes, we compiled a sample of European and Southwest Asian subadult and adult Middle-to-Late Pleistocene hominins (≈MIS 12-MIS 1; N = 65). We sampled both a Preneanderthal-Neanderthal group and a Homo sapiens group. The Preneanderthal-Neanderthal group was further divided into three time-successive subgroups defined by associated MIS stages. Metric and morphological observations were made on original fossils and physical and virtual endocranial reconstructions. Guercy 1 and other Early Neanderthals, differ from Preneanderthals by increased development of the prefrontal cortex, precentral and postcentral gyri, inferior parietal lobule, and frontoparietal operculum. Early Neanderthal differ, in general, from Late Neanderthals by exhibiting less development in most of the latter brain structures. The late group additionally differentiates itself from the early group by a greater development of the rostral superior parietal lobule, angular gyrus, superior and middle temporal gyri, and caudal branches of the superior temporal gyrus. Endocranial morphology assessed along the Preneanderthal-Neanderthal sequence show that brain structures prominent in Preneanderthals are accentuated in Early-to-Late Neanderthals. However, both the Early and Late groups differentiate themselves by also showing regionally specific changes in brain development. This pattern of morphological change is consistent with a mosaic pattern of neural evolution in these Middle-to-Late Pleistocene hominins.},
}

@article {pmid36323899,
year = {2022},
author = {Graham, F},
title = {Daily briefing: First known Neanderthal family discovered.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-03378-0},
pmid = {36323899},
issn = {1476-4687},
}

@article {pmid36322514,
year = {2022},
author = {Campelo Dos Santos, AL and Owings, A and Sullasi, HSL and Gokcumen, O and DeGiorgio, M and Lindo, J},
title = {Genomic evidence for ancient human migration routes along South America's Atlantic coast.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1986},
pages = {20221078},
pmid = {36322514},
issn = {1471-2954},
support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; History, Ancient ; Animals ; *Human Migration ; Genomics ; Genome, Human ; *Neanderthals ; Brazil ; },
abstract = {An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.},
}

Humans
History, Ancient
Animals
*Human Migration
Genomics
Genome, Human
*Neanderthals
Brazil

@article {pmid36313404,
year = {2022},
author = {Mortazavi, SA and Bevelacqua, JJ and Welsh, JS and Masoumi, SJ and Bahaaddini Beigy Zarandi, BF and Ghadimi-Moghadam, A and Haghani, M and Mortazavi, SMJ},
title = {The Paradox of COVID-19 in Sub-Saharan Africa: Why it is More Unethical Not to Investigate Low Dose Radiotherapy for COVID-19.},
journal = {Journal of biomedical physics & engineering},
volume = {12},
number = {5},
pages = {539-542},
pmid = {36313404},
issn = {2251-7200},
abstract = {An accumulating body of evidence shows that various ethnicities are differentially affected by SARS-COV-2 infection. Moreover, some evidence shows that due to the vaccine inequity and millions of people living with HIV, a major catastrophe could occur in African countries that possibly affects the whole world. Given the possibility that Neanderthal genes confer a slight increase in susceptibility, this difference, at least to some extent, might possibly decrease the risk of the emergence of new SARS-CoV-2 variants among black people in Africa. Recent studies show less death and fewer cases among the ethnic group classified as "Black Africans". Although Neanderthal DNA might explain some differences in morbidity and mortality of COVID-19, a multitude of confounders complicate things to where drawing definite conclusions is hard or even impossible. Using selective-pressure-free treatments (e.g. low dose radiotherapy) for COVID-19 pneumonia would be of crucial importance everywhere, but particularly in sub-Saharan Africa, where "long COVID" in millions of people with HIV paves the road for the more frequent emergence of new variants.},
}

@article {pmid36289417,
year = {2022},
author = {Thompson, B and Bundell, S},
title = {Ancient DNA reveals family of Neanderthals living in Siberian cave.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-03460-7},
pmid = {36289417},
issn = {1476-4687},
}

@article {pmid36271299,
year = {2022},
author = {Vidal-Cordasco, M and Ocio, D and Hickler, T and Marín-Arroyo, AB},
title = {Publisher Correction: Ecosystem productivity affected the spatiotemporal disappearance of Neanderthals in Iberia.},
journal = {Nature ecology & evolution},
volume = {6},
number = {11},
pages = {1789},
doi = {10.1038/s41559-022-01917-6},
pmid = {36271299},
issn = {2397-334X},
}

@article {pmid36261727,
year = {2022},
author = {Callaway, E},
title = {First known Neanderthal family discovered in Siberian cave.},
journal = {Nature},
volume = {610},
number = {7933},
pages = {615-616},
pmid = {36261727},
issn = {1476-4687},
mesh = {Animals ; *Caves ; *Fossils ; *Neanderthals/genetics ; History, Ancient ; },
}

Animals
*Caves
*Fossils
*Neanderthals/genetics
History, Ancient

@article {pmid36261548,
year = {2022},
author = {Skov, L and Peyrégne, S and Popli, D and Iasi, LNM and Devièse, T and Slon, V and Zavala, EI and Hajdinjak, M and Sümer, AP and Grote, S and Bossoms Mesa, A and López Herráez, D and Nickel, B and Nagel, S and Richter, J and Essel, E and Gansauge, M and Schmidt, A and Korlević, P and Comeskey, D and Derevianko, AP and Kharevich, A and Markin, SV and Talamo, S and Douka, K and Krajcarz, MT and Roberts, RG and Higham, T and Viola, B and Krivoshapkin, AI and Kolobova, KA and Kelso, J and Meyer, M and Pääbo, S and Peter, BM},
title = {Genetic insights into the social organization of Neanderthals.},
journal = {Nature},
volume = {610},
number = {7932},
pages = {519-525},
pmid = {36261548},
issn = {1476-4687},
support = {803147/ERC_/European Research Council/International ; 715069/ERC_/European Research Council/International ; FP7/2007-2013/ERC_/European Research Council/International ; 694707/ERC_/European Research Council/International ; },
mesh = {Animals ; Female ; Humans ; Caves ; Genome/genetics ; Hybridization, Genetic ; *Neanderthals/genetics ; Siberia ; DNA, Mitochondrial/genetics ; Y Chromosome/genetics ; Male ; Family ; Homozygote ; },
abstract = {Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans[1-8], but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave[9,10] and 2 from Okladnikov Cave[11]-making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father-daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals' genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.},
}

Animals
Female
Humans
Caves
Genome/genetics
Hybridization, Genetic
*Neanderthals/genetics
Siberia
DNA, Mitochondrial/genetics
Y Chromosome/genetics
Male
Family
Homozygote

@article {pmid36261544,
year = {2022},
author = {Cassidy, LM},
title = {The first genomic portrait of a Neanderthal family.},
journal = {Nature},
volume = {610},
number = {7932},
pages = {454-455},
pmid = {36261544},
issn = {1476-4687},
mesh = {Animals ; *Neanderthals/genetics ; Genome/genetics ; Genomics ; },
}

Animals
*Neanderthals/genetics
Genome/genetics
Genomics

@article {pmid36261474,
year = {2022},
author = {Mayoral, E and Duveau, J and Santos, A and Ramírez, AR and Morales, JA and Díaz-Delgado, R and Rivera-Silva, J and Gómez-Olivencia, A and Díaz-Martínez, I},
title = {New dating of the Matalascañas footprints provides new evidence of the Middle Pleistocene (MIS 9-8) hominin paleoecology in southern Europe.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {17505},
pmid = {36261474},
issn = {2045-2322},
mesh = {Animals ; Humans ; *Hominidae ; Fossils ; *Neanderthals ; Europe ; Luminescence ; },
abstract = {Hominin footprints were recently discovered at Matalascañas (Huelva; South of Iberian Peninsula). They were dated thanks to a previous study in deposits of the Asperillo cliff to 106 ± 19 ka, Upper Pleistocene, making Neandertals the most likely track-makers. In this paper, we report new Optically Stimulated Luminescence dating that places the hominin footprints surface in the range of 295.8 ± 17 ka (MIS 9-MIS 8 transition, Middle Pleistocene). This new age implies that the possible track-makers are individuals more likely from the Neandertal evolutionary lineage. Regardless of the taxon attributed to the Matalascañas footprints, they supplement the existing partial fossil record for the European Middle Pleistocene Hominins being notably the first palaeoanthropological evidence (hominin skeleton or footprints) from the MIS 9 and MIS 8 transition discovered in the Iberian Peninsula, a moment of climatic evolution from warm to cool. Thus, the Matalascañas footprints represent a crucial record for understanding human occupations in Europe in the Pleistocene.},
}

Animals
Humans
*Hominidae
Fossils
*Neanderthals
Europe
Luminescence

@article {pmid36253794,
year = {2022},
author = {Bergman, J and Schierup, MH},
title = {Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {215},
pmid = {36253794},
issn = {1474-760X},
mesh = {Animals ; Female ; *Hominidae/genetics ; Humans ; Male ; Nucleotides ; *Pseudoautosomal Regions ; Receptor, PAR-1/genetics ; Y Chromosome/genetics ; },
abstract = {BACKGROUND: The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes, and two archaic human genome sequences.

RESULTS: We find that PAR1 is fast evolving and closer to evolutionary nucleotide equilibrium than autosomal telomeres. We detect a difference between substitution patterns and extant diversity in PAR1, mainly driven by the conflict between strong mutation and recombination-associated fixation bias at CpG sites. We detect excess C-to-G mutations in PAR1 of all great apes, specific to the mutagenic effect of male recombination. Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. We find differences between substitution spectra of these archaics suggesting rapid evolution of PAR1 in recent hominin history. Frequency analysis of alleles segregating in females and males provided no evidence for recent sexual antagonism in this region. We study repeat content and double-strand break hotspot regions in PAR1 and find that they may play roles in ensuring the obligate X-Y recombination event during male meiosis.

CONCLUSIONS: Our study provides an unprecedented quantification of population genetic forces governing PAR1 biology across extant and extinct hominids. PAR1 evolutionary dynamics are predominantly governed by recombination processes with a strong impact on mutation patterns across all species.},
}

Animals
Female
*Hominidae/genetics
Humans
Male
Nucleotides
*Pseudoautosomal Regions
Receptor, PAR-1/genetics
Y Chromosome/genetics

@article {pmid36252021,
year = {2022},
author = {Jaouen, K and Villalba-Mouco, V and Smith, GM and Trost, M and Leichliter, J and Lüdecke, T and Méjean, P and Mandrou, S and Chmeleff, J and Guiserix, D and Bourgon, N and Blasco, F and Mendes Cardoso, J and Duquenoy, C and Moubtahij, Z and Salazar Garcia, DC and Richards, M and Tütken, T and Hublin, JJ and Utrilla, P and Montes, L},
title = {A Neandertal dietary conundrum: Insights provided by tooth enamel Zn isotopes from Gabasa, Spain.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {43},
pages = {e2109315119},
pmid = {36252021},
issn = {1091-6490},
mesh = {Animals ; Carbon/analysis ; Carbon Isotopes/analysis ; *Carnivora ; Collagen ; Dental Enamel/chemistry ; Diet ; *Neanderthals ; Nitrogen Isotopes/analysis ; Oxygen/analysis ; Spain ; Strontium/analysis ; *Tooth/chemistry ; *Trace Elements/analysis ; Zinc/analysis ; Zinc Isotopes/analysis ; },
abstract = {The characterization of Neandertals' diets has mostly relied on nitrogen isotope analyses of bone and tooth collagen. However, few nitrogen isotope data have been recovered from bones or teeth from Iberia due to poor collagen preservation at Paleolithic sites in the region. Zinc isotopes have been shown to be a reliable method for reconstructing trophic levels in the absence of organic matter preservation. Here, we present the results of zinc (Zn), strontium (Sr), carbon (C), and oxygen (O) isotope and trace element ratio analysis measured in dental enamel on a Pleistocene food web in Gabasa, Spain, to characterize the diet and ecology of a Middle Paleolithic Neandertal individual. Based on the extremely low δ[66]Zn value observed in the Neandertal's tooth enamel, our results support the interpretation of Neandertals as carnivores as already suggested by δ[15]N isotope values of specimens from other regions. Further work could help identify if such isotopic peculiarities (lowest δ[66]Zn and highest δ[15]N of the food web) are due to a metabolic and/or dietary specificity of the Neandertals.},
}

Animals
Carbon/analysis
Carbon Isotopes/analysis
*Carnivora
Collagen
Dental Enamel/chemistry
Diet
*Neanderthals
Nitrogen Isotopes/analysis
Oxygen/analysis
Spain
Strontium/analysis
*Tooth/chemistry
*Trace Elements/analysis
Zinc/analysis
Zinc Isotopes/analysis