@article {pmid33077870,
year = {2020},
author = {Yang, S and Varghese, AM and Sood, N and Chiattone, C and Akinola, NO and Huang, X and Gale, RP},
title = {Ethnic and geographic diversity of chronic lymphocytic leukaemia.},
journal = {Leukemia},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41375-020-01057-5},
pmid = {33077870},
issn = {1476-5551},
abstract = {East Asians, Asian Indians and Amerindians have a five to ten-fold lower age-adjusted incidence rate (AAIR) of chronic lymphocytic leukaemia (CLL) compared with persons of predominately European descent. The data we review suggest a genetic rather than environmental basis for this discordance. All these populations arose from a common African Black ancestor but different clades have different admixture with archaic hominins including Neanderthals, Denisovans and Homo erectus, which may explain different CLL incidences. There are also some differences in clinical laboratory and molecular co-variates of CLL between these populations. Because the true age-adjusted incidence rate in African Blacks is unknown it is not possible to determine whether modern Europeans acquired susceptibility to CLL or the other populations lost susceptibility and/or developed resistance to developing CLL. We also found other B-cell lymphomas and T- and NK-cell cancers had different incidences in the populations we studied. These data provide clues to determining the cause(s) of CLL.},
}

@article {pmid31386798,
year = {2020},
author = {Mikaeeli, S and Susan-Resiga, D and Girard, E and Ben Djoudi Ouadda, A and Day, R and Prost, S and Seidah, NG},
title = {Functional analysis of natural PCSK9 mutants in modern and archaic humans.},
journal = {The FEBS journal},
volume = {287},
number = {3},
pages = {515-528},
doi = {10.1111/febs.15036},
pmid = {31386798},
issn = {1742-4658},
support = {148363//CIHR/Canada ; },
mesh = {Animals ; Binding Sites ; DNA Methylation ; Humans ; *Loss of Function Mutation ; Neanderthals/*genetics ; Proprotein Convertase 9/chemistry/*genetics/metabolism ; Protein Binding ; Receptors, LDL/metabolism ; },
abstract = {PCSK9 is the last member of the proprotein convertases (PCs) family and its gene is mutated in ~ 2% to 3% of individuals with familial hypercholesterolemia (FH). This protein enhances the degradation of the low-density lipoprotein receptor (LDLR) and hence increases the levels of circulating LDL-cholesterol (LDLc). Studies of the underlying mechanism(s) regulating the activity of different mutations in the PCSK9 gene are ongoing as they enhance our understanding of the biology and clinical relevance of PCSK9 and its partners. In an attempt to unravel the regulation of PCSK9 transcription and possibly identify mutation 'hot spot' regions with alterations in CpG methylation, we present for the first time the complete methylome profile of the PCSK9 gene in modern and archaic humanoids. Our data showed that the genomes of modern humans and archaic PCSK9 exhibit a similar methylation pattern. Next, we defined the mechanistic consequences of three PCSK9 natural mutations (PCSK9-R96L, -R105W, and -P174S) and one archaic Denisovan mutation (PCSK9-H449L) using various complementary cellular and in vitro binding assays. Our results showed that the PCSK9-H449L is a loss-of-function (LOF) mutation, likely due to its lower binding affinity to the LDLR. Similarly, PCSK9-R96L and -R105W are LOF mutations, even though they have been identified in FH patients. The PCSK9-R105W mutation leads to a significantly lower autocatalytic processing of proPCSK9. PCSK9-P174S resulted in a LOF in both extracellular and intracellular pathways. In conclusion, our extensive analyses revealed that all studied mutations result in PCSK9 LOF, via various mechanisms, leading to lower levels of LDLc.},
}

Animals
Binding Sites
DNA Methylation
Humans
*Loss of Function Mutation
Neanderthals/*genetics
Proprotein Convertase 9/chemistry/*genetics/metabolism
Protein Binding
Receptors, LDL/metabolism

@article {pmid33043635,
year = {2020},
author = {},
title = {Risk Variant for Severe COVID-19 Inherited from Neanderthals.},
journal = {American journal of medical genetics. Part A},
volume = {182},
number = {10},
pages = {2203-2204},
doi = {10.1002/ajmg.a.61247},
pmid = {33043635},
issn = {1552-4833},
}

@article {pmid33039881,
year = {2020},
author = {Pan, L and Dumoncel, J and Mazurier, A and Zanolli, C},
title = {Hominin diversity in East Asia during the Middle Pleistocene: A premolar endostructural perspective.},
journal = {Journal of human evolution},
volume = {148},
number = {},
pages = {102888},
doi = {10.1016/j.jhevol.2020.102888},
pmid = {33039881},
issn = {1095-8606},
abstract = {Following the recent studies of East Asian mid-Middle to early Late Pleistocene hominin material, a large spectrum of morphological diversity has been recognized and the coexistence of archaic ('Homo erectus-like') and derived ('modern-like') dental morphological patterns has been highlighted. In fact, for most of these Chinese fossils, generally categorized as 'archaic Homo sapiens' or 'post-H. erectus Homo', the taxonomic attribution is a matter of contention. With the help of μCT techniques and a deformation-based 3D geometric morphometric approach, we focused on the morphological variation in the enamel-dentine junction (EDJ) of 18 upper and lower premolars from Chinese Middle Pleistocene hominins. We then compared our results with a number of fossil and modern human groups, including Early Pleistocene H. erectus from Sangiran; late Early Pleistocene hominins from Tighenif, Algeria; classic Neanderthals; and modern humans. Our results highlight an evolutionary/chronological trend of crown base reduction, elevation of EDJ topography, and EDJ surface simplification in the hominin groups studied here. Moreover, this study brings insights to the taxonomy/phylogeny of 6 late Middle Pleistocene specimens whose evolutionary placement has been debated for decades. Among these specimens, Changyang premolars show features that can be aligned with the Asian H. erectus hypodigm, whereas Panxian Dadong and Tongzi premolars are more similar to Late Pleistocene Homo. Compared with early to mid-Middle Pleistocene hominins in East Asia, late Middle Pleistocene hominins evince an enlarged morphological variation. A persistence of archaic morphotypes and possible admixture among populations during the late Middle Pleistocene are discussed.},
}

@article {pmid33028520,
year = {2020},
author = {García-Martínez, D and Bastir, M and Gómez-Olivencia, A and Maureille, B and Golovanova, L and Doronichev, V and Akazawa, T and Kondo, O and Ishida, H and Gascho, D and Zollikofer, CPE and de León, MP and Heuzé, Y},
title = {Early development of the Neanderthal ribcage reveals a different body shape at birth compared to modern humans.},
journal = {Science advances},
volume = {6},
number = {41},
pages = {},
doi = {10.1126/sciadv.abb4377},
pmid = {33028520},
issn = {2375-2548},
abstract = {Ontogenetic studies provide clues for understanding important paleobiological aspects of extinct species. When compared to that of modern humans, the adult Neanderthal thorax was shorter, deeper, and wider. This is related to the wide Neanderthal body and is consistent with their hypothetical large requirements for energy and oxygen. Whether these differences were already established at birth or appeared later during development is unknown. To delve into this question, we use virtual reconstruction tools and geometric morphometrics to recover the 3D morphology of the ribcages of four Neanderthal individuals from birth to around 3 years old: Mezmaiskaya 1, Le Moustier 2, Dederiyeh 1, and Roc de Marsal. Our results indicate that the comparatively deep and short ribcage of the Neanderthals was already present at birth, as were other skeletal species-specific traits. This morphology possibly represents the plesiomorphic condition shared with Homo erectus, and it is likely linked to large energetic requirements.},
}

@article {pmid32998156,
year = {2020},
author = {Zeberg, H and Pääbo, S},
title = {The major genetic risk factor for severe COVID-19 is inherited from Neanderthals.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-020-2818-3},
pmid = {32998156},
issn = {1476-4687},
abstract = {A recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)2 comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in south Asia and around 16% of people in Europe.},
}

@article {pmid32989161,
year = {2020},
author = {Haws, JA and Benedetti, MM and Talamo, S and Bicho, N and Cascalheira, J and Ellis, MG and Carvalho, MM and Friedl, L and Pereira, T and Zinsious, BK},
title = {The early Aurignacian dispersal of modern humans into westernmost Eurasia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.2016062117},
pmid = {32989161},
issn = {1091-6490},
abstract = {Documenting the first appearance of modern humans in a given region is key to understanding the dispersal process and the replacement or assimilation of indigenous human populations such as the Neanderthals. The Iberian Peninsula was the last refuge of Neanderthal populations as modern humans advanced across Eurasia. Here we present evidence of an early Aurignacian occupation at Lapa do Picareiro in central Portugal. Diagnostic artifacts were found in a sealed stratigraphic layer dated 41.1 to 38.1 ka cal BP, documenting a modern human presence on the western margin of Iberia ∼5,000 years earlier than previously known. The data indicate a rapid modern human dispersal across southern Europe, reaching the westernmost edge where Neanderthals were thought to persist. The results support the notion of a mosaic process of modern human dispersal and replacement of indigenous Neanderthal populations.},
}

@article {pmid32975051,
year = {2020},
author = {Chirchir, H},
title = {Trabecular bone in domestic dogs and wolves: Implications for understanding human self-domestication.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {},
number = {},
pages = {},
doi = {10.1002/ar.24510},
pmid = {32975051},
issn = {1932-8494},
support = {//NASA WV Space Grant Consortium Research Seed Grant/ ; },
abstract = {The process of domestication is complex and results in significant morphological, cognitive, and physiological changes. In canids, some of the traits indicative of domestication of domestic dogs compared to their wild counterparts the wolves are prosociality toward humans, reduced stress hormone levels, and reduced cranial capacity. Research suggests that selection for prosociality among dogs resulted in morphological changes such as reduction in cranial capacity, juvenilization of the face, and overall gracile morphology. Interestingly, similar features have been described in modern humans compared to extinct species of Homo, for example, Neanderthals. Therefore, the human self-domestication hypothesis has been proposed to partially explain the gracile modern human skeleton. Specifically, that as modern humans settled in communities, there was increased selection for prosociality (intergroup cooperation); and one of the by-products of this selection was the evolution of a gracile skeleton, including a slight reduction in cranial capacity, reduced brow ridge and tooth size, and low trabecular bone fraction (TBF). However, TBF variation has not been tested between domestic dogs and wolves, who underwent self-domestication. Thus, this study tests the hypothesis that dogs have low TBF as a consequence of domestication compared to their wild counterparts, the wolves, by comparing TBF in the hindlimbs-proximal femur and distal tibia- of the two species. Wilcoxon rank sum tests show that dogs have lower TBF values than wolves in both elements. These preliminary results add to the literature documenting changes in self-domesticated species and provide a potential analog to further the understanding of self-domestication.},
}

@article {pmid32973032,
year = {2020},
author = {Petr, M and Hajdinjak, M and Fu, Q and Essel, E and Rougier, H and Crevecoeur, I and Semal, P and Golovanova, LV and Doronichev, VB and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Vernot, B and Meyer, M and Kelso, J},
title = {The evolutionary history of Neanderthal and Denisovan Y chromosomes.},
journal = {Science (New York, N.Y.)},
volume = {369},
number = {6511},
pages = {1653-1656},
doi = {10.1126/science.abb6460},
pmid = {32973032},
issn = {1095-9203},
support = {/ERC_/European Research Council/International ; },
abstract = {Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.},
}

@article {pmid32973019,
year = {2020},
author = {Schierup, MH},
title = {The last pieces of a puzzling early meeting.},
journal = {Science (New York, N.Y.)},
volume = {369},
number = {6511},
pages = {1565-1566},
doi = {10.1126/science.abe2766},
pmid = {32973019},
issn = {1095-9203},
mesh = {Animals ; Biological Evolution ; *Neanderthals ; Y Chromosome ; },
}

Animals
Biological Evolution
*Neanderthals
Y Chromosome

@article {pmid32963029,
year = {2020},
author = {Bokelmann, L and Glocke, I and Meyer, M},
title = {Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples.},
journal = {Genome research},
volume = {30},
number = {10},
pages = {1449-1457},
doi = {10.1101/gr.263863.120},
pmid = {32963029},
issn = {1549-5469},
abstract = {Extensive manipulations involved in the preparation of DNA samples for sequencing have hitherto made it impossible to determine the precise structure of double-stranded DNA fragments being sequenced, such as the presence of blunt ends, single-stranded overhangs, or single-strand breaks. We here describe MatchSeq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded DNA, reveals that 1- or 2-nt overhangs and blunt ends dominate the ends of ancient DNA molecules and that short gaps exist, which are predominantly caused by the loss of individual purines. We further show that deamination of cytosine to uracil occurs in both single- and double-stranded contexts close to the ends of molecules, and that single-stranded parts of DNA fragments are enriched in pyrimidines. MatchSeq provides unprecedented resolution for interrogating the structures of fragmented double-stranded DNA and can be applied to fragmented double-stranded DNA isolated from any biological source. The method relies on well-established laboratory techniques and can easily be integrated into routine data generation. This possibility is shown by the successful reconstruction of double-stranded DNA fragments from previously published single-stranded sequence data, allowing a more comprehensive characterization of the biochemical properties not only of ancient DNA but also of cell-free DNA from human blood plasma, a clinically relevant marker for the diagnosis and monitoring of disease.},
}

@article {pmid32927399,
year = {2020},
author = {Bailey, SE and Sorrentino, R and Mancuso, G and Hublin, JJ and Benazzi, S},
title = {Taxonomic differences in deciduous lower first molar crown outlines of Homo sapiens and Homo neanderthalensis.},
journal = {Journal of human evolution},
volume = {147},
number = {},
pages = {102864},
doi = {10.1016/j.jhevol.2020.102864},
pmid = {32927399},
issn = {1095-8606},
abstract = {Recent studies have demonstrated that the outline shapes of deciduous upper and lower second molars and the deciduous upper first molar are useful for diagnosing hominin taxa-especially Homo neanderthalensis and Homo sapiens. Building on these studies, we use geometric morphometric methods to assess the taxonomic significance of the crown outline of the lower first deciduous molar (dm1). We test whether the crown shape of the dm1 distinguishes H. neanderthalensis from H. sapiens and explore whether dm1 crown shape can be used to accurately assign individuals to taxa. Our fossil sample includes 3 early H. sapiens, 7 Upper Paleolithic H. sapiens, and 13 H. neanderthalensis individuals. Our recent human sample includes 103 individuals from Africa, Australia, Europe, South America, and South Asia. Our results indicate that H. neanderthalensis dm1s cluster fairly tightly and separate well from those of Upper Paleolithic H. sapiens. However, we also found that the range of shapes in the recent human sample completely overlaps the ranges of all fossil samples. Consequently, results of the quadratic discriminant analysis based on the first 8 principal components (PCs) representing more than 90% of the variation were mixed. Lower dm1s were correctly classified in 87.3% of the individuals; the combined H. sapiens sample had greater success (90.2%) in assigning individuals than did the H. neanderthalensis sample (61.5%). When the analysis was run removing the highly variable recent human sample, accuracy increased to 84.6% for H. neanderthalensis, and 57.1% of Upper Paleolithic H. sapiens were classified correctly by using the first 4 PCs (70.3%). We conclude that caution is warranted when assigning isolated dm1 crowns to taxa; while an assignment to H. neanderthalensis has a high probability of being correct, assignment to Upper Paleolithic H. sapiens is less certain.},
}

@article {pmid32918796,
year = {2020},
author = {Breyl, M},
title = {Triangulating Neanderthal cognition: A tale of not seeing the forest for the trees.},
journal = {Wiley interdisciplinary reviews. Cognitive science},
volume = {},
number = {},
pages = {e1545},
doi = {10.1002/wcs.1545},
pmid = {32918796},
issn = {1939-5086},
abstract = {The inference of Neanderthal cognition, including their cultural and linguistic capabilities, has persisted as a fiercely debated research topic for decades. This lack of consensus is substantially based on inherent uncertainties in reconstructing prehistory out of indirect evidence as well as other methodological limitations. Further factors include systemic difficulties within interdisciplinary discourse, data artifacts, historic research biases, and the sheer scope of the relevant research. Given the degrees of freedom in interpretation ensuing from these complications, any attempt to find approximate answers to the yet unsettled pertinent discourse may not rest on single studies, but instead a careful and comprehensive interdisciplinary synthesis of findings. Triangulating Neanderthals' cognition by considering the plethora of data, diverse perspectives and aforementioned complexities present within the literature constitutes the currently most reliable pathway to tentative conclusions. While some uncertainties remain, such an approach paints the picture of an extensive shared humanity between anatomically modern humans and Neanderthals. This article is categorized under: Cognitive Biology > Evolutionary Roots of Cognition Linguistics > Evolution of Language.},
}

@article {pmid32914870,
year = {2020},
author = {Oxilia, G and Bortolini, E and Badino, F and Bernardini, F and Gazzoni, V and Lugli, F and Romandini, M and Radini, A and Terlato, G and Marciani, G and Silvestrini, S and Menghi Sartorio, JC and Thun Hohenstein, U and Fiorenza, L and Kullmer, O and Tuniz, C and Moggi Cecchi, J and Talamo, S and Fontana, F and Peresani, M and Benazzi, S and Cristiani, E},
title = {Exploring late Paleolithic and Mesolithic diet in the Eastern Alpine region of Italy through multiple proxies.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.24128},
pmid = {32914870},
issn = {1096-8644},
support = {639286//European Union's Horizon 2020/ ; 724046//European Union's Horizon 2020/ ; },
abstract = {OBJECTIVES: The analysis of prehistoric human dietary habits is key for understanding the effects of paleoenvironmental changes on the evolution of cultural and social human behaviors. In this study, we compare results from zooarchaeological, stable isotope and dental calculus analyses as well as lower second molar macrowear patterns to gain a broader understanding of the diet of three individuals who lived between the end of the Late Pleistocene and the Early Holocene (ca., 17-8 ky cal BP) in the Eastern Alpine region of Italy.

MATERIALS AND METHODS: We analyze individuals buried at the sites of Riparo Tagliente (Verona), Riparo Villabruna, and Mondeval de Sora (Belluno). The three burials provide a unique dataset for diachronically exploring the influence of climatic changes on human subsistence strategies.

RESULTS: Isotopic results indicate that all individuals likely relied on both terrestrial and freshwater animal proteins. Even though dental calculus analysis was, in part, hindered by the amount of mineral deposit available on the teeth, tooth macrowear study suggests that the dietary habits of the individuals included plant foods. Moreover, differences in macrowear patterns of lower second molars have been documented between Neanderthals and modern humans in the present sample, due to a prevalence of Buccal wear among the former as opposed to higher values of Lingual wear in modern human teeth.

DISCUSSION: Isotopic analyses have emphasized the contribution of animal proteins in the diet of the three foragers from the Eastern Alpine region. The possible intake of carbohydrate-rich plant foods, suggested by the retrieval of plant remains in dental calculus, is supported by the signal of macrowear analysis. Moreover, the latter method indicates that the distribution of macrowear in lower second molars (M2 s) allows us to discriminate between Neanderthals and modern humans within the present reference sample. Overall, our results show these three prehistoric hunter-gatherers were well adapted to the environment in which they lived exploiting many natural resources.},
}

@article {pmid32901061,
year = {2020},
author = {Picin, A and Hajdinjak, M and Nowaczewska, W and Benazzi, S and Urbanowski, M and Marciszak, A and Fewlass, H and Socha, P and Stefaniak, K and Żarski, M and Wiśniewski, A and Hublin, JJ and Nadachowski, A and Talamo, S},
title = {New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14778},
pmid = {32901061},
issn = {2045-2322},
abstract = {The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.},
}

@article {pmid32889336,
year = {2020},
author = {Romandini, M and Oxilia, G and Bortolini, E and Peyrégne, S and Delpiano, D and Nava, A and Panetta, D and Di Domenico, G and Martini, P and Arrighi, S and Badino, F and Figus, C and Lugli, F and Marciani, G and Silvestrini, S and Menghi Sartorio, JC and Terlato, G and Hublin, JJ and Meyer, M and Bondioli, L and Higham, T and Slon, V and Peresani, M and Benazzi, S},
title = {A late Neanderthal tooth from northeastern Italy.},
journal = {Journal of human evolution},
volume = {147},
number = {},
pages = {102867},
doi = {10.1016/j.jhevol.2020.102867},
pmid = {32889336},
issn = {1095-8606},
abstract = {The site of Riparo Broion (Vicenza, northeastern Italy) preserves a stratigraphic sequence documenting the Middle-to-Upper Paleolithic transition, in particular the final Mousterian and the Uluzzian cultures. In 2018, a human tooth was retrieved from a late Mousterian level, representing the first human remain ever found from this rock shelter (Riparo Broion 1). Here, we provide the morphological description and taxonomic assessment of Riparo Broion 1 with the support of classic and virtual morphology, 2D and 3D analysis of the topography of enamel thickness, and DNA analysis. The tooth is an exfoliated right upper deciduous canine, and its general morphology and enamel thickness distribution support attribution to a Neanderthal child. Correspondingly, the mitochondrial DNA sequence from Riparo Broion 1 falls within the known genetic variation of Late Pleistocene Neanderthals, in accordance with newly obtained radiocarbon dates that point to approximately 48 ka cal BP as the most likely minimum age for this specimen. The present work describes novel and direct evidence of the late Neanderthal occupation in northern Italy that preceded the marked cultural and technological shift documented by the Uluzzian layers in the archaeological sequence at Riparo Broion. Here, we provide a new full morphological, morphometric, and taxonomic analysis of Riparo Broion 1, in addition to generating the wider reference sample of Neanderthal and modern human upper deciduous canines. This research contributes to increasing the sample of fossil remains from Italy, as well as the number of currently available upper deciduous canines, which are presently poorly documented in the scientific literature.},
}

@article {pmid32874601,
year = {2020},
author = {Amos, W},
title = {Signals interpreted as archaic introgression appear to be driven primarily by faster evolution in Africa.},
journal = {Royal Society open science},
volume = {7},
number = {7},
pages = {191900},
pmid = {32874601},
issn = {2054-5703},
abstract = {Non-African humans appear to carry a few per cent archaic DNA due to ancient inter-breeding. This modest legacy and its likely recent timing imply that most introgressed fragments will be rare and hence will occur mainly in the heterozygous state. I tested this prediction by calculating D statistics, a measure of legacy size, for pairs of humans where one of the pair was conditioned always to be either homozygous or heterozygous. Using coalescent simulations, I confirmed that conditioning the non-African to be heterozygous increased D, while conditioning the non-African to be homozygous reduced D to zero. Repeating with real data reveals the exact opposite pattern. In African-non-African comparisons, D is near-zero if the African individual is held homozygous. Conditioning one of two Africans to be either homozygous or heterozygous invariably generates large values of D, even when both individuals are drawn from the same population. Invariably, the African with more heterozygous sites (conditioned heterozygous > unconditioned > conditioned homozygous) appears less related to the archaic. By contrast, the same analysis applied to pairs of non-Africans always yields near-zero D, showing that conditioning does not create large D without an underlying signal to expose. Large D values in humans are therefore driven almost entirely by heterozygous sites in Africans acting to increase divergence from related taxa such as Neanderthals. In comparison with heterozygous Africans, individuals that lack African heterozygous sites, whether non-African or conditioned homozygous African, always appear more similar to archaic outgroups, a signal previously interpreted as evidence for introgression. I hope these analyses will encourage others to consider increased divergence as well as increased similarity to archaics as mechanisms capable of driving asymmetrical base-sharing.},
}

@article {pmid32859969,
year = {2020},
author = {Yousefi, M and Heydari-Guran, S and Kafash, A and Ghasidian, E},
title = {Species distribution models advance our knowledge of the Neanderthals' paleoecology on the Iranian Plateau.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14248},
pmid = {32859969},
issn = {2045-2322},
abstract = {Neanderthals (Homo neanderthalensis) were distributed across a vast region from Europe to western and Central Asia. The Neanderthals' paleoecology and distribution has been extensively studied in Europe where the species originated. However, very little is known about their paleoecology in south-western Asia. Here, we employed species distribution modelling and 45 Middle Palaeolithic (c. 200,000-40,000 years BCE) sites location associated with fossil and/or lithic artefacts made by the Neanderthals to examine the expansion of the Neanderthals on the Iranian Plateau in south-western Asia. We estimated the niche overlap between Neanderthals and wild goat, wild sheep and Persian gazelle by modelling their past distribution using 200, 143 and 110 occurrence records respectively. The results show that Neanderthals had highest niche overlap with wild goat in the study area. This analysis revealed that the most suitable Neanderthals' habitats in south-western Asia were located in the Zagros Mountains stretches from north-western and western and some isolated patches in the central parts of the Iranian Plateau. The annual precipitation and maximum temperature of the warmest month were the most important predictor of the species' distribution. This finding shows that the southern edge of the Neanderthals distribution was limited by warm summer. Our results provide important information for future field investigations and excavations in the area.},
}

@article {pmid32853200,
year = {2020},
author = {Mughal, MR and Koch, H and Huang, J and Chiaromonte, F and DeGiorgio, M},
title = {Learning the properties of adaptive regions with functional data analysis.},
journal = {PLoS genetics},
volume = {16},
number = {8},
pages = {e1008896},
pmid = {32853200},
issn = {1553-7404},
support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; F31 HG010574/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; DNA-Binding Proteins/genetics ; European Continental Ancestry Group/*genetics ; Genetic Variation ; Humans ; Membrane Transport Proteins ; *Models, Genetic ; *Mutation Rate ; Neanderthals/genetics ; Selection, Genetic ; Software ; },
abstract = {Identifying regions of positive selection in genomic data remains a challenge in population genetics. Most current approaches rely on comparing values of summary statistics calculated in windows. We present an approach termed SURFDAWave, which translates measures of genetic diversity calculated in genomic windows to functional data. By transforming our discrete data points to be outputs of continuous functions defined over genomic space, we are able to learn the features of these functions that signify selection. This enables us to confidently identify complex modes of natural selection, including adaptive introgression. We are also able to predict important selection parameters that are responsible for shaping the inferred selection events. By applying our model to human population-genomic data, we recapitulate previously identified regions of selective sweeps, such as OCA2 in Europeans, and predict that its beneficial mutation reached a frequency of 0.02 before it swept 1,802 generations ago, a time when humans were relatively new to Europe. In addition, we identify BNC2 in Europeans as a target of adaptive introgression, and predict that it harbors a beneficial mutation that arose in an archaic human population that split from modern humans within the hypothesized modern human-Neanderthal divergence range.},
}

Animals
DNA-Binding Proteins/genetics
European Continental Ancestry Group/*genetics
Genetic Variation
Humans
Membrane Transport Proteins
*Models, Genetic
*Mutation Rate
Neanderthals/genetics
Selection, Genetic
Software

@article {pmid32839541,
year = {2020},
author = {Telis, N and Aguilar, R and Harris, K},
title = {Selection against archaic hominin genetic variation in regulatory regions.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-020-01284-0},
pmid = {32839541},
issn = {2397-334X},
support = {Graduate Research Fellowship//National Science Foundation (NSF)/ ; 1R35GM133428-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Career Award at the Scientific Interface//Burroughs Wellcome Fund (BWF)/ ; Sloan Research Fellowship//Alfred P. Sloan Foundation/ ; Pew Scholarship//Pew Charitable Trusts/ ; Searle Scholarship//Kinship Foundation/ ; },
abstract = {Traces of Neandertal and Denisovan DNA persist in the modern human gene pool, but have been systematically purged by natural selection from genes and other functionally important regions. This implies that many archaic alleles harmed the fitness of hybrid individuals, but the nature of this harm is poorly understood. Here, we show that enhancers contain less Neandertal and Denisovan variation than expected given the background selection they experience, suggesting that selection acted to purge these regions of archaic alleles that disrupted their gene regulatory functions. We infer that selection acted mainly on young archaic variation that arose in Neandertals or Denisovans shortly before their contact with humans; enhancers are not depleted of older variants found in both archaic species. Some types of enhancer appear to have tolerated introgression better than others; compared with tissue-specific enhancers, pleiotropic enhancers show stronger depletion of archaic single-nucleotide polymorphisms. To some extent, evolutionary constraint is predictive of introgression depletion, but certain tissues' enhancers are more depleted of Neandertal and Denisovan alleles than expected given their comparative tolerance to new mutations. Foetal brain and muscle are the tissues whose enhancers show the strongest depletion of archaic alleles, but only brain enhancers show evidence of unusually stringent purifying selection. We conclude that epistatic incompatibilities between human and archaic alleles are needed to explain the degree of archaic variant depletion from foetal muscle enhancers, perhaps due to divergent selection for higher muscle mass in archaic hominins compared with humans.},
}

@article {pmid32817536,
year = {2020},
author = {Bard, E and Heaton, TJ and Talamo, S and Kromer, B and Reimer, RW and Reimer, PJ},
title = {Extended dilation of the radiocarbon time scale between 40,000 and 48,000 y BP and the overlap between Neanderthals and Homo sapiens.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {35},
pages = {21005-21007},
pmid = {32817536},
issn = {1091-6490},
abstract = {The new radiocarbon calibration curve (IntCal20) allows us to calculate the gradient of the relationship between 14C age and calendar age over the past 55 millennia before the present (55 ka BP). The new gradient curve exhibits a prolonged and prominent maximum between 48 and 40 ka BP during which the radiocarbon clock runs almost twice as fast as it should. This radiocarbon time dilation is due to the increase in the atmospheric 14C/12C ratio caused by the 14C production rise linked to the transition into the Laschamp geomagnetic excursion centered around 41 ka BP. The major maximum in the gradient from 48 to 40 ka BP is a new feature of the IntCal20 calibration curve, with far-reaching impacts for scientific communities, such as prehistory and paleoclimatology, relying on accurate ages in this time range. To illustrate, we consider the duration of the overlap between Neanderthals and Homo sapiens in Eurasia.},
}

@article {pmid32813722,
year = {2020},
author = {Delpiano, D and Uthmeier, T},
title = {Techno-functional and 3D shape analysis applied for investigating the variability of backed tools in the Late Middle Paleolithic of Central Europe.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0236548},
pmid = {32813722},
issn = {1932-6203},
mesh = {Animals ; Archaeology/*instrumentation ; Artifacts ; Behavior Rating Scale ; Fossils/*diagnostic imaging ; Humans ; Neanderthals ; Paleontology/*instrumentation ; Technology/*instrumentation ; Tool Use Behavior/classification ; },
abstract = {In the Late Middle Paleolithic of Central Europe, two main cultural complexes have been distinguished: the Micoquian or Keilmessergruppe (KMG), and the Mousterian. Their differences mainly consist in the frequence of some retouched tools and the presence of bifacial technology. When these industries coexist, one element of discussion is the application of different concepts to manufacture tools with the same techno-functionality. This is particularly true for backed artifacts, such as Keilmesser (backed, asymmetrical bifacially-shaped knives) opposed to flake-tools equipped with a natural or knapped back. We conducted a techno-functional analysis of the backed tools from the G-Layer-Complex of Sesselfelsgrotte, one of the main Late Middle Paleolithic sequences in Central Europe, characterized by a combination of KMG and Mousterian aspects. In order to better understand the morpho-metrical data, 3D scans were used for recording technical features and performing semi-automatic geometric morphometrics. Results indicate that the techno-functional schemes of Keilmesser show a moderate variability and often overlap with the schemes of other typological groups. Within bifacial backed knives, a process of imitation of unifacial flake tools' functionaly was recognized particularly in the cutting edge manufacturing. Keilmesser proved to be the long-life, versatile version of backed flake-tools, also due to the recurrent valence as both tool and core. This is why Keilmesser represent an ideal strategic blank when a mobile and multi-functional tool is needed. Based on these data, it is assumed that the relationship between Mousterian and KMG is deeply rooted and the emergence of KMG aspects could be related to constrained situations characterizing the long cold stages of the Early Weichselian. A higher regional mobility caused by the comparably low predictability of resources characterized the subsistence tactics of Neanderthal groups especially at the borders of their overall distribution. For this reason, Keilmesser could have represented an ecological answer before possibly becoming a marker of cultural identity.},
}

Animals
Archaeology/*instrumentation
Artifacts
Behavior Rating Scale
Fossils/*diagnostic imaging
Humans
Neanderthals
Paleontology/*instrumentation
Technology/*instrumentation
Tool Use Behavior/classification

@article {pmid32805525,
year = {2020},
author = {Torres-Tamayo, N and Schlager, S and García-Martínez, D and Sanchis-Gimeno, JA and Nalla, S and Ogihara, N and Oishi, M and Martelli, S and Bastir, M},
title = {Three-dimensional geometric morphometrics of thorax-pelvis covariation and its potential for predicting the thorax morphology: A case study on Kebara 2 Neandertal.},
journal = {Journal of human evolution},
volume = {147},
number = {},
pages = {102854},
doi = {10.1016/j.jhevol.2020.102854},
pmid = {32805525},
issn = {1095-8606},
abstract = {The skeletal torso is a complex structure of outstanding importance in understanding human body shape evolution, but reconstruction usually entails an element of subjectivity as researchers apply their own anatomical expertise to the process. Among different fossil reconstruction methods, 3D geometric morphometric techniques have been increasingly used in the last decades. Two-block partial least squares analysis has shown great potential for predicting missing elements by exploiting the covariation between two structures (blocks) in a reference sample: one block can be predicted from the other one based on the strength of covariation between blocks. The first aim of this study is to test whether this predictive approach can be used for predicting thorax morphologies from pelvis morphologies within adult Homo sapiens reference samples with known covariation between the thorax and the pelvis. The second aim is to apply this method to Kebara 2 Neandertal (Israel, ∼60 ka) to predict its thorax morphology using two different pelvis reconstructions as predictors. We measured 134 true landmarks, 720 curve semilandmarks, and 160 surface semilandmarks on 60 3D virtual torso models segmented from CT scans. We conducted three two-block partial least squares analyses between the thorax (block 1) and the pelvis (block 2) based on the H. sapiens reference samples after performing generalized Procrustes superimposition on each block separately. Comparisons of these predictions in full shape space by means of Procrustes distances show that the male-only predictive model yields the most reliable predictions within modern humans. In addition, Kebara 2 thorax predictions based on this model concur with the thorax morphology proposed for Neandertals. The method presented here does not aim to replace other techniques, but to rather complement them through quantitative prediction of a virtual 'scaffold' to articulate the thoracic fossil elements, thus extending the potential of missing data estimation beyond the methods proposed in previous works.},
}

@article {pmid32760067,
year = {2020},
author = {Hubisz, MJ and Williams, AL and Siepel, A},
title = {Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph.},
journal = {PLoS genetics},
volume = {16},
number = {8},
pages = {e1008895},
pmid = {32760067},
issn = {1553-7404},
support = {R35 GM127070/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Evolution, Molecular ; *Gene Flow ; Human Migration ; Humans ; *Models, Genetic ; Neanderthals/*genetics ; Population/*genetics ; *Recombination, Genetic ; },
abstract = {The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present a major extension of the ARGweaver algorithm, called ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topologies and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these "super-archaic" regions-comprising at least about 4Mb-were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.},
}

Animals
Evolution, Molecular
*Gene Flow
Human Migration
Humans
*Models, Genetic
Neanderthals/*genetics
Population/*genetics
*Recombination, Genetic

@article {pmid32750315,
year = {2020},
author = {Course, MM and Gudsnuk, K and Smukowski, SN and Winston, K and Desai, N and Ross, JP and Sulovari, A and Bourassa, CV and Spiegelman, D and Couthouis, J and Yu, CE and Tsuang, DW and Jayadev, S and Kay, MA and Gitler, AD and Dupre, N and Eichler, EE and Dion, PA and Rouleau, GA and Valdmanis, PN},
title = {Evolution of a Human-Specific Tandem Repeat Associated with ALS.},
journal = {American journal of human genetics},
volume = {107},
number = {3},
pages = {445-460},
pmid = {32750315},
issn = {1537-6605},
support = {R01 DK078424/DK/NIDDK NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; T32 GM007454/GM/NIGMS NIH HHS/United States ; U24 AG041689/AG/NIA NIH HHS/United States ; },
abstract = {Tandem repeats are proposed to contribute to human-specific traits, and more than 40 tandem repeat expansions are known to cause neurological disease. Here, we characterize a human-specific 69 bp variable number tandem repeat (VNTR) in the last intron of WDR7, which exhibits striking variability in both copy number and nucleotide composition, as revealed by long-read sequencing. In addition, greater repeat copy number is significantly enriched in three independent cohorts of individuals with sporadic amyotrophic lateral sclerosis (ALS). Each unit of the repeat forms a stem-loop structure with the potential to produce microRNAs, and the repeat RNA can aggregate when expressed in cells. We leveraged its remarkable sequence variability to align the repeat in 288 samples and uncover its mechanism of expansion. We found that the repeat expands in the 3'-5' direction, in groups of repeat units divisible by two. The expansion patterns we observed were consistent with duplication events, and a replication error called template switching. We also observed that the VNTR is expanded in both Denisovan and Neanderthal genomes but is fixed at one copy or fewer in non-human primates. Evaluating the repeat in 1000 Genomes Project samples reveals that some repeat segments are solely present or absent in certain geographic populations. The large size of the repeat unit in this VNTR, along with our multiplexed sequencing strategy, provides an unprecedented opportunity to study mechanisms of repeat expansion, and a framework for evaluating the roles of VNTRs in human evolution and disease.},
}

@article {pmid32745133,
year = {2020},
author = {Örd, T and Puurand, T and Örd, D and Annilo, T and Möls, M and Remm, M and Örd, T},
title = {A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals.},
journal = {PLoS genetics},
volume = {16},
number = {8},
pages = {e1008981},
pmid = {32745133},
issn = {1553-7404},
support = {HHSN268201000029C/HL/NHLBI NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; },
mesh = {Cell Cycle Proteins/*genetics ; Estonia/epidemiology ; Female ; Gene Expression Regulation/genetics ; *Genetic Heterogeneity ; *Genetics, Population ; Genotype ; Humans ; Male ; Minisatellite Repeats/*genetics ; Promoter Regions, Genetic ; Protein-Serine-Threonine Kinases/*antagonists & inhibitors/genetics ; RNA-Seq ; Repressor Proteins/*genetics ; Whole Genome Sequencing ; },
abstract = {Tribbles homolog 3 (TRIB3) is pseudokinase involved in intracellular regulatory processes and has been implicated in several diseases. In this article, we report that human TRIB3 promoter contains a 33-bp variable number tandem repeat (VNTR) and characterize the heterogeneity and function of this genetic element. Analysis of human populations around the world uncovered the existence of alleles ranging from 1 to 5 copies of the repeat, with 2-, 3- and 5-copy alleles being the most common but displaying considerable geographical differences in frequency. The repeated sequence overlaps a C/EBP-ATF transcriptional regulatory element and is highly conserved, but not repeated, in various mammalian species, including great apes. The repeat is however evident in Neanderthal and Denisovan genomes. Reporter plasmid experiments in human cell culture reveal that an increased copy number of the TRIB3 promoter 33-bp repeat results in increased transcriptional activity. In line with this, analysis of whole genome sequencing and RNA-Seq data from human cohorts demonstrates that the copy number of TRIB3 promoter 33-bp repeats is positively correlated with TRIB3 mRNA expression level in many tissues throughout the body. Moreover, the copy number of the TRIB3 33-bp repeat appears to be linked to known TRIB3 eQTL SNPs as well as TRIB3 SNPs reported in genetic association studies. Taken together, the results indicate that the promoter 33-bp VNTR constitutes a causal variant for TRIB3 expression variation between individuals and could underlie the results of SNP-based genetic studies.},
}

Cell Cycle Proteins/*genetics
Estonia/epidemiology
Female
Gene Expression Regulation/genetics
*Genetic Heterogeneity
*Genetics, Population
Genotype
Humans
Male
Minisatellite Repeats/*genetics
Promoter Regions, Genetic
Protein-Serine-Threonine Kinases/*antagonists & inhibitors/genetics
RNA-Seq
Repressor Proteins/*genetics
Whole Genome Sequencing

@article {pmid32735718,
year = {2020},
author = {Ríos, L and Cardoso, HFV},
title = {Comment on 'Krapina atlases suggest a high prevalence of anatomical variations in the first cervical vertebra of Neanderthals'.},
journal = {Journal of anatomy},
volume = {},
number = {},
pages = {},
doi = {10.1111/joa.13268},
pmid = {32735718},
issn = {1469-7580},
abstract = {A review of the observation of an anterior cleft on the atlas of a Neanderthal from Krapina.},
}

@article {pmid32732402,
year = {2020},
author = {Gibbons, A},
title = {How an ancient microbial arms race remodeled human cells.},
journal = {Science (New York, N.Y.)},
volume = {369},
number = {6503},
pages = {491-492},
doi = {10.1126/science.369.6503.491},
pmid = {32732402},
issn = {1095-9203},
mesh = {Animals ; Cell Membrane/chemistry/microbiology ; Communicable Diseases/*genetics ; *Evolution, Molecular ; Host-Pathogen Interactions/*genetics ; Humans ; Immune System/*cytology ; N-Acetylneuraminic Acid/metabolism ; Neanderthals/*genetics/*microbiology ; Selection, Genetic ; },
}

Animals
Cell Membrane/chemistry/microbiology
Communicable Diseases/*genetics
*Evolution, Molecular
Host-Pathogen Interactions/*genetics
Humans
Immune System/*cytology
N-Acetylneuraminic Acid/metabolism
Neanderthals/*genetics/*microbiology
Selection, Genetic

@article {pmid32728251,
year = {2020},
author = {},
title = {Dinosaur retraction, Neanderthal pain and EU budget woe.},
journal = {Nature},
volume = {583},
number = {7818},
pages = {665},
doi = {10.1038/d41586-020-02204-9},
pmid = {32728251},
issn = {1476-4687},
}

@article {pmid32721654,
year = {2020},
author = {Grine, FE and Mongle, CS and Smith, SL and Black, W and du Plessis, A and Braga, J},
title = {Human manual distal phalanges from the Middle Stone Age deposits of Klasies River Main Site, Western Cape Province, South Africa.},
journal = {Journal of human evolution},
volume = {146},
number = {},
pages = {102849},
doi = {10.1016/j.jhevol.2020.102849},
pmid = {32721654},
issn = {1095-8606},
abstract = {Two new distal manual phalanges from the Middle Stone Age deposits of Klasies River Main Site are described. One (SAM-AP 6387) likely derives from ray II or ray III, whereas the other (SAM-AP 6388) is from the thumb. Both derive from a late adolescent or fully adult individual. They were recovered by H. Deacon from the same stratigraphic unit (submember W or possibly submember R) of the Shell and Sand Member of Cave 1, which places them between 100 and 90 ka. Both are comparatively small elements, and the possibility that they came from the same hand cannot be discounted at this time. These bones add to the meager and all too fragmentary postcranial human fossil sample from the Late Pleistocene of South Africa. These two specimens provide some additional evidence pertaining to the morphological attributes of the distal phalanges of the Middle Stone Age inhabitants of South Africa. Together with the distal pollical phalanx from Die Kelders (SAM-AP 6402), they are relatively small in comparison with homologs from recent human samples as well as Late Pleistocene specimens from Eurasia. Given their small sizes, the distal pollical phalanges from Klasies and Die Kelders are not dissimilar to Holocene Khoesan homologs. As expected, the Klasies elements differ noticeably from Neandertal homologs, especially in the narrowness of their shafts and distal tuberosities.},
}

@article {pmid32719451,
year = {2020},
author = {Rinker, DC and Simonti, CN and McArthur, E and Shaw, D and Hodges, E and Capra, JA},
title = {Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations.},
journal = {Nature ecology & evolution},
volume = {4},
number = {10},
pages = {1332-1341},
pmid = {32719451},
issn = {2397-334X},
support = {T32GM080178//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; K22 CA184308/CA/NCI NIH HHS/United States ; T32 GM080178/GM/NIGMS NIH HHS/United States ; R35GM127087//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; K22CA184308//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; T32 EY021453/EY/NEI NIH HHS/United States ; F30HG011200//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; T32EY021453//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; T32GM007347//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM115836/GM/NIGMS NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; },
abstract = {Neanderthal ancestry remains across modern Eurasian genomes and introgressed sequences influence diverse phenotypes. Here, we demonstrate that introgressed sequences reintroduced thousands of ancestral alleles that were lost in Eurasian populations before introgression. Our simulations and variant effect predictions argue that these reintroduced alleles (RAs) are more likely to be tolerated by modern humans than are introgressed Neanderthal-derived alleles (NDAs) due to their distinct evolutionary histories. Consistent with this, we show enrichment for RAs and depletion for NDAs on introgressed haplotypes with expression quantitative trait loci (eQTL) and phenotype associations. Analysis of available cross-population eQTLs and massively parallel reporter assay data show that RAs commonly influence gene expression independent of linked NDAs. We further validate these independent effects for one RA in vitro. Finally, we demonstrate that NDAs are depleted for regulatory activity compared to RAs, while RAs have activity levels similar to non-introgressed variants. In summary, our study reveals that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these RAs were more tolerated than NDAs. Thus, RAs and their distinct evolutionary histories must be considered when evaluating the effects of introgression.},
}

@article {pmid32707058,
year = {2020},
author = {Zeberg, H and Dannemann, M and Sahlholm, K and Tsuo, K and Maricic, T and Wiebe, V and Hevers, W and Robinson, HPC and Kelso, J and Pääbo, S},
title = {A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans.},
journal = {Current biology : CB},
volume = {30},
number = {17},
pages = {3465-3469.e4},
doi = {10.1016/j.cub.2020.06.045},
pmid = {32707058},
issn = {1879-0445},
abstract = {The sodium channel Nav1.7 is crucial for impulse generation and conduction in peripheral pain pathways [1]. In Neanderthals, the Nav1.7 protein carried three amino acid substitutions (M932L, V991L, and D1908G) relative to modern humans. We expressed Nav1.7 proteins carrying all combinations of these substitutions and studied their electrophysiological effects. Whereas the single amino acid substitutions do not affect the function of the ion channel, the full Neanderthal variant carrying all three substitutions, as well as the combination of V991L with D1908G, shows reduced inactivation, suggesting that peripheral nerves were more sensitive to painful stimuli in Neanderthals than in modern humans. We show that, due to gene flow from Neanderthals, the three Neanderthal substitutions are found in ∼0.4% of present-day Britons, where they are associated with heightened pain sensitivity.},
}

@article {pmid32704108,
year = {2020},
author = {Callaway, E},
title = {Neanderthal gene linked to increased pain sensitivity.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-020-02202-x},
pmid = {32704108},
issn = {1476-4687},
}

@article {pmid32699254,
year = {2020},
author = {Sánchez-Romero, L and Benito-Calvo, A and Marín-Arroyo, AB and Agudo-Pérez, L and Karampaglidis, T and Rios-Garaizar, J},
title = {Author Correction: New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in the Amalda I cave (Gipuzkoa, Spain).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12456},
doi = {10.1038/s41598-020-68761-1},
pmid = {32699254},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid32697783,
year = {2020},
author = {Baumann, C and Bocherens, H and Drucker, DG and Conard, NJ},
title = {Fox dietary ecology as a tracer of human impact on Pleistocene ecosystems.},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0235692},
pmid = {32697783},
issn = {1932-6203},
mesh = {Animals ; Archaeology ; Bayes Theorem ; Bone and Bones/metabolism ; Carbon Isotopes/analysis ; Collagen/chemistry/metabolism ; Diet/*veterinary ; *Ecosystem ; Fossils/history ; Foxes/*physiology ; History, Ancient ; Humans ; Neanderthals ; Nitrogen Isotopes/analysis ; },
abstract = {Nowadays, opportunistic small predators, such as foxes (Vulpes vulpes and Vulpes lagopus), are well known to be very adaptable to human modified ecosystems. However, the timing of the start of this phenomenon in terms of human impact on ecosystems and of the implications for foxes has hardly been studied. We hypothesize that foxes can be used as an indicator of past human impact on ecosystems, as a reflection of population densities and consequently to track back the influence of humans on the Pleistocene environment. To test this hypothesis, we used stable isotope analysis (δ13C, δ15N) of bone collagen extracted from faunal remains from several archaeological sites located in the Swabian Jura (southwest Germany) and covering a time range over three important cultural periods, namely the Middle Palaeolithic (older than 42,000 years ago) attributed to Neanderthals, and the early Upper Palaeolithic periods Aurignacian and Gravettian (42,000 to 30,000 years ago) attributed to modern humans. We then ran Bayesian statistic systems (SIBER, mixSIAR) to reconstruct the trophic niches and diets of Pleistocene foxes. We observed that during the Middle Palaeolithic period, when Neanderthals sparsely populated the Swabian Jura, the niches occupied by foxes suggest a natural trophic behavior. In contrast, during the early Upper Palaeolithic periods, a new trophic fox niche appeared, characterized by a restricted diet on reindeer. This trophic niche could be due to the consumption of human subsidies related to a higher human population density and the resulting higher impact on the Pleistocene environment by modern humans compared to Neanderthals. Furthermore, our study suggests that, a synanthropic commensal behavior of foxes started already in the Aurignacian, around 42,000 years ago.},
}

Animals
Archaeology
Bayes Theorem
Bone and Bones/metabolism
Carbon Isotopes/analysis
Collagen/chemistry/metabolism
Diet/*veterinary
*Ecosystem
Fossils/history
Foxes/*physiology
History, Ancient
Humans
Neanderthals
Nitrogen Isotopes/analysis

@article {pmid32696095,
year = {2020},
author = {Peeters, S and Zwart, H},
title = {Neanderthals as familiar strangers and the human spark: How the 'golden years' of Neanderthal research reopen the question of human uniqueness.},
journal = {History and philosophy of the life sciences},
volume = {42},
number = {3},
pages = {33},
pmid = {32696095},
issn = {1742-6316},
abstract = {During the past decades, our image of Homo neanderthalensis has changed dramatically. Initially, Neanderthals were seen as primitive brutes. Increasingly, however, Neanderthals are regarded as basically human. New discoveries and technologies have led to an avalanche of data, and as a result of that it becomes increasingly difficult to pinpoint what the difference between modern humans and Neanderthals really is. And yet, the persistent quest for a minimal difference which separates them from us is still noticeable in Neanderthal research. Neanderthal discourse is a vantage point from which the logic of 'us' versus 'other' is critically reconsidered. Studying contemporary academic literature and science autobiographies from an oblique perspective, focusing not on Neanderthals as objects, but on the dynamics of interaction between Neanderthal researchers and their finds, basic convictions at work in this type of research are retrieved. What is at issue is not the actual distinction between modern humans and Neanderthals (which is continuously being redefined), but rather the dualistic construction of human and nonhuman. Neanderthal understanding is affected by the desire to safeguard human uniqueness. The overall trend is to identify the human mark or spark, which defines us as favoured 'winners'. The paradoxes emerging in contemporary Neanderthal discourse are symptomatic of the fact that a dualistic style of thinking is no longer tenable.},
}

@article {pmid32690317,
year = {2020},
author = {Montinaro, F and Capelli, C},
title = {A Worldwide Map of Human Structural Variants.},
journal = {Trends in genetics : TIG},
volume = {36},
number = {10},
pages = {722-725},
doi = {10.1016/j.tig.2020.07.002},
pmid = {32690317},
issn = {0168-9525},
abstract = {Genomic variation extends from single nucleotide variants to large chromosomal rearrangements, but the extent of structural variation in Homo sapiens is still unclear. Almarri et al. provide a worldwide catalogue of structural variants present in human populations. Most of the reported variation is novel, with some variants being inherited from Neanderthals and Denisovans. Drift and selection shaped the distribution of these variants with some suggested to have functional implications.},
}

@article {pmid32681013,
year = {2020},
author = {Marra, F and Rolfo, MF and Gaeta, M and Florindo, F},
title = {Anomalous Last Interglacial Tyrrhenian sea levels and Neanderthal settling at Guattari and Moscerini caves (central Italy).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {11929},
pmid = {32681013},
issn = {2045-2322},
abstract = {We present a geological-stratigraphical study aimed to provide chronologic constraints to the sea-level markers occurring at two coastal caves of central Italy (Grotta Guattari and Grotta dei Moscerini) and to the Neanderthal frequentation of these caves, in the light of recent archaeological and geomorphological-geochronological studies suggesting similar sea levels during MIS 5.5 and MIS 5.3, and only few m below the Present during MIS 5.1 in this region. Based on the review of previous literature data, combined with new stratigraphic observations at Grotta Guattari and re-analysis of archive material including unpublished field notes from Grotta dei Moscerini, we reconstruct a plausible sea-level history accounting for the lithological and paleoenvironmental features of their sedimentary fillings. In particular, we outline the abundant occurrence of well-rounded pumice clasts within the sedimentary deposits of Moscerini Cave, attesting for the proximity to the beach where this pumice was gathered by wave action. Through the petrographic and geochemical analysis of this pumice we evidence provenance from Phlegraean Fields and Ischia Island volcanic districts, framing their chronology in the time span 118-40 ka, consistent with literature ESR-U/Th dates providing ages ranging 101 ± 5-74 ± 7 ka for the sedimentary filling of both Moscerini and Guattari caves.},
}

@article {pmid32666166,
year = {2020},
author = {Hallast, P and Agdzhoyan, A and Balanovsky, O and Xue, Y and Tyler-Smith, C},
title = {A Southeast Asian origin for present-day non-African human Y chromosomes.},
journal = {Human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00439-020-02204-9},
pmid = {32666166},
issn = {1432-1203},
support = {PUT1036//Eesti Teadusagentuur/ ; 098051/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000-70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000-55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion.},
}

@article {pmid32661407,
year = {2020},
author = {Columbu, A and Chiarini, V and Spötl, C and Benazzi, S and Hellstrom, J and Cheng, H and De Waele, J},
title = {Author Correction: Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.},
journal = {Nature ecology & evolution},
volume = {4},
number = {9},
pages = {1279},
doi = {10.1038/s41559-020-1267-6},
pmid = {32661407},
issn = {2397-334X},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid32652819,
year = {2020},
author = {Pomeroy, E and Hunt, CO and Reynolds, T and Abdulmutalb, D and Asouti, E and Bennett, P and Bosch, M and Burke, A and Farr, L and Foley, R and French, C and Frumkin, A and Goldberg, P and Hill, E and Kabukcu, C and Lahr, MM and Lane, R and Marean, C and Maureille, B and Mutri, G and Miller, CE and Mustafa, KA and Nymark, A and Pettitt, P and Sala, N and Sandgathe, D and Stringer, C and Tilby, E and Barker, G},
title = {Issues of theory and method in the analysis of Paleolithic mortuary behavior: A view from Shanidar Cave.},
journal = {Evolutionary anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/evan.21854},
pmid = {32652819},
issn = {1520-6505},
support = {//British Academy/ ; //Calleva Foundation/ ; //Human Origins Research Fund/ ; ECF-2017-284//Leverhulme Trust/ ; RPG-2013-105//Leverhulme Trust/ ; //McDonald Institute for Archaeological Research/ ; NE/L002507/1//Natural Environment Research Council/ ; NF/2016/2/14//Natural Environment Research Council/ ; //Rust Family Foundation/ ; //Society of Antiquaries of London/ ; CONF-788//Wenner-Gren Foundation/ ; },
abstract = {Mortuary behavior (activities concerning dead conspecifics) is one of many traits that were previously widely considered to have been uniquely human, but on which perspectives have changed markedly in recent years. Theoretical approaches to hominin mortuary activity and its evolution have undergone major revision, and advances in diverse archeological and paleoanthropological methods have brought new ways of identifying behaviors such as intentional burial. Despite these advances, debates concerning the nature of hominin mortuary activity, particularly among the Neanderthals, rely heavily on the rereading of old excavations as new finds are relatively rare, limiting the extent to which such debates can benefit from advances in the field. The recent discovery of in situ articulated Neanderthal remains at Shanidar Cave offers a rare opportunity to take full advantage of these methodological and theoretical developments to understand Neanderthal mortuary activity, making a review of these advances relevant and timely.},
}

@article {pmid32632262,
year = {2020},
author = {Columbu, A and Chiarini, V and Spötl, C and Benazzi, S and Hellstrom, J and Cheng, H and De Waele, J},
title = {Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.},
journal = {Nature ecology & evolution},
volume = {4},
number = {9},
pages = {1188-1195},
doi = {10.1038/s41559-020-1243-1},
pmid = {32632262},
issn = {2397-334X},
support = {NSFC 41888101//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
abstract = {The causes of Neanderthal-modern human (MH) turnover are ambiguous. While potential biocultural interactions between the two groups are still little known, it is clear that Neanderthals in southern Europe disappeared about 42 thousand years ago (ka) after cohabitation for ~3,000 years with MH. Among a plethora of hypotheses on Neanderthal extinction, rapid climate changes during the Middle to Upper Palaeolithic transition (MUPT) are regarded as a primary factor. Here we show evidence for stable climatic and environmental conditions during the MUPT in a region (Apulia) where Neanderthals and MH coexisted. We base our findings on a rare glacial stalagmite deposited between ~106 and ~27 ka, providing the first continuous western Mediterranean speleothem palaeoclimate archive for this period. The uninterrupted growth of the stalagmite attests to the constant availability of rainfall and vegetated soils, while its δ13C-δ18O palaeoclimate proxies demonstrate that Apulia was not affected by dramatic climate oscillations during the MUPT. Our results imply that, because climate did not play a key role in the disappearance of Neanderthals in this area, Neanderthal-MH turnover must be approached from a perspective that takes into account climatic and environmental conditions favourable for both species.},
}

@article {pmid32632258,
year = {2020},
author = {Bastir, M and García-Martínez, D and Torres-Tamayo, N and Palancar, CA and Beyer, B and Barash, A and Villa, C and Sanchis-Gimeno, JA and Riesco-López, A and Nalla, S and Torres-Sánchez, I and García-Río, F and Been, E and Gómez-Olivencia, A and Haeusler, M and Williams, SA and Spoor, F},
title = {Rib cage anatomy in Homo erectus suggests a recent evolutionary origin of modern human body shape.},
journal = {Nature ecology & evolution},
volume = {4},
number = {9},
pages = {1178-1187},
doi = {10.1038/s41559-020-1240-4},
pmid = {32632258},
issn = {2397-334X},
support = {CGL2015-63648-P//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; CGL2015-63648-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España (Ministerio de Economía, Industria y Competitividad)/ ; },
abstract = {The tall and narrow body shape of anatomically modern humans (Homo sapiens) evolved via changes in the thorax, pelvis and limbs. It is debated, however, whether these modifications first evolved together in African Homo erectus, or whether H. erectus had a more primitive body shape that was distinct from both the more ape-like Australopithecus species and H. sapiens. Here we present the first quantitative three-dimensional reconstruction of the thorax of the juvenile H. erectus skeleton, KNM-WT 15000, from Nariokotome, Kenya, along with its estimated adult rib cage, for comparison with H. sapiens and the Kebara 2 Neanderthal. Our three-dimensional reconstruction demonstrates a short, mediolaterally wide and anteroposteriorly deep thorax in KNM-WT 15000 that differs considerably from the much shallower thorax of H. sapiens, pointing to a recent evolutionary origin of fully modern human body shape. The large respiratory capacity of KNM-WT 15000 is compatible with the relatively stocky, more primitive, body shape of H. erectus.},
}

@article {pmid32615344,
year = {2020},
author = {Yan, SM and McCoy, RC},
title = {Archaic hominin genomics provides a window into gene expression evolution.},
journal = {Current opinion in genetics & development},
volume = {62},
number = {},
pages = {44-49},
pmid = {32615344},
issn = {1879-0380},
support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; },
abstract = {Differences in gene expression are thought to account for most phenotypic differences within and between species. Consequently, gene expression is a powerful lens through which to study divergence between modern humans and our closest evolutionary relatives, the Neanderthals and Denisovans. Such insights complement biological knowledge gleaned from the fossil record, while also revealing general features of the mode and tempo of regulatory evolution. Because of the degradation of ancient RNA, gene expression profiles of archaic hominins must be studied by indirect means. As such, conclusions drawn from these studies are often laden with assumptions about the genetic architecture of gene expression, the complexity of which is increasingly apparent. Despite these challenges, rapid technical and conceptual advances in the fields of ancient genomics, functional genomics, statistical genomics, and genome engineering are revolutionizing understanding of hominin gene expression evolution.},
}

@article {pmid32612423,
year = {2020},
author = {Senturk, N and Ergoren, MC},
title = {Developing an Online Portal for Determining the Genomic Signature of Archaic DNA that are Associated to Modern Human Genetic Diseases: A Meta-Analysis Study.},
journal = {The Eurasian journal of medicine},
volume = {52},
number = {2},
pages = {153-160},
pmid = {32612423},
issn = {1308-8734},
abstract = {Objective: Mutations or introgression can cause and rise adaptive alleles of which some can be beneficial. Archaic humans lived more than 200,000 years ago in Europe and Western Asia. They were adapted to the environment and pathogens that prevailed in these locations. It can therefore be thought that modern humans obtained significant immune advantage from the archaic alleles.

Materials and Methods: First, data were collected by meta-analysis from previously identified genetic diseases caused by alleles that were introgressed from archaics. Second, the in silico model portal (http://www.archaics2phenotype.xxx.edu.tr) was designed to trace the history of the Neanderthal allele. The portal also shows the current distribution of the genotypes of the selected alleles within different populations and correlates with the individuals phenotype.

Results: Our developed model provides a better understanding for the origin of genetic diseases or traits that are associated with the Neanderthal genome.

Conclusion: The developed medicine model will help individuals and their populations to receive the best treatment. It also clarifies why there are differences in disease phenotypes in modern humans.},
}

@article {pmid32594872,
year = {2020},
author = {Nielsen, M and Langley, MC and Shipton, C and Kapitány, R},
title = {Homo neanderthalensis and the evolutionary origins of ritual in Homo sapiens.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1805},
pages = {20190424},
pmid = {32594872},
issn = {1471-2970},
abstract = {There is a large, if disparate, body of archaeological literature discussing specific instantiations of symbolic material culture and the possibility of ritual practices in Neanderthal populations. Despite this attention, however, no single synthesis exists that draws upon cognitive, psychological and cultural evolutionary theories of ritual. Here, we review the evidence for ritual-practice among now-extinct Homo neanderthalensis, as well as the necessary cognitive pre-conditions for such behaviour, in order to explore the evolution of ritual in Homo sapiens. We suggest that the currently available archaeological evidence indicates that Neanderthals may have used 'ritualization' to increase the successful transmission of technical knowledge across generations-providing an explanation for the technological stability of the Middle Palaeolithic and attesting to a survival strategy differing from near-contemporary H. sapiens. This article is part of the theme issue 'Ritual renaissance: new insights into the most human of behaviours'.},
}

@article {pmid32593870,
year = {2020},
author = {Martínez de Pinillos, M and Martín-Francés, L and de Castro, JMB and García-Campos, C and Modesto-Mata, M and Martinón-Torres, M and Vialet, A},
title = {Inner morphological and metric characterization of the molar remains from the Montmaurin-La Niche mandible: The Neanderthal signal.},
journal = {Journal of human evolution},
volume = {145},
number = {},
pages = {102739},
doi = {10.1016/j.jhevol.2019.102739},
pmid = {32593870},
issn = {1095-8606},
abstract = {Here, we present a metric and morphological study of the molar remains from the Montmaurin-La Niche mandible by means of microcomputed tomography. According to the last analysis, based on the combination of geomorphological and paleontological data, the level bearing this human mandible probably corresponds to the marine isotope stages (MIS) 7. These data place the Montmaurin-La Niche in a chronologically intermediate position between the Neanderthals and the Middle Pleistocene fossils (e.g., Sima de los Huesos, la Caune de l'Arago). A recent study has revealed that while the mandible is more closely related to the Early and Middle Pleistocene African and Eurasian populations, the morphology of the outer enamel surfaces of its molars is typical of the Neanderthal linage. The data presented here are in line with this finding because the morphology of the enamel-dentine junction of the molars is similar to that of Neanderthals, whereas the absolute and relative enamel thickness values (2D and 3D) are closer to those exhibited by some Early Pleistocene hominins. Moreover, the pulp cavity morphology and proportions are in concordance with the Neanderthal populations. Our results strengthen the hypothesis that the settlement of Europe could be the result of several migrations, at different times, originated from a common source population. Thus, the variability in the European Middle Pleistocene populations (e.g., Montmaurin, Sima de los Huesos, Arago, Mala Balanica) could indicate different migrations at different times and/or population fragmentation, without excluding the possible hybridization between residents and new settlers.},
}

@article {pmid32586278,
year = {2020},
author = {Weiß, CL and Gansauge, MT and Aximu-Petri, A and Meyer, M and Burbano, HA},
title = {Mining ancient microbiomes using selective enrichment of damaged DNA molecules.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {432},
pmid = {32586278},
issn = {1471-2164},
support = {Presidential Innovation Fund//Max-Planck-Gesellschaft/ ; },
abstract = {BACKGROUND: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains.

RESULTS: We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach.

CONCLUSIONS: Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.},
}

@article {pmid32580077,
year = {2020},
author = {Bosman, AM and Reyes-Centeno, H and Harvati, K},
title = {A virtual assessment of the suprainiac depressions on the Eyasi I (Tanzania) and Aduma ADU-VP-1/3 (Ethiopia) Pleistocene hominin crania.},
journal = {Journal of human evolution},
volume = {145},
number = {},
pages = {102815},
doi = {10.1016/j.jhevol.2020.102815},
pmid = {32580077},
issn = {1095-8606},
abstract = {Despite a steady increase in our understanding of the phenotypic variation of Pleistocene Homo, debate continues over phylogenetically informative features. One such trait is the suprainiac fossa, a depression on the occipital bone above inion that is commonly considered an autapomorphy of the Neanderthal lineage. Challenging this convention, depressions in the suprainiac region have also been described for two Pleistocene hominin crania from sub-Saharan Africa: Eyasi I (Tanzania) and ADU-VP-1/3 (Ethiopia). Here, we use a combined quantitative and qualitative approach, using μCT imaging, to investigate the occipital depressions on these specimens. The results show that neither the external nor the internal morphologies of these depressions bear any resemblance to the Neanderthal condition. A principal component analysis based on multiple thickness measurements along the occipital squama demonstrates that the relative thickness values for the internal structures in Eyasi I and ADU-VP-1/3 are within the range of Homo sapiens. Thus, our results support the autapomorphic status of the Neanderthal suprainiac fossa and highlight the need to use nuanced approaches and multiple lines of evidence.},
}

@article {pmid32574964,
year = {2020},
author = {Mathov, Y and Batyrev, D and Meshorer, E and Carmel, L},
title = {Harnessing epigenetics to study human evolution.},
journal = {Current opinion in genetics & development},
volume = {62},
number = {},
pages = {23-29},
doi = {10.1016/j.gde.2020.05.023},
pmid = {32574964},
issn = {1879-0380},
abstract = {Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.},
}

@article {pmid32559457,
year = {2020},
author = {Dannemann, M and He, Z and Heide, C and Vernot, B and Sidow, L and Kanton, S and Weigert, A and Treutlein, B and Pääbo, S and Kelso, J and Camp, JG},
title = {Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions.},
journal = {Stem cell reports},
volume = {15},
number = {1},
pages = {214-225},
pmid = {32559457},
issn = {2213-6711},
abstract = {Induced pluripotent stem cells (iPSCs) from diverse humans offer the potential to study human functional variation in controlled culture environments. A portion of this variation originates from an ancient admixture between modern humans and Neandertals, which introduced alleles that left a phenotypic legacy on individual humans today. Here, we show that a large iPSC repository harbors extensive Neandertal DNA, including alleles that contribute to human phenotypes and diseases, encode hundreds of amino acid changes, and alter gene expression in specific tissues. We provide a database of the inferred introgressed Neandertal alleles for each individual iPSC line, together with the annotation of the predicted functional variants. We also show that transcriptomic data from organoids generated from iPSCs can be used to track Neandertal-derived RNA over developmental processes. Human iPSC resources provide an opportunity to experimentally explore Neandertal DNA function and its contribution to present-day phenotypes, and potentially study Neandertal traits.},
}

@article {pmid32556248,
year = {2020},
author = {Khan, N and de Manuel, M and Peyregne, S and Do, R and Prufer, K and Marques-Bonet, T and Varki, N and Gagneux, P and Varki, A},
title = {Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins.},
journal = {Genome biology and evolution},
volume = {12},
number = {7},
pages = {1040-1050},
pmid = {32556248},
issn = {1759-6653},
support = {R01 GM032373/GM/NIGMS NIH HHS/United States ; U01 MH106874/MH/NIMH NIH HHS/United States ; },
abstract = {Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface "self-associated molecular patterns" that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2-3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a "hotspot" in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human-Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal-human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.},
}

@article {pmid32546518,
year = {2020},
author = {Mafessoni, F and Grote, S and de Filippo, C and Slon, V and Kolobova, KA and Viola, B and Markin, SV and Chintalapati, M and Peyrégne, S and Skov, L and Skoglund, P and Krivoshapkin, AI and Derevianko, AP and Meyer, M and Kelso, J and Peter, B and Prüfer, K and Pääbo, S},
title = {A high-coverage Neandertal genome from Chagyrskaya Cave.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {26},
pages = {15132-15136},
pmid = {32546518},
issn = {1091-6490},
mesh = {Animals ; Biological Evolution ; Female ; Fossils ; Gene Expression Regulation ; Genetic Variation ; *Genome ; Humans ; Inbreeding ; Neanderthals/*genetics ; Population Density ; Russia ; },
abstract = {We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prüfer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prüfer et al., Nature 505, 43-49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.},
}

Animals
Biological Evolution
Female
Fossils
Gene Expression Regulation
Genetic Variation
*Genome
Humans
Inbreeding
Neanderthals/*genetics
Population Density
Russia

@article {pmid32531199,
year = {2020},
author = {Almarri, MA and Bergström, A and Prado-Martinez, J and Yang, F and Fu, B and Dunham, AS and Chen, Y and Hurles, ME and Tyler-Smith, C and Xue, Y},
title = {Population Structure, Stratification, and Introgression of Human Structural Variation.},
journal = {Cell},
volume = {182},
number = {1},
pages = {189-199.e15},
doi = {10.1016/j.cell.2020.05.024},
pmid = {32531199},
issn = {1097-4172},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.},
}

@article {pmid32511250,
year = {2020},
author = {Martín-Francés, L and Martinón-Torres, M and Martínez de Pinillos, M and García-Campos, C and Zanolli, C and Bayle, P and Modesto-Mata, M and Arsuaga, JL and Bermúdez de Castro, JM},
title = {Crown tissue proportions and enamel thickness distribution in the Middle Pleistocene hominin molars from Sima de los Huesos (SH) population (Atapuerca, Spain).},
journal = {PloS one},
volume = {15},
number = {6},
pages = {e0233281},
pmid = {32511250},
issn = {1932-6203},
mesh = {Animals ; Biological Evolution ; Dental Enamel/anatomy & histology/metabolism ; Fossils/*anatomy & histology ; Hominidae/*anatomy & histology ; Humans ; Molar/*anatomy & histology/metabolism ; Neanderthals ; Phylogeny ; Spain ; Tooth ; Tooth Crown/anatomy & histology/metabolism ; },
abstract = {Dental enamel thickness, topography, growth and development vary among hominins. In Homo, the thickness of dental enamel in most Pleistocene hominins display variations from thick to hyper-thick, while Neanderthals exhibit proportionally thinner enamel. The origin of the thin trait remains unclear. In this context, the Middle Pleistocene human dental assemblage from Atapuerca-Sima de los Huesos (SH) provides a unique opportunity to trace the evolution of enamel thickness in European hominins. In this study, we aim to test the hypothesis if the SH molar sample approximates the Neanderthal condition for enamel thickness and/or distribution. This study includes 626 molars, both original and comparative data. We analysed the molar inner structural organization of the original collections (n = 124), belonging to SH(n = 72) and modern humans from Spanish origin (n = 52). We compared the SH estimates to those of extinct and extant populations of the genus Homo from African, Asian and European origin (estimates extracted from literature n = 502). The comparative sample included maxillary and mandibular molars belonging to H. erectus, East and North African Homo, European Middle Pleistocene Homo, Neanderthals, and fossil and extant H. sapiens. We used high-resolution images to investigate the endostructural configuration of SH molars (tissue proportions, enamel thickness and distribution). The SH molars exhibit on average thick absolute and relative enamel in 2D and 3D estimates, both in the complete crown and the lateral enamel. This primitive condition is shared with the majority of extinct and extant hominin sample, except for Neanderthals and some isolated specimens. On the contrary, the SH molar enamel distribution maps reveal a distribution pattern similar to the Neanderthal signal (with thicker enamel on the lingual cusps and more peripherally distributed), compared to H. antecessor and modern humans. Due to the phylogenetic position of the SH population, the thick condition in molars could represent the persistence of the plesiomorphic condition in this group. Still, more data is needed on other Early and Middle Pleistocene populations to fully understand the evolutionary meaning of this trait.},
}

Animals
Biological Evolution
Dental Enamel/anatomy & histology/metabolism
Fossils/*anatomy & histology
Hominidae/*anatomy & histology
Humans
Molar/*anatomy & histology/metabolism
Neanderthals
Phylogeny
Spain
Tooth
Tooth Crown/anatomy & histology/metabolism

@article {pmid32494067,
year = {2020},
author = {Skov, L and Coll Macià, M and Sveinbjörnsson, G and Mafessoni, F and Lucotte, EA and Einarsdóttir, MS and Jonsson, H and Halldorsson, B and Gudbjartsson, DF and Helgason, A and Schierup, MH and Stefansson, K},
title = {The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes.},
journal = {Nature},
volume = {582},
number = {7810},
pages = {78-83},
doi = {10.1038/s41586-020-2225-9},
pmid = {32494067},
issn = {1476-4687},
mesh = {Animals ; Female ; Genetic Association Studies ; Genetic Introgression/*genetics ; Genome, Human/*genetics ; *Genomics ; Haploidy ; Humans ; Iceland ; Male ; *Mutation ; Neanderthals/*genetics ; Phenotype ; Phylogeny ; },
abstract = {Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50-60 thousand years ago1. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388-112,709 unique archaic fragments that cover 38.0-48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500 thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types-perhaps due to different generation intervals for males and females. Finally, we assessed 271 phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.},
}

Animals
Female
Genetic Association Studies
Genetic Introgression/*genetics
Genome, Human/*genetics
*Genomics
Haploidy
Humans
Iceland
Male
*Mutation
Neanderthals/*genetics
Phenotype
Phylogeny

@article {pmid32490227,
year = {2020},
author = {Kolendrianou, M and Ligkovanlis, S and Maniakas, I and Tzortzi, M and Iliopoulos, G},
title = {The Palaeolithic cave of Kalamakia (Mani Peninsula), Greece: new insights on the palaeoenvironment using microvertebrates and mesowear analysis of ruminant teeth.},
journal = {Heliyon},
volume = {6},
number = {5},
pages = {e03958},
pmid = {32490227},
issn = {2405-8440},
abstract = {In the present study, results from the examination of mammalian teeth from the cave of Kalamakia with modern techniques, as well as a qualitative overview of the microvertebrate and lithic material, are presented together with a revision of previous related work done for the site, in order to assess the palaeoenvironmental conditions in the area and the role they played in the Neanderthal's repeated occupation of the cave. Geometric morphometrics analyses performed on the first lower molars of Microtus spp. individuals revealed persistent populations of the subgenus Terricola, in which the presence of Microtus thomasi and Microtus subterraneus are continuous through the stratigraphic units. Mesowear analyses performed on ruminant teeth showed no significant variation in toothwear through time, except for relatively elevated levels of dietary abrasion for the more recent samples. The study of the lithics revealed that Neanderthals visited the cave in alternating short and more permanent episodes of occupation, with the human occupants exhibiting special concern for raw material economy, while exploiting poor raw materials for the construction of their tools. The overview of the microvertebrate remains showed a growing trend towards the upper stratigraphic units, where taxa typical of temperate climate, open woodland and shrubland become more dominant. These results, along with observations derived from previous studies, suggest that temperate climate and open environment were the factors that mainly contributed to making the cave of Kalamakia attractive as a habitation site to the humans of the area.},
}

@article {pmid32457436,
year = {2020},
author = {Sánchez-Romero, L and Benito-Calvo, A and Marín-Arroyo, AB and Agudo-Pérez, L and Karampaglidis, T and Rios-Garaizar, J},
title = {New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in theAmalda I cave (Gipuzkoa, Spain).},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {8733},
pmid = {32457436},
issn = {2045-2322},
abstract = {The Level VII of Amalda I cave (Gipuzkoa, Spain) represents one of the latest Middle Palaeolithic occupations in the Cantabrian Region. It is characterized by the presence of Middle Palaeolithic lithic industry and animal remains, with clear evidences of anthropic and carnivore manipulation. At this site, the Neanderthal presence has been questioned in relation to the role of carnivores in the accumulation of large, medium-sized and small mammals. It has also been proposed that the Neanderthal occupation could have consisted of short-term occupations, where different activities took place in a structured space within the cave. However, all hypotheses lacked any integrative analysis of the site formation processes. With the aim of understanding these processes, a combination of spatial techniques, based on GIS and inferential statistics (density analysis, hotspots tools and palaeotopographic reconstruction), along with the taphonomic study of identifiable and non-identifiable macromammals remains, were employed. This study has revealed distinct use of the cave space by Neanderthals and carnivores. The major concentrations of lithics and medium-size mammal remains were clearly accumulated by humans at the cave entrance, while the small-size mammals were gathered by carnivores in an inner zone. The activities of the Neanderthals seem to be distinctly structured, suggesting a parallel exploitation of resources.},
}

@article {pmid32453742,
year = {2020},
author = {Natri, HM and Bobowik, KS and Kusuma, P and Crenna Darusallam, C and Jacobs, GS and Hudjashov, G and Lansing, JS and Sudoyo, H and Banovich, NE and Cox, MP and Gallego Romero, I},
title = {Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago.},
journal = {PLoS genetics},
volume = {16},
number = {5},
pages = {e1008749},
pmid = {32453742},
issn = {1553-7404},
mesh = {CpG Islands ; *DNA Methylation ; Environment ; Epigenesis, Genetic/physiology ; Ethnic Groups/*genetics/statistics & numerical data ; Gene Expression Profiling/statistics & numerical data ; *Gene-Environment Interaction ; Genetics, Population ; Genome-Wide Association Study/statistics & numerical data ; Genomics/methods ; Humans ; Indonesia/epidemiology ; Islands/epidemiology ; Pacific Islands/epidemiology ; Pedigree ; Phenotype ; Polymorphism, Single Nucleotide ; RNA-Seq ; *Transcriptome ; },
abstract = {Indonesia is the world's fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.},
}

CpG Islands
*DNA Methylation
Environment
Epigenesis, Genetic/physiology
Ethnic Groups/*genetics/statistics & numerical data
Gene Expression Profiling/statistics & numerical data
*Gene-Environment Interaction
Genetics, Population
Genome-Wide Association Study/statistics & numerical data
Genomics/methods
Humans
Indonesia/epidemiology
Islands/epidemiology
Pacific Islands/epidemiology
Pedigree
Phenotype
Polymorphism, Single Nucleotide
RNA-Seq
*Transcriptome

@article {pmid32451437,
year = {2020},
author = {Esteller-Cucala, P and Maceda, I and Børglum, AD and Demontis, D and Faraone, SV and Cormand, B and Lao, O},
title = {Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {8622},
doi = {10.1038/s41598-020-65322-4},
pmid = {32451437},
issn = {2045-2322},
support = {U01 MH109536/MH/NIMH NIH HHS/United States ; R01 MH101519/MH/NIMH NIH HHS/United States ; },
abstract = {Attention-deficit/hyperactivity disorder (ADHD) is an impairing neurodevelopmental condition highly prevalent in current populations. Several hypotheses have been proposed to explain this paradox, mainly in the context of the Paleolithic versus Neolithic cultural shift but especially within the framework of the mismatch theory. This theory elaborates on how a particular trait once favoured in an ancient environment might become maladaptive upon environmental changes. However, given the lack of genomic data available for ADHD, these theories have not been empirically tested. We took advantage of the largest GWAS meta-analysis available for this disorder consisting of over 20,000 individuals diagnosed with ADHD and 35,000 controls, to assess the evolution of ADHD-associated alleles in European populations using archaic, ancient and modern human samples. We also included Approximate Bayesian computation coupled with deep learning analyses and singleton density scores to detect human adaptation. Our analyses indicate that ADHD-associated alleles are enriched in loss of function intolerant genes, supporting the role of selective pressures in this early-onset phenotype. Furthermore, we observed that the frequency of variants associated with ADHD has steadily decreased since Paleolithic times, particularly in Paleolithic European populations compared to samples from the Neolithic Fertile Crescent. We demonstrate this trend cannot be explained by African admixture nor Neanderthal introgression, since introgressed Neanderthal alleles are enriched in ADHD risk variants. All analyses performed support the presence of long-standing selective pressures acting against ADHD-associated alleles until recent times. Overall, our results are compatible with the mismatch theory for ADHD but suggest a much older time frame for the evolution of ADHD-associated alleles compared to previous hypotheses.},
}

@article {pmid32451090,
year = {2020},
author = {Hoffmann, DL and Standish, CD and García-Diez, M and Pettitt, PB and Milton, JA and Zilhão, J and Alcolea-González, JJ and Cantalejo-Duarte, P and Collado, H and de Balbín, R and Lorblanchet, M and Ramos-Muñoz, J and Weniger, GC and Pike, AWG},
title = {Response to White et al.'s reply: 'Still no archaeological evidence that Neanderthals created Iberian cave art' [J. Hum. Evol. (2020) 102640].},
journal = {Journal of human evolution},
volume = {144},
number = {},
pages = {102810},
doi = {10.1016/j.jhevol.2020.102810},
pmid = {32451090},
issn = {1095-8606},
}

@article {pmid32437543,
year = {2020},
author = {Zeberg, H and Kelso, J and Pääbo, S},
title = {The Neandertal Progesterone Receptor.},
journal = {Molecular biology and evolution},
volume = {37},
number = {9},
pages = {2655-2660},
pmid = {32437543},
issn = {1537-1719},
abstract = {The hormone progesterone is important for preparing the uterine lining for egg implantation and for maintaining the early stages of pregnancy. The gene encoding the progesterone receptor (PGR) carries introgressed Neandertal haplotypes with two missense substitutions and a mobile Alu element. These Neandertal gene variants have reached nearly 20% frequency in non-Africans and have been associated with preterm birth. Here, we show that one of the missense substitutions appears fixed in Neandertals, while the other substitution as well as the Alu insertion were polymorphic among Neandertals. We show that two Neandertal haplotypes carrying the PGR gene entered the modern human population and that present-day carriers of the Neandertal haplotypes express higher levels of the receptor. In a cohort of present-day Britons, these carriers have more siblings, fewer miscarriages, and less bleeding during early pregnancy suggesting that the Neandertal progesterone receptor alleles promote fertility. This may explain their high frequency in modern human populations.},
}

@article {pmid32436615,
year = {2020},
author = {Palancar, CA and García-Martínez, D and Radovčić, D and Llidó, S and Mata-Escolano, F and Bastir, M and Sanchis-Gimeno, JA},
title = {Krapina atlases suggest a high prevalence of anatomical variations in the first cervical vertebra of Neanderthals.},
journal = {Journal of anatomy},
volume = {},
number = {},
pages = {},
doi = {10.1111/joa.13215},
pmid = {32436615},
issn = {1469-7580},
support = {CGL2015-63648-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; FJCI-2017-32157//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; UV-INV_AE18-773873//Universitat de València/ ; },
abstract = {The first cervical vertebra, atlas, and its anatomical variants have been widely studied in Homo sapiens. However, in Neanderthals, the presence of anatomical variants of the atlas has been very little studied until very recently. Only the Neanderthal group from the El Sidrón site (Spain) has been analysed with regard to the anatomical variants of the atlas. A high prevalence of anatomical variants has been described in this sample, which points to low genetic diversity in this Neanderthal group. Even so, the high prevalence of anatomical variations detected in El Sidrón Neanderthal atlases needs to be confirmed by analysing more Neanderthal remains. In this context, we analysed the possible presence of anatomical variants in the three Neanderthal atlases recovered from the Krapina site (Croatia) within the Neanderthal lineage. Two of the three Krapina atlases presented anatomical variations. One atlas (Krapina 98) had an unclosed transverse foramen and the other (Krapina 99) presented a non-fused anterior atlas arch. Moreover, an extended review of the bibliography also showed these anatomical variations in other Middle and Upper Pleistocene hominins, leading us to hypothesise that anatomical variations of the atlas had a higher prevalence in extinct hominins than in modern humans.},
}

@article {pmid32436183,
year = {2020},
author = {Ricci, C and Kakularam, KR and Marzocchi, C and Capecchi, G and Riolo, G and Boschin, F and Kuhn, H and Castagna, MG and Cantara, S},
title = {Thr92Ala polymorphism in the type 2 deiodinase gene: an evolutionary perspective.},
journal = {Journal of endocrinological investigation},
volume = {},
number = {},
pages = {},
doi = {10.1007/s40618-020-01287-5},
pmid = {32436183},
issn = {1720-8386},
support = {KU 961-14/1//German Research Council/ ; },
abstract = {PURPOSE: In the past, a role of thyroid hormones in human evolution has been hypothesized. T3, the metabolically active form, derives from extrathyroidal conversion of T4 by deionidase 2 (D2) enzyme encoded by DIO2 gene. In thyroid-deficient patients, decreased levels of free T3 have been associated with the polymorphism rs225014 A/G in DIO2, which causes the substitution of Threonine with Alanine (p.Thr92Ala) at protein level.

METHODS: We compared DNA and protein sequences of D2 from archaic human subspecies with those of contemporary humans.

RESULTS: Neanderthals and Denisovans displayed only the G allele at the rs225014 polymorphism, which encodes for an Alanine on the amino acid level. These data suggest that these hominines were homozygous for the Ala amino acid. These arcaic humans often lived in condition of iodine deficiency and thus, defective mechanisms of T3 biosynthesis could be life threatining. A reduced D2 activity is likely to cause decreased T3 levels, which could be critical for those individuals. Neanderthals and Denisovans were hunters/gatherers, and their diet was mainly based on the consumption of meat, with a low intake of carbohydrates. The need for circulating T3 is reduced at such alimentary conditions. On the basis of our genome comparisons the A allele, corresponding to Threonine and associated with higher levels of circulating T3 in thyroid-deficient patients, appeared for the first time during evolution in Anatomically Modern Humans during the Upper Pleistocene and has been conserved during the Neolithic age. With the advent of agriculture and herding, individuals carrying A allele might have a higher probability for surviving and reproducing. Thus, the variant was positively selected during the evolution.

CONCLUSION: Here we present an evolutionary perspective for p.Thr92Ala variant of D2 from Neanderthals to Anatomically Modern Humans.},
}

@article {pmid32433609,
year = {2020},
author = {Hublin, JJ and Sirakov, N and Aldeias, V and Bailey, S and Bard, E and Delvigne, V and Endarova, E and Fagault, Y and Fewlass, H and Hajdinjak, M and Kromer, B and Krumov, I and Marreiros, J and Martisius, NL and Paskulin, L and Sinet-Mathiot, V and Meyer, M and Pääbo, S and Popov, V and Rezek, Z and Sirakova, S and Skinner, MM and Smith, GM and Spasov, R and Talamo, S and Tuna, T and Wacker, L and Welker, F and Wilcke, A and Zahariev, N and McPherron, SP and Tsanova, T},
title = {Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.},
journal = {Nature},
volume = {581},
number = {7808},
pages = {299-302},
doi = {10.1038/s41586-020-2259-z},
pmid = {32433609},
issn = {1476-4687},
support = {/ERC_/European Research Council/International ; },
mesh = {Animals ; Asia ; Bone and Bones/metabolism ; Bulgaria ; Caves ; DNA, Ancient/isolation & purification ; DNA, Mitochondrial/genetics/isolation & purification ; Europe ; *Fossils ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; Phylogeny ; Tool Use Behavior ; Tooth/anatomy & histology/metabolism ; },
abstract = {The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin1. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts2, from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago3. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe4-6. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations7,8.},
}

Animals
Asia
Bone and Bones/metabolism
Bulgaria
Caves
DNA, Ancient/isolation & purification
DNA, Mitochondrial/genetics/isolation & purification
Europe
*Fossils
History, Ancient
Human Migration/*history
Humans
Neanderthals/genetics
Phylogeny
Tool Use Behavior
Tooth/anatomy & histology/metabolism

@article {pmid32409455,
year = {2020},
author = {Gibbons, A},
title = {Oldest Homo sapiens bones found in Europe.},
journal = {Science (New York, N.Y.)},
volume = {368},
number = {6492},
pages = {697},
doi = {10.1126/science.368.6492.697},
pmid = {32409455},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Bone and Bones ; Bulgaria ; Humans ; Molar/anatomy & histology ; *Neanderthals ; },
}

Animals
*Biological Evolution
Bone and Bones
Bulgaria
Humans
Molar/anatomy & histology
*Neanderthals

@article {pmid32398823,
year = {2020},
author = {Hardy, BL and Moncel, MH and Kerfant, C and Lebon, M and Bellot-Gurlet, L and Mélard, N},
title = {Author Correction: Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {8167},
doi = {10.1038/s41598-020-65143-5},
pmid = {32398823},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid32380300,
year = {2020},
author = {Verna, C and Détroit, F and Kupczik, K and Arnaud, J and Balzeau, A and Grimaud-Hervé, D and Bertrand, S and Riou, B and Moncel, MH},
title = {The Middle Pleistocene hominin mandible from Payre (Ardèche, France).},
journal = {Journal of human evolution},
volume = {144},
number = {},
pages = {102775},
doi = {10.1016/j.jhevol.2020.102775},
pmid = {32380300},
issn = {1095-8606},
abstract = {Although Neandertals are the best-known fossil hominins, the tempo and evolutionary processes in their lineage are strongly debated. This is in part due to the scarcity of the fossil record, in particular before the marine isotopic stage (MIS) 5. In 2010, a partial hominin mandible was discovered at the Middle Paleolithic site of Payre (France) in a layer that is dated to the end of MIS 8/beginning of MIS 7, a time period for which very few fossils are known in Europe. The Payre 15 mandible retains the complete symphyseal region and right lateral corpus with heavily worn P4, M1, and M2 in situ. Taphonomic modifications in the form of three notches suggest that this individual was chewed by a carnivore. We provide here the first detailed description of this specimen and a comparative analysis that includes morphological features, linear mandibular dimensions, an elliptic Fourier analysis of the symphysis, and a morphometric analysis of the M1 roots (based on segmented CT scan data). Our comparative sample encompasses European Middle and Upper Pleistocene specimens attributed to Homo heidelbergensis and Homo neanderthalensis, Upper Pleistocene Homo sapiens, and Holocene Homo sapiens. The Payre 15 mandible shows a combination of primitive and Neandertal-like features, with a receding symphyseal profile without any element of the mentum osseum, a posterior location of the mental foramen and lateral prominence. Its mandibular body is tall and thick anteriorly. Payre 15 has mesotaurodont M1 roots and a three-rooted M2. By its dimensions and combination of features, Payre 15 aligns better with Middle Pleistocene European hominins than with MIS 6-3 Neandertals. Noteworthy, it falls well within the range of variation of the Sima de los Huesos sample. Our results underscore that the total pattern of Neandertal-derived morphology was not achieved at the beginning of the MIS 7 and suggest a low level of mandibular diachronic changes for the period MIS 11-7.},
}

@article {pmid32371290,
year = {2020},
author = {Yeshurun, R and Malkinson, D and Crater Gershtein, KM and Zaidner, Y and Weinstein-Evron, M},
title = {Site occupation dynamics of early modern humans at Misliya Cave (Mount Carmel, Israel): Evidence from the spatial taphonomy of faunal remains.},
journal = {Journal of human evolution},
volume = {143},
number = {},
pages = {102797},
doi = {10.1016/j.jhevol.2020.102797},
pmid = {32371290},
issn = {1095-8606},
abstract = {Space use in Middle Paleolithic (MP) camps has been suggested as a source of information on the intensity and repetition of occupations and, by extension, of demographics. In the Levant, clear evidence for differential intrasite use and maintenance was important in viewing the late MP Neanderthal sites as base camps inhabited for a significant duration, relative to the Early MP (EMP). We test this model with the rich faunal assemblage from the EMP (>140 ka) site of Misliya Cave, Mount Carmel, Israel. Excavations in Misliya yielded a large and diverse lithic assemblage, combustion features, and a modern human maxilla, together with a large archaeofaunal assemblage that we use as a spatial marker. We analyzed the distribution of bone items with variable taphonomic properties (anthropogenic, biogenic, and abiotic bone-surface modifications) in a hearth-related context, both by comparing grid squares and point patterns. Both analyses are largely congruent. They indicate repeated and consistent use of the site's space that includes hearth-related consumption activities and peripheral activities further away, albeit with little evidence for site maintenance. Thus, the Misliya results display a mixed signal of clear around-the-fire pattern and differential space use in the EMP that is reminiscent of the much later MP sites in the Levant, but without the more elaborate camp maintenance. More case studies and detailed proxies are needed before we can fine-tune our understanding of camp structure in the Levantine MP and its bearing to site occupation dynamics.},
}

@article {pmid32356723,
year = {2020},
author = {Jordan, B},
title = {[Neandertal DNA in Africans].},
journal = {Medecine sciences : M/S},
volume = {36},
number = {4},
pages = {421-423},
doi = {10.1051/medsci/2020055},
pmid = {32356723},
issn = {1958-5381},
mesh = {Africa ; Animals ; DNA/analysis/*genetics ; Evolution, Molecular ; Genetics, Population ; Genome ; History, 21st Century ; History, Ancient ; Hominidae/classification/*genetics ; Humans ; Hybridization, Genetic ; Neanderthals/classification/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; },
abstract = {Sophisticated analyses of current human populations compared to a high-coverage Neandertal genome sequence indicate that, contrary to the previous consensus, African genomes carry a small but significant amount of Neandertal-specific DNA. This indicates back-migration into Africa of modern humans (carrying some Neandertal sequences) and underlines the complexity of ancient human migrations.},
}

Africa
Animals
DNA/analysis/*genetics
Evolution, Molecular
Genetics, Population
Genome
History, 21st Century
History, Ancient
Hominidae/classification/*genetics
Humans
Hybridization, Genetic
Neanderthals/classification/*genetics
Sequence Alignment
Sequence Homology, Nucleic Acid

@article {pmid32330268,
year = {2020},
author = {Lodewijk, GA and Fernandes, DP and Vretzakis, I and Savage, JE and Jacobs, FMJ},
title = {Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels.},
journal = {Molecular biology and evolution},
volume = {37},
number = {9},
pages = {2531-2548},
pmid = {32330268},
issn = {1537-1719},
abstract = {Ever since the availability of genomes from Neanderthals, Denisovans, and ancient humans, the field of evolutionary genomics has been searching for protein-coding variants that may hold clues to how our species evolved over the last ∼600,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive toward low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.},
}

@article {pmid32318238,
year = {2020},
author = {Zeng, Y and Pu, X and Du, J and Yang, X and Li, X and Mandal, MSN and Yang, T and Yang, J},
title = {Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases.},
journal = {Oxidative medicine and cellular longevity},
volume = {2020},
number = {},
pages = {3836172},
pmid = {32318238},
issn = {1942-0994},
abstract = {Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.},
}

@article {pmid32299352,
year = {2020},
author = {Moriano, J and Boeckx, C},
title = {Modern human changes in regulatory regions implicated in cortical development.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {304},
pmid = {32299352},
issn = {1471-2164},
support = {FFI2016-78034-C2-1-P//SpanishMinistry of Economy and Competitiveness/FEDER/ ; PIRG-GA-2009-256413//Marie Curie International Reintegration Grant/ ; Evolinguistics: JP17H06379//MEXT/JSPS/ ; -//Fundació Bosch i Gimpera (ES)/ ; 2017-SGR-341//Generalitat de Catalunya (ES)/ ; },
abstract = {BACKGROUND: Recent paleogenomic studies have highlighted a very small set of proteins carrying modern human-specific missense changes in comparison to our closest extinct relatives. Despite being frequently alluded to as highly relevant, species-specific differences in regulatory regions remain understudied. Here, we integrate data from paleogenomics, chromatin modification and physical interaction, and single-cell gene expression of neural progenitor cells to identify derived regulatory changes in the modern human lineage in comparison to Neanderthals/Denisovans. We report a set of genes whose enhancers and/or promoters harbor modern human single nucleotide changes and are active at early stages of cortical development.

RESULTS: We identified 212 genes controlled by regulatory regions harboring modern human changes where Neanderthals/Denisovans carry the ancestral allele. These regulatory regions significantly overlap with putative modern human positively-selected regions and schizophrenia-related genetic loci. Among the 212 genes, we identified a substantial proportion of genes related to transcriptional regulation and, specifically, an enrichment for the SETD1A histone methyltransferase complex, known to regulate WNT signaling for the generation and proliferation of intermediate progenitor cells.

CONCLUSIONS: This study complements previous research focused on protein-coding changes distinguishing our species from Neanderthals/Denisovans and highlights chromatin regulation as a functional category so far overlooked in modern human evolution studies. We present a set of candidates that will help to illuminate the investigation of modern human-specific ontogenetic trajectories.},
}

@article {pmid32285198,
year = {2020},
author = {Barreiro, LB and Quintana-Murci, L},
title = {Evolutionary and population (epi)genetics of immunity to infection.},
journal = {Human genetics},
volume = {139},
number = {6-7},
pages = {723-732},
pmid = {32285198},
issn = {1432-1203},
support = {ANR-10-LABX-69-01//ANR/ ; R01 GM115656/GM/NIGMS NIH HHS/United States ; R01-GM115656/GM/NIGMS NIH HHS/United States ; R01-GM134376/GM/NIGMS NIH HHS/United States ; R01 GM134376/GM/NIGMS NIH HHS/United States ; ANR-10- LABX-62-IBEID//ANR/ ; },
mesh = {Animals ; *Biological Evolution ; *Epigenesis, Genetic ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Humans ; Infections/epidemiology/genetics/*immunology ; Selection, Genetic ; },
abstract = {Immune response is one of the functions that have been more strongly targeted by natural selection during human evolution. The evolutionary genetic dissection of the immune system has greatly helped to distinguish genes and functions that are essential, redundant or advantageous for human survival. It is also becoming increasingly clear that admixture between early Eurasians with now-extinct hominins such as Neanderthals or Denisovans, or admixture between modern human populations, can be beneficial for human adaptation to pathogen pressures. In this review, we discuss how the integration of population genetics with functional genomics in diverse human populations can inform about the changes in immune functions related to major lifestyle transitions (e.g., from hunting and gathering to farming), the action of natural selection to the evolution of the immune system, and the history of past epidemics. We also highlight the need of expanding the characterization of the immune system to a larger array of human populations-particularly neglected human groups historically exposed to different pathogen pressures-to fully capture the relative contribution of genetic, epigenetic, and environmental factors to immune response variation in humans.},
}

Animals
*Biological Evolution
*Epigenesis, Genetic
*Genetic Variation
*Genetics, Population
*Genome, Human
Humans
Infections/epidemiology/genetics/*immunology
Selection, Genetic

@article {pmid32273518,
year = {2020},
author = {Hardy, BL and Moncel, MH and Kerfant, C and Lebon, M and Bellot-Gurlet, L and Mélard, N},
title = {Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {4889},
doi = {10.1038/s41598-020-61839-w},
pmid = {32273518},
issn = {2045-2322},
abstract = {Neanderthals are often considered as less technologically advanced than modern humans. However, we typically only find faunal remains or stone tools at Paleolithic sites. Perishable materials, comprising the vast majority of material culture items, are typically missing. Individual twisted fibres on stone tools from the Abri du Maras led to the hypothesis of Neanderthal string production in the past, but conclusive evidence was lacking. Here we show direct evidence of fibre technology in the form of a 3-ply cord fragment made from inner bark fibres on a stone tool recovered in situ from the same site. Twisted fibres provide the basis for clothing, rope, bags, nets, mats, boats, etc. which, once discovered, would have become an indispensable part of daily life. Understanding and use of twisted fibres implies the use of complex multi-component technology as well as a mathematical understanding of pairs, sets, and numbers. Added to recent evidence of birch bark tar, art, and shell beads, the idea that Neanderthals were cognitively inferior to modern humans is becoming increasingly untenable.},
}

@article {pmid32269345,
year = {2020},
author = {Welker, F and Ramos-Madrigal, J and Gutenbrunner, P and Mackie, M and Tiwary, S and Rakownikow Jersie-Christensen, R and Chiva, C and Dickinson, MR and Kuhlwilm, M and de Manuel, M and Gelabert, P and Martinón-Torres, M and Margvelashvili, A and Arsuaga, JL and Carbonell, E and Marques-Bonet, T and Penkman, K and Sabidó, E and Cox, J and Olsen, JV and Lordkipanidze, D and Racimo, F and Lalueza-Fox, C and Bermúdez de Castro, JM and Willerslev, E and Cappellini, E},
title = {The dental proteome of Homo antecessor.},
journal = {Nature},
volume = {580},
number = {7802},
pages = {235-238},
doi = {10.1038/s41586-020-2153-8},
pmid = {32269345},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Dental Enamel/*chemistry/*metabolism ; *Fossils ; Georgia (Republic) ; *Hominidae ; Humans ; Male ; Molar/chemistry/metabolism ; Neanderthals ; Phosphoproteins/analysis/chemistry/metabolism ; Phosphorylation ; Phylogeny ; Proteome/*analysis/chemistry/*metabolism ; Spain ; },
abstract = {The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1-5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6-8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.},
}

Amino Acid Sequence
Animals
Dental Enamel/*chemistry/*metabolism
*Fossils
Georgia (Republic)
*Hominidae
Humans
Male
Molar/chemistry/metabolism
Neanderthals
Phosphoproteins/analysis/chemistry/metabolism
Phosphorylation
Phylogeny
Proteome/*analysis/chemistry/*metabolism
Spain

@article {pmid32268436,
year = {2020},
author = {Merseburger, AS and Rüssel, C and Belz, H and Spiegelhalder, P and Feyerabend, S and Tran, N and Kruetzfeldt, K and Baurecht, W and Bögemann, M},
title = {[Early- vs. late-onset treatment using abiraterone acetate plus prednisone in chemo-naïve, asymptomatic or mildly symptomatic patients with metastatic CRPC after androgen deprivation therapy].},
journal = {Aktuelle Urologie},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-1121-7593},
pmid = {32268436},
issn = {1438-8820},
abstract = {BACKGROUND: Abiraterone acetate (AA) is a prodrug of abiraterone, which is an irreversible inhibitor of 17α-hydroxylase/C17, 20-lyase. Since 2011, abiraterone acetate has been available in combination with prednisone/prednisolone (AA + P) for the treatment of metastatic castration-resistant prostate cancer (mCRPC) after pre-treatment with docetaxel, and since 2012 for the treatment of chemotherapy-naïve asymptomatic or mildly symptomatic mCRPC patients. A revision of the guidelines of the European Association of Urology in 2014 redefining castration resistance gave rise to the question of when the treatment of mCRPC with abiraterone acetate plus prednisone should be initiated after prior hormone treatment and how successful it would be. This led us to observe an early-onset AA + P therapy cohort (EC) and a late-onset therapy cohort (LC) of patients.

PATIENTS AND METHODS: We designed a combined retrospective and prospective, multicentre, non-interventional two-cohort study to obtain data on the effectiveness and safety of an early-onset AA + P therapy in mCRPC patients in the clinical routine compared to a late therapy onset. The EC comprised patients who received AA + P immediately after castration resistance without a prior first-generation antiandrogen such as bicalutamide or flutamide. The LC included patients who, after castration resistance had occurred, started treatment with AA + P only after unsuccessful treatment with a first-generation antiandrogen. Patients with mCRPC who received AA + P therapy according to the physician's routine clinical practice decision were considered. The patients were consecutively included in the study on the basis of their medical records, with the treatment decision having been made independently of and before patient enrolment. Patients were documented or followed from the beginning of AA + P therapy until the start of a carcinoma-specific systemic follow-up therapy (retrospectively if before and prospectively if after start of data collection). Effectiveness analyses were done for all patients with at least two AA + P administrations and safety analyses for all treated patients.

RESULTS: Of the 159 patients included, 44 received early therapy and 105 received later therapy with AA + P. 10 patients could not be clearly assigned and were summarised in a third cohort (missed early-onset therapy assignment; MEC). 56/159 patients (35.2 %) were still alive at study start and 103/159 patients (64.8 %) had already deceased (31/44 [70.5 %] in EC, 64/105 [61.0 %] in LC, and 8/10 [80.0 %] in MEC). 24/159 patients (15.1 %) were documented both retrospectively and prospectively. The median duration of AA + P treatment was 11.3 months for EC, 12.0 months for LC, and 8.3 months for MEC patients. The median time to next systemic cancer therapy or death was 12.3 months for EC and 12.8 months for LC patients (p = 0.2820). The median time to the next systemic cancer therapy alone (i. e. without the event 'death') was 22.7 months for EC and 23.3 months for LC patients (p = 0.5995). Median overall survival (OS) was 22.3 months for EC and 39.2 months for LC patients (p = 0.0232). The incidence of serious adverse events (SAEs) was low. SAEs occurred in 3/44 EC (6.8 %), 4/105 LC (3.8 %), and 1/10 MEC patients (10.0 %). One SAE in EC and one in LC resulted in death.

CONCLUSIONS: In contrast to the new definition of castration resistance, AA + P was still more frequently used in daily clinical practice during the study observation period in patients treated with antiandrogens of the first generation after occurrence of castration resistance. Nevertheless, AA + P therapy appears to be effective and well tolerated during clinical routine in mCRPC patients. A comparison of the study results with earlier 'real-world' studies, however, has to take limiting factors into account. The observed difference in median overall survival might be explained by the imbalance of baseline characteristics between both cohorts with regard to number of patients, patients already deceased at start of documentation, patients with visceral metastases and patients with opioids at start of AA + P. For these reasons, patients in the EC initially might have had a poorer prognosis. A prospective randomised and controlled clinical trial would therefore be necessary to assess a possible difference in overall survival and response of the AA + P treatment with respect to therapy onset.},
}

@article {pmid32247528,
year = {2020},
author = {Grimaud-Hervé, D and Albessard-Ball, L and Pokhojaev, A and Balzeau, A and Sarig, R and Latimer, B and McDermott, Y and May, H and Hershkovitz, I},
title = {The endocast of the late Middle Paleolithic Manot 1 specimen, Western Galilee, Israel.},
journal = {Journal of human evolution},
volume = {},
number = {},
pages = {102734},
doi = {10.1016/j.jhevol.2019.102734},
pmid = {32247528},
issn = {1095-8606},
abstract = {Studying endocasts has long allowed anthropologists to examine changes in the external topography and the overall size of the brain throughout the evolutionary history of hominins. The nearly complete calvaria of Manot 1 presents an opportunity to gain insights into the external brain morphology, vascular system, and dimensions of the brain of this late Middle Paleolithic hominin. Detailed size and shape analyses of the Manot 1 endocast indicate a modern Homo sapiens anatomy, despite the presence of some primitive features of the calvaria. Traits considered to be derived endocranial features for H. sapiens are present in Manot 1, including an elongated parietal sagittal chord with an elevated superior part of the hemisphere, a widened posterior part of the frontal lobes, a considerable development of the parietal reliefs such as the supramarginal lobules, and a slight posterior projection of the occipital lobes. These findings, together with data presented in previous studies, rule out the possibility of a direct Neanderthal ancestry for the Manot 1 hominin and instead confirm its affiliation with H. sapiens. The Manot 1 calvaria is more similar to that of later Upper Paleolithic H. sapiens than it is to the earlier Levantine populations of Skhul and Qafzeh. The late Middle Paleolithic date of Manot 1 provides an opportunity to analyze the recent developments in human cerebral morphology and organization.},
}

@article {pmid32247107,
year = {2020},
author = {Pereira-Pedro, AS and Bruner, E and Gunz, P and Neubauer, S},
title = {A morphometric comparison of the parietal lobe in modern humans and Neanderthals.},
journal = {Journal of human evolution},
volume = {142},
number = {},
pages = {102770},
doi = {10.1016/j.jhevol.2020.102770},
pmid = {32247107},
issn = {1095-8606},
abstract = {The modern human brain and braincase have a characteristic globular shape including parietal and cerebellar bulging. In contrast, Neanderthals, although having similar endocranial volume, displayed more elongated endocrania with flatter parietal and cerebellar regions. Based on endocranial imprints, we compare the parietal lobe morphology of modern humans and Neanderthals, as this brain region is central to several cognitive functions including tool use and visual imaging. In paleoneurology, shape analyses of endocasts are based either on anatomical landmarks that represent endocranial surface features homologous to cortical convolutions (impressions of brain gyri and sulci) or on dense meshes of semilandmarks that capture overall endocranial shape. Previous analyses using the former suggested that modern humans have relatively longer and taller parietal lobes than extinct human species, while the latter emphasized parietal bulging without a significant size difference of parietal regions. In the present study, we combine both anatomical landmarks and surface semilandmarks to investigate the morphological differences of the parietal lobes between modern humans and Neanderthals. Despite limitations by landmark uncertainty, our analyses were able to detect and confirm average different parietal shapes, with modern humans displaying taller and anteroposteriorly extended parietal lobes. We also show mean size differences, with modern humans displaying slightly larger surface areas on the dorsal posterior parietal region, and on a lateral region comprising the supramarginal gyrus, angular gyrus, and intraparietal sulcus. While we observed average differences in the parietal form between the two species, their ranges of distribution overlap, indicating the differences could be a matter of degree. Thus, further analyses on intraspecific variation in parietal lobe morphology within modern human brains should help understand the differences between globular and elongated endocrania. This is crucial because changes to the parietal cortex might affect associative and integrative functions between somatic and visual primary inputs.},
}

@article {pmid32234956,
year = {2020},
author = {Taskent, O and Lin, YL and Patramanis, I and Pavlidis, P and Gokcumen, O},
title = {Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage.},
journal = {Genetics},
volume = {215},
number = {2},
pages = {497-509},
pmid = {32234956},
issn = {1943-2631},
abstract = {The time, extent, and genomic effect of the introgressions from archaic humans into ancestors of extant human populations remain some of the most exciting venues of population genetics research in the past decade. Several studies have shown population-specific signatures of introgression events from Neanderthals, Denisovans, and potentially other unknown hominin populations in different human groups. Moreover, it was shown that these introgression events may have contributed to phenotypic variation in extant humans, with biomedical and evolutionary consequences. In this study, we present a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and show that they can be traced back to multiple introgression events. In parallel, we document hundreds of deletion polymorphisms shared with Neanderthals. A locus-specific analysis of one such shared deletion suggests the existence of a direct introgression event from the Altai Neanderthal lineage into the ancestors of extant East Asian populations. Overall, our study is in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.},
}

@article {pmid32217711,
year = {2020},
author = {Will, M},
title = {Neanderthal surf and turf.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6485},
pages = {1422-1423},
doi = {10.1126/science.abb3568},
pmid = {32217711},
issn = {1095-9203},
mesh = {Animals ; Fossils ; *Hominidae ; *Neanderthals ; },
}

Animals
Fossils
*Hominidae
*Neanderthals

@article {pmid32217702,
year = {2020},
author = {Zilhão, J and Angelucci, DE and Igreja, MA and Arnold, LJ and Badal, E and Callapez, P and Cardoso, JL and d'Errico, F and Daura, J and Demuro, M and Deschamps, M and Dupont, C and Gabriel, S and Hoffmann, DL and Legoinha, P and Matias, H and Monge Soares, AM and Nabais, M and Portela, P and Queffelec, A and Rodrigues, F and Souto, P},
title = {Last Interglacial Iberian Neandertals as fisher-hunter-gatherers.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6485},
pages = {},
doi = {10.1126/science.aaz7943},
pmid = {32217702},
issn = {1095-9203},
mesh = {Animal Shells ; Animals ; Archaeology ; Atlantic Ocean ; Birds ; Caves ; *Diet ; Fishes ; Mammals ; *Neanderthals ; Nuts ; Pinus ; Portugal ; Seafood ; Turtles ; },
abstract = {Marine food-reliant subsistence systems such as those in the African Middle Stone Age (MSA) were not thought to exist in Europe until the much later Mesolithic. Whether this apparent lag reflects taphonomic biases or behavioral distinctions between archaic and modern humans remains much debated. Figueira Brava cave, in the Arrábida range (Portugal), provides an exceptionally well preserved record of Neandertal coastal resource exploitation on a comparable scale to the MSA and dated to ~86 to 106 thousand years ago. The breadth of the subsistence base-pine nuts, marine invertebrates, fish, marine birds and mammals, tortoises, waterfowl, and hoofed game-exceeds that of regional early Holocene sites. Fisher-hunter-gatherer economies are not the preserve of anatomically modern people; by the Last Interglacial, they were in place across the Old World in the appropriate settings.},
}

Animal Shells
Animals
Archaeology
Atlantic Ocean
Birds
Caves
*Diet
Fishes
Mammals
*Neanderthals
Nuts
Pinus
Portugal
Seafood
Turtles

@article {pmid32199301,
year = {2020},
author = {Hunt, KD},
title = {Obituary of Charles Loring Brace, IV (1930-2019).},
journal = {Journal of human evolution},
volume = {142},
number = {},
pages = {102743},
doi = {10.1016/j.jhevol.2020.102743},
pmid = {32199301},
issn = {1095-8606},
}

@article {pmid32193295,
year = {2020},
author = {Bergström, A and McCarthy, SA and Hui, R and Almarri, MA and Ayub, Q and Danecek, P and Chen, Y and Felkel, S and Hallast, P and Kamm, J and Blanché, H and Deleuze, JF and Cann, H and Mallick, S and Reich, D and Sandhu, MS and Skoglund, P and Scally, A and Xue, Y and Durbin, R and Tyler-Smith, C},
title = {Insights into human genetic variation and population history from 929 diverse genomes.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6484},
pages = {},
pmid = {32193295},
issn = {1095-9203},
support = {FC001595/MRC_/Medical Research Council/United Kingdom ; /ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; 206194/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; //Medical Research Council,/International ; 207492/WT_/Wellcome Trust/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Africa ; Americas ; Animals ; Asia ; Continental Population Groups/genetics ; DNA Copy Number Variations ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Haplotypes ; Hominidae/genetics ; Humans ; INDEL Mutation ; Neanderthals/genetics ; Oceania ; Phylogeny ; Polymorphism, Single Nucleotide ; Population Density ; *Whole Genome Sequencing ; },
abstract = {Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.},
}

Africa
Americas
Animals
Asia
Continental Population Groups/genetics
DNA Copy Number Variations
*Genetic Variation
*Genetics, Population
*Genome, Human
Haplotypes
Hominidae/genetics
Humans
INDEL Mutation
Neanderthals/genetics
Oceania
Phylogeny
Polymorphism, Single Nucleotide
Population Density
*Whole Genome Sequencing

@article {pmid32170098,
year = {2020},
author = {Modesto-Mata, M and Dean, MC and Lacruz, RS and Bromage, TG and García-Campos, C and Martínez de Pinillos, M and Martín-Francés, L and Martinón-Torres, M and Carbonell, E and Arsuaga, JL and Bermúdez de Castro, JM},
title = {Short and long period growth markers of enamel formation distinguish European Pleistocene hominins.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {4665},
pmid = {32170098},
issn = {2045-2322},
abstract = {Characterizing dental development in fossil hominins is important for distinguishing between them and for establishing where and when the slow overall growth and development of modern humans appeared. Dental development of australopiths and early Homo was faster than modern humans. The Atapuerca fossils (Spain) fill a barely known gap in human evolution, spanning ~1.2 to ~0.4 million years (Ma), during which H. sapiens and Neandertal dental growth characteristics may have developed. We report here perikymata counts, perikymata distributions and periodicities of all teeth belonging to the TE9 level of Sima del Elefante, level TD6.2 of Gran Dolina (H. antecessor) and Sima de los Huesos. We found some components of dental growth in the Atapuerca fossils resembled more recent H. sapiens. Mosaic evolution of perikymata counts and distribution generate three distinct clusters: H. antecessor, Sima de los Huesos and H. sapiens.},
}

@article {pmid32163763,
year = {2020},
author = {Belcastro, MG and Mariotti, V and Pietrobelli, A and Sorrentino, R and García-Tabernero, A and Estalrrich, A and Rosas, A},
title = {The study of the lower limb entheses in the Neanderthal sample from El Sidrón (Asturias, Spain): How much musculoskeletal variability did Neanderthals accumulate?.},
journal = {Journal of human evolution},
volume = {141},
number = {},
pages = {102746},
doi = {10.1016/j.jhevol.2020.102746},
pmid = {32163763},
issn = {1095-8606},
abstract = {Entheses have rarely been systematically studied in the field of human evolution. However, the investigation of their morphological variability (e.g., robusticity) could provide new insight into their evolutionary significance in the European Neanderthal populations. The aim of this work is to study the entheses and joint features of the lower limbs of El Sidrón Neanderthals (Spain; 49 ka), using standardized scoring methods developed on modern samples. Paleobiology, growth, and development of both juveniles and adults from El Sidrón are studied and compared with those of Krapina Neanderthals (Croatia, 130 ka) and extant humans. The morphological patterns of the gluteus maximus and vastus intermedius entheses in El Sidrón, Krapina, and modern humans differ from one another. Both Neanderthal groups show a definite enthesis design for the gluteus maximus, with little intrapopulation variability with respect to modern humans, who are characterized by a wider range of morphological variability. The gluteus maximus enthesis in the El Sidrón sample shows the osseous features of fibrous entheses, as in modern humans, whereas the Krapina sample shows the aspects of fibrocartilaginous ones. The morphology and anatomical pattern of this enthesis has already been established during growth in all three human groups. One of two and three of five adult femurs from El Sidrón and from Krapina, respectively, show the imprint of the vastus intermedius, which is absent among juveniles from those Neanderthal samples and in modern samples. The scant intrapopulation and the high interpopulation variability in the two Neanderthal samples is likely due to a long-term history of small, isolated populations with high levels of inbreeding, who also lived in different ecological conditions. The comparison of different anatomical entheseal patterns (fibrous vs. fibrocartilaginous) in the Neanderthals and modern humans provides additional elements in the discussion of their functional and genetic origin.},
}

@article {pmid32146203,
year = {2020},
author = {Rosas, A and Losada Agustina, B and García-Martínez, D and Torres-Tamayo, N and García-Tabernero, A and Pastor, JF and Rasilla, M and Bastir, M},
title = {Analyses of the neandertal patellae from El Sidrón (Asturias, Spain) with implications for the evolution of body form in Homo.},
journal = {Journal of human evolution},
volume = {141},
number = {},
pages = {102738},
doi = {10.1016/j.jhevol.2019.102738},
pmid = {32146203},
issn = {1095-8606},
abstract = {The evolution of the body form in Homo and its potential morphological connection to the arrangement of different skeletal systems is of major interest in human evolution. Patella morphology as part of the knee is potentially influenced by body form. Here, we describe for the first time the patellae remains recovered at El Sidrón Neandertal site and analyze them in a comparative evolutionary framework. We aim to clarify whether morphometric features frequently observed in Neandertal and modern human patellae are retained from a primitive anatomical arrangement or whether they represent derived features (apomorphies). For this purpose, we combine analyses of discrete features, classic anthropological measurements, and 3D geometric morphometrics based on generalized Procrustes analysis, mean size and shape comparisons, and principal components analysis. We found a size increment of the patella in hominin evolution, with large species showing a larger patella. Modern humans and Neandertals exhibit overall larger patellae, with maximum values observed in the latter, likely as a consequence of their broader body shape. Also, some Neandertals display a thicker patella, which has been linked to larger quadriceps muscles. However, Neandertals retain a primitive morphology in their patellar articular surfaces, with similar-sized lateral and medial articular facets, leading to a more symmetrical internal face. This feature is inherited from a primitive Homo ancestor and suggests a different configuration of the knee in Neandertals. Conversely, Homo sapiens exhibits an autoapomorphic patellar anatomy with expanded lateral articular facets. We propose that these distinct configurations of the patella within Homo may be a consequence of different body forms rather than specific functional adaptations of the knee. Thus, the slender body form of modern humans may entail a medial reorientation of the tibial tuberosity (patellar ligament), allowing lateral surface expansion. These anatomical evolutionary variations may involve subtle secondary differences in bipedalism within Homo.},
}

@article {pmid32132541,
year = {2020},
author = {Gokhman, D and Nissim-Rafinia, M and Agranat-Tamir, L and Housman, G and García-Pérez, R and Lizano, E and Cheronet, O and Mallick, S and Nieves-Colón, MA and Li, H and Alpaslan-Roodenberg, S and Novak, M and Gu, H and Osinski, JM and Ferrando-Bernal, M and Gelabert, P and Lipende, I and Mjungu, D and Kondova, I and Bontrop, R and Kullmer, O and Weber, G and Shahar, T and Dvir-Ginzberg, M and Faerman, M and Quillen, EE and Meissner, A and Lahav, Y and Kandel, L and Liebergall, M and Prada, ME and Vidal, JM and Gronostajski, RM and Stone, AC and Yakir, B and Lalueza-Fox, C and Pinhasi, R and Reich, D and Marques-Bonet, T and Meshorer, E and Carmel, L},
title = {Differential DNA methylation of vocal and facial anatomy genes in modern humans.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {1189},
pmid = {32132541},
issn = {2041-1723},
support = {U01 MH106874/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adult ; Aged ; Animals ; Cells, Cultured ; Child ; Chondrocytes ; *DNA Methylation ; *DNA, Ancient ; Evolution, Molecular ; Face/*anatomy & histology ; Female ; Gene Regulatory Networks ; Genetic Speciation ; Humans ; Larynx/anatomy & histology ; Male ; Middle Aged ; Neanderthals/genetics ; Pan troglodytes/genetics ; *Phenotype ; Phonation/*genetics ; Primary Cell Culture ; Tongue/anatomy & histology ; Vocal Cords/anatomy & histology ; Vocalization, Animal ; },
abstract = {Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.},
}

Adult
Aged
Animals
Cells, Cultured
Child
Chondrocytes
*DNA Methylation
*DNA, Ancient
Evolution, Molecular
Face/*anatomy & histology
Female
Gene Regulatory Networks
Genetic Speciation
Humans
Larynx/anatomy & histology
Male
Middle Aged
Neanderthals/genetics
Pan troglodytes/genetics
*Phenotype
Phonation/*genetics
Primary Cell Culture
Tongue/anatomy & histology
Vocal Cords/anatomy & histology
Vocalization, Animal

@article {pmid32128408,
year = {2020},
author = {Rogers, AR and Harris, NS and Achenbach, AA},
title = {Neanderthal-Denisovan ancestors interbred with a distantly related hominin.},
journal = {Science advances},
volume = {6},
number = {8},
pages = {eaay5483},
pmid = {32128408},
issn = {2375-2548},
abstract = {Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans.},
}

@article {pmid32099103,
year = {2020},
author = {Willson, J},
title = {There and back again - ancient genes reveal early migrations.},
journal = {Nature reviews. Genetics},
volume = {21},
number = {4},
pages = {205},
doi = {10.1038/s41576-020-0222-3},
pmid = {32099103},
issn = {1471-0064},
mesh = {DNA, Mitochondrial ; Human Migration ; Humans ; *Neanderthals ; },
}

DNA, Mitochondrial
Human Migration
Humans
*Neanderthals

@article {pmid32095519,
year = {2020},
author = {Durvasula, A and Sankararaman, S},
title = {Recovering signals of ghost archaic introgression in African populations.},
journal = {Science advances},
volume = {6},
number = {7},
pages = {eaax5097},
pmid = {32095519},
issn = {2375-2548},
support = {R35 GM125055/GM/NIGMS NIH HHS/United States ; R00 GM111744/GM/NIGMS NIH HHS/United States ; },
abstract = {While introgression from Neanderthals and Denisovans has been documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations.},
}

@article {pmid32078934,
year = {2020},
author = {Moncel, MH and Ashton, N and Arzarello, M and Fontana, F and Lamotte, A and Scott, B and Muttillo, B and Berruti, G and Nenzioni, G and Tuffreau, A and Peretto, C},
title = {Early Levallois core technology between Marine Isotope Stage 12 and 9 in Western Europe.},
journal = {Journal of human evolution},
volume = {139},
number = {},
pages = {102735},
doi = {10.1016/j.jhevol.2019.102735},
pmid = {32078934},
issn = {1095-8606},
mesh = {Animals ; Archaeology ; *Biological Evolution ; France ; *Hominidae ; Italy ; Neanderthals ; *Technology ; United Kingdom ; },
abstract = {Early Levallois core technology is usually dated in Europe to the end of Marine Isotope Stage (MIS) 9 and particularly from the beginning of MIS 8 to MIS 6. This technology is considered as one of the markers of the transition from lower to Middle Paleolithic or from Mode 2 to Mode 3. Recent discoveries show that some lithic innovations actually appeared earlier in western Europe, from MIS 12 to MIS 9, contemporaneous with changes in subsistence strategies and the first appearance of early Neanderthal anatomical features. Among these discoveries, there is the iconic Levallois core technology. A selection of well-dated assemblages in the United Kingdom, France, and Italy dated from MIS 12 to 9, which include both cores and flakes with Levallois features, has been described and compared with the aim of characterizing this technology. The conclusion supports the interpretation that several technical features may be attributed to a Levallois technology similar to those observed in younger Middle Paleolithic sites, distinct from the main associated core technologies in each level. Some features in the sample of sites suggest a gradual transformation of existing core technologies. The small evidence of Levallois could indicate occasional local innovations from different technological backgrounds and would explain the diversity of Levallois methods that is observed from MIS 12. The technological roots of Levallois technology in the Middle Pleistocene would suggest a multiregional origin and diffusion in Europe and early evidence of regionalization of local traditions through Europe from MIS 12 to 9. The relationships of Levallois technology with new needs and behaviors are discussed, such as flake preference, functional reasons related to hunting and hafting, an increase in the use of mental templates in European populations, and changes in the structure of hominin groups adapting to climatic and environmental changes.},
}

Animals
Archaeology
*Biological Evolution
France
*Hominidae
Italy
Neanderthals
*Technology
United Kingdom

@article {pmid32062432,
year = {2020},
author = {Weissbrod, L and Weinstein-Evron, M},
title = {Climate variability in early expansions of Homo sapiens in light of the new record of micromammals in Misliya Cave, Israel.},
journal = {Journal of human evolution},
volume = {139},
number = {},
pages = {102741},
doi = {10.1016/j.jhevol.2020.102741},
pmid = {32062432},
issn = {1095-8606},
mesh = {Animals ; *Biological Evolution ; Caves ; *Climate ; Climate Change ; Fossils ; *Human Migration ; Humans ; Israel ; Mammals ; Neanderthals ; },
abstract = {In this study, we provide the first taphonomic and taxonomic descriptions of the micromammals from Misliya Cave, where recently a Homo sapiens hemimaxilla has been reported. This finding significantly extends the time frame for the out-of-Africa presence of anatomically modern humans. It also provides an opportunity to reassess variation in early modern human population responses to climate change in the Levantine sequence. Information on species ranking and diversity estimations (Shannon functions) is obtained from quantitative data across 31 Levantine assemblages and investigated in a broad comparative frame using multivariate analyses. Recent models of human-climate interactions in the late Early-Middle Paleolithic of the southern Levant have drawn heavily on on-site associations of human fossils with remains of micromammals. However, there has been little, if any, attempt to examine the long-term picture of how paleocommunities of micromammals responded qualitatively and quantitatively to climatic oscillations of the region by altering their compositional complexity. Consequently, our understanding is vastly limited in regard to the paleoecosystem functions that linked past precipitation shifts to changes in primary producers and consumers or as to the background climatic conditions that allowed for the development of highly nonanalog ancient communities in the region. Although previous studies argued for a correspondence between alternations in H. sapiens and Neanderthal occupations of the Levant and faunal shifts in key biostratigraphic indicator taxa (such as Euro-Siberian Ellobius versus Saharo-Arabian Mastomys and Arvicanthis), our data indicate the likelihood that early H. sapiens populations (Misliya and Qafzeh hominins) persisted through high amplitudes of paleoecological and climatic oscillations. It is unlikely, given these results, that climate functioned as a significant filter of early modern human persistence and genetic interactions with Neanderthals in the Levant.},
}

Animals
*Biological Evolution
Caves
*Climate
Climate Change
Fossils
*Human Migration
Humans
Israel
Mammals
Neanderthals

@article {pmid32062431,
year = {2020},
author = {Meignen, L and Bar-Yosef, O},
title = {Acheulo-Yabrudian and Early Middle Paleolithic at Hayonim Cave (Western Galilee, Israel): Continuity or break?.},
journal = {Journal of human evolution},
volume = {139},
number = {},
pages = {102733},
doi = {10.1016/j.jhevol.2019.102733},
pmid = {32062431},
issn = {1095-8606},
mesh = {Animals ; Archaeology ; *Biological Evolution ; Caves ; *Hominidae ; Israel ; Neanderthals ; *Technology ; },
abstract = {The long archeological sequence exposed during our renewed excavations in Hayonim Cave sheds new light on the striking technological changes observed at the boundary between the Acheulo-Yabrudian (end of the Lower Paleolithic) and Early Middle Paleolithic in the Levant, as well as on their meaning in terms of population movements. The recent, as yet unpublished, technological studies highlight a clear technological break between these two entities. In Hayonim, the Acheulo-Yabrudian assemblages found at the bottom of the archeological sequence display the specific combination of bifacial shaping and the production of thick, often cortical, flakes frequently shaped into scrapers by Quina retouch. Neither of these lithic production systems is observed in the succeeding Levantine Middle Paleolithic assemblages. In contrast, the Early Middle Paleolithic is characterized by the expansion and diversification of the Levallois production system in its full-fledged form, the emergence of a specific Laminar technology, and a high proportion of retouched tools made on elongated blanks (points and blades). These technological features are unknown in the previous Acheulo-Yabrudian assemblages in the cave. Based on this information, we attempt to determine if the observed changes in stone tool production strategies resulted from an autochthonous development or a dispersal out of Africa.},
}

Animals
Archaeology
*Biological Evolution
Caves
*Hominidae
Israel
Neanderthals
*Technology

@article {pmid32047045,
year = {2020},
author = {Schmidt, P and Rageot, M and Blessing, M and Tennie, C},
title = {The Zandmotor data do not resolve the question whether Middle Paleolithic birch tar making was complex or not.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {9},
pages = {4456-4457},
pmid = {32047045},
issn = {1091-6490},
mesh = {Archaeology ; Betula ; Humans ; *Neanderthals ; North Sea ; Technology ; },
}

Archaeology
Betula
Humans
*Neanderthals
North Sea
Technology

@article {pmid32047044,
year = {2020},
author = {Kozowyk, PRB and Langejans, GHJ and Dusseldorp, GL and Niekus, MJLT},
title = {Reply to Schmidt et al.: Interpretation of Paleolithic adhesive production: Combining experimental and paleoenvironmental information.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {9},
pages = {4458-4459},
pmid = {32047044},
issn = {1091-6490},
mesh = {Adhesives ; Archaeology ; *Neanderthals ; North Sea ; Technology ; },
}

Adhesives
Archaeology
*Neanderthals
North Sea
Technology

@article {pmid32031468,
year = {2020},
author = {Le Tortorec, A and Matusali, G and Mahé, D and Aubry, F and Mazaud-Guittot, S and Houzet, L and Dejucq-Rainsford, N},
title = {From Ancient to Emerging Infections: The Odyssey of Viruses in the Male Genital Tract.},
journal = {Physiological reviews},
volume = {100},
number = {3},
pages = {1349-1414},
doi = {10.1152/physrev.00021.2019},
pmid = {32031468},
issn = {1522-1210},
mesh = {Communicable Diseases, Emerging/*virology ; Genitalia, Male/*virology ; Humans ; Male ; Virus Diseases/pathology/*virology ; },
abstract = {The male genital tract (MGT) is the target of a number of viral infections that can have deleterious consequences at the individual, offspring, and population levels. These consequences include infertility, cancers of male organs, transmission to the embryo/fetal development abnormalities, and sexual dissemination of major viral pathogens such as human immunodeficiency virus (HIV) and hepatitis B virus. Lately, two emerging viruses, Zika and Ebola, have additionally revealed that the human MGT can constitute a reservoir for viruses cleared from peripheral circulation by the immune system, leading to their sexual transmission by cured men. This represents a concern for future epidemics and further underlines the need for a better understanding of the interplay between viruses and the MGT. We review here how viruses, from ancient viruses that integrated the germline during evolution through old viruses (e.g., papillomaviruses originating from Neanderthals) and more modern sexually transmitted infections (e.g., simian zoonotic HIV) to emerging viruses (e.g., Ebola and Zika) take advantage of genital tract colonization for horizontal dissemination, viral persistence, vertical transmission, and endogenization. The MGT immune responses to viruses and the impact of these infections are discussed. We summarize the latest data regarding the sources of viruses in semen and the complex role of this body fluid in sexual transmission. Finally, we introduce key animal findings that are relevant for our understanding of viral infection and persistence in the human MGT and suggest future research directions.},
}

Communicable Diseases, Emerging/*virology
Genitalia, Male/*virology
Humans
Male
Virus Diseases/pathology/*virology

@article {pmid32004458,
year = {2020},
author = {Chen, L and Wolf, AB and Fu, W and Li, L and Akey, JM},
title = {Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.},
journal = {Cell},
volume = {180},
number = {4},
pages = {677-687.e16},
doi = {10.1016/j.cell.2020.01.012},
pmid = {32004458},
issn = {1097-4172},
support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; },
mesh = {African Continental Ancestry Group/*genetics ; Animals ; *Evolution, Molecular ; Gene Flow ; Human Migration ; Humans ; Models, Genetic ; Neanderthals/*genetics ; Pedigree ; Polymorphism, Genetic ; },
abstract = {Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.},
}

African Continental Ancestry Group/*genetics
Animals
*Evolution, Molecular
Gene Flow
Human Migration
Humans
Models, Genetic
Neanderthals/*genetics
Pedigree
Polymorphism, Genetic

@article {pmid32001636,
year = {2020},
author = {Price, M},
title = {Africans, too, carry Neanderthal genetic legacy.},
journal = {Science (New York, N.Y.)},
volume = {367},
number = {6477},
pages = {497},
doi = {10.1126/science.367.6477.497},
pmid = {32001636},
issn = {1095-9203},
mesh = {Africa ; African Continental Ancestry Group/*genetics ; Animals ; Europe ; Fossils ; *Gene Flow ; Humans ; Neanderthals/*genetics ; },
}

Africa
African Continental Ancestry Group/*genetics
Animals
Europe
Fossils
*Gene Flow
Humans
Neanderthals/*genetics

@article {pmid31988114,
year = {2020},
author = {Kolobova, KA and Roberts, RG and Chabai, VP and Jacobs, Z and Krajcarz, MT and Shalagina, AV and Krivoshapkin, AI and Li, B and Uthmeier, T and Markin, SV and Morley, MW and O'Gorman, K and Rudaya, NA and Talamo, S and Viola, B and Derevianko, AP},
title = {Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {6},
pages = {2879-2885},
pmid = {31988114},
issn = {1091-6490},
mesh = {Animals ; *Archaeology ; Caves ; Fossils/history ; History, Ancient ; Neanderthals/*genetics ; Siberia ; },
abstract = {Neanderthals were once widespread across Europe and western Asia. They also penetrated into the Altai Mountains of southern Siberia, but the geographical origin of these populations and the timing of their dispersal have remained elusive. Here we describe an archaeological assemblage from Chagyrskaya Cave, situated in the Altai foothills, where around 90,000 Middle Paleolithic artifacts and 74 Neanderthal remains have been recovered from deposits dating to between 59 and 49 thousand years ago (age range at 95.4% probability). Environmental reconstructions suggest that the Chagyrskaya hominins were adapted to the dry steppe and hunted bison. Their distinctive toolkit closely resembles Micoquian assemblages from central and eastern Europe, including the northern Caucasus, more than 3,000 kilometers to the west of Chagyrskaya Cave. At other Altai sites, evidence of earlier Neanderthal populations lacking associated Micoquian-like artifacts implies two or more Neanderthal incursions into this region. We identify eastern Europe as the most probable ancestral source region for the Chagyrskaya toolmakers, supported by DNA results linking the Neanderthal remains with populations in northern Croatia and the northern Caucasus, and providing a rare example of a long-distance, intercontinental population movement associated with a distinctive Paleolithic toolkit.},
}

Animals
*Archaeology
Caves
Fossils/history
History, Ancient
Neanderthals/*genetics
Siberia