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31 Jul 2021 at 01:49
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Bibliography on: Neanderthals


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Wikipedia: Neanderthals or Neandertals — named for the Neandertal region in Germany — were a species or subspecies of archaic human, in the genus Homo. Neanderthals became extinct around 40,000 years ago. They were closely related to modern humans, sharing 99.7% of DNA. Remains left by Neanderthals include bone and stone tools, which are found in Eurasia, from Western Europe to Central and Northern Asia. Neanderthals are generally classified by paleontologists as the species Homo neanderthalensis, having separated from the Homo sapiens lineage 600,000 years ago, but a minority consider them to be a subspecies of Homo sapiens (Homo sapiens neanderthalensis). Several cultural assemblages have been linked to the Neanderthals in Europe. The earliest, the Mousterian stone tool culture, dates to about 160,000 years ago. Late Mousterian artifacts were found in Gorham's Cave on the south-facing coast of Gibraltar. Compared to Homo sapiens, Neanderthals had a lower surface-to-volume ratio, with shorter legs and a bigger body, in conformance with Bergmann's rule, as an energy-loss reduction adaptation to life in a high-latitude (i.e. seasonally cold) climate. Their average cranial capacity was notably larger than typical for modern humans: 1600 cm3 vs. 1250-1400 cm3. The Neanderthal genome project published papers in 2010 and 2014 stating that Neanderthals contributed to the DNA of modern humans, including most humans outside sub-Saharan Africa, as well as a few populations in sub-Saharan Africa, through interbreeding, likely between 50,000 and 60,000 years ago.

Created with PubMed® Query: Neanderthal OR Neandertal NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2021-07-28

Condemi S, Mazières S, Faux P, et al (2021)

Blood groups of Neandertals and Denisova decrypted.

PloS one, 16(7):e0254175 pii:PONE-D-20-40264.

Blood group systems were the first phenotypic markers used in anthropology to decipher the origin of populations, their migratory movements, and their admixture. The recent emergence of new technologies based on the decoding of nucleic acids from an individual's entire genome has relegated them to their primary application, blood transfusion. Thus, despite the finer mapping of the modern human genome in relation to Neanderthal and Denisova populations, little is known about red cell blood groups in these archaic populations. Here we analyze the available high-quality sequences of three Neanderthals and one Denisovan individuals for 7 blood group systems that are used today in transfusion (ABO including H/Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, Diego). We show that Neanderthal and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing from viral gut infection and Neanderthal RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to low reproductive success and with their inevitable demise. Lastly, we connect a Neanderthal RHD allele to two present-day Aboriginal Australian and Papuan, suggesting that a segment of archaic genome was introgressed in this gene in non-Eurasian populations. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems are a relevant piece of the puzzle helping to decipher it.

RevDate: 2021-07-27

Alcaraz-Castaño M, Alcolea-González JJ, de Andrés-Herrero M, et al (2021)

First modern human settlement recorded in the Iberian hinterland occurred during Heinrich Stadial 2 within harsh environmental conditions.

Scientific reports, 11(1):15161.

As the south-westernmost region of Europe, the Iberian Peninsula stands as a key area for understanding the process of modern human dispersal into Eurasia. However, the precise timing, ecological setting and cultural context of this process remains controversial concerning its spatiotemporal distribution within the different regions of the peninsula. While traditional models assumed that the whole Iberian hinterland was avoided by modern humans due to ecological factors until the retreat of the Last Glacial Maximum, recent research has demonstrated that hunter-gatherers entered the Iberian interior at least during Solutrean times. We provide a multi-proxy geoarchaeological, chronometric and paleoecological study on human-environment interactions based on the key site of Peña Capón (Guadalajara, Spain). Results show (1) that this site hosts the oldest modern human presence recorded to date in central Iberia, associated to pre-Solutrean cultural traditions around 26,000 years ago, and (2) that this presence occurred during Heinrich Stadial 2 within harsh environmental conditions. These findings demonstrate that this area of the Iberian hinterland was recurrently occupied regardless of climate and environmental variability, thus challenging the widely accepted hypothesis that ecological risk hampered the human settlement of the Iberian interior highlands since the first arrival of modern humans to Southwest Europe.

RevDate: 2021-07-23

McArthur E, Rinker DC, JA Capra (2021)

Quantifying the contribution of Neanderthal introgression to the heritability of complex traits.

Nature communications, 12(1):4481.

Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Here, we quantify the contribution of introgressed alleles to the heritability of more than 400 diverse traits. We show that genomic regions in which detectable Neanderthal ancestry remains are depleted of heritability for all traits considered, except those related to skin and hair. Introgressed variants themselves are also depleted for contributions to the heritability of most traits. However, introgressed variants shared across multiple Neanderthal populations are enriched for heritability and have consistent directions of effect on several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. Integrating our results, we propose a model in which selection against introgressed functional variation was the dominant trend (especially for cognitive traits); however, for a few traits, introgressed variants provided beneficial variation via uni-directional (e.g., lightening skin color) or bi-directional (e.g., modulating immune response) effects.

RevDate: 2021-07-27
CmpDate: 2021-07-27

Bataille G, Falcucci A, Tafelmaier Y, et al (2020)

Technological differences between Kostenki 17/II (Spitsynskaya industry, Central Russia) and the Protoaurignacian: Reply to Dinnis et al. (2019).

Journal of human evolution, 146:102685.

RevDate: 2021-07-27
CmpDate: 2021-07-27

Jelinek AJ (2020)

Comments on "Dating the Middle Paleolithic deposits of La Quina Amont (Charente, France) using luminescence methods" [J. Hum. Evol. 109 (2017) 30-45].

Journal of human evolution, 149:102575.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Cullen VL, Smith VC, Tushabramishvili N, et al (2021)

A revised AMS and tephra chronology for the Late Middle to Early Upper Paleolithic occupations of Ortvale Klde, Republic of Georgia.

Journal of human evolution, 151:102908.

The nature and timing of the shift from the Late Middle Paleolithic (LMP) to the Early Upper Paleolithic (EUP) varied geographically, temporally, and substantively across the Near East and Eurasia; however, the result of this process was the archaeological disappearance of Middle Paleolithic technologies across the length and breadth of their geographic distribution. Ortvale Klde rockshelter (Republic of Georgia) contains the most detailed LMP-EUP archaeological sequence in the Caucasus, an environmentally and topographically diverse region situated between southwest Asia and Europe. Tephrochronological investigations at the site reveal volcanic ash (tephra) from various volcanic sources and provide a tephrostratigraphy for the site that will facilitate future correlations in the region. We correlate one of the cryptotephra layers to the large, caldera-forming Nemrut Formation eruption (30,000 years ago) from Nemrut volcano in Turkey. We integrate this tephrochronological constraint with new radiocarbon dates and published ages in an OxCal Bayesian age model to produce a revised chronology for the site. This model increases the ages for the end of the LMP (∼47.5-44.2 ka cal BP) and appearance of the EUP (∼46.7-43.6 ka cal BP) at Ortvale Klde, which are earlier than those currently reported for other sites in the Caucasus but similar to estimates for specific sites in southwest Asia and eastern Europe. These data, coupled with archaeological, stratigraphic, and taphonomic observations, suggest that at Ortvale Klde, (1) the appearance of EUP technologies of bone and stone has no technological roots in the preceding LMP, (2) a LMP population vacuum likely preceded the appearance of these EUP technologies, and (3) the systematic combination of tephra correlations and absolute dating chronologies promises to substantially improve our inter-regional understanding of this critical time interval of human evolution and the potential interconnectedness of hominins at different sites.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Shimelmitz R, Groman-Yaroslavski I, Weinstein-Evron M, et al (2021)

A Middle Pleistocene abrading tool from Tabun Cave, Israel: A search for the roots of abrading technology in human evolution.

Journal of human evolution, 150:102909.

During the reanalysis of the finds from Jelinek's and Ronen's excavations at Tabun Cave, Israel, we encountered a cobble bearing traces of mechanical alterations similar to those recorded on grinding tools. However, the artifact derives from the early layers of the Acheulo-Yabrudian complex of the late Lower Paleolithic (ca. 350 ka), a time with no evidence for grinding or abrasion. Accordingly, we sought to determine whether the traces on the artifact can be attributed to purposeful human action. We conducted a detailed use-wear analysis of the cobble and implemented an experimental program, gaining positive results for the hypothesis of purposeful human practice. We argue that the significance and novelty of early abrading technology is that it marks a new mode of raw material manipulation-one that is categorically different from other modes of tool use observed among earlier hominins or other primates and animals. Throughout the Early Pleistocene, use of stone tools was associated with vertical motions (battering, pounding, striking) or with the application of a thin or narrow working edge, leveled at cutting or scraping. Conversely, abrading consists in applying a wide working surface in a continuous sequence of horizontal motions, geared to modify or reduce the surfaces of a targeted material. The emergence of this technology joins additional behavioral changes recently identified and attributed to the Middle Pleistocene, illustrating the growing and diversifying capabilities of early hominins to harness technology to shape their environment.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Kuzmin YV, SG Keates (2020)

The chronology of hominin fossils from the Altai Mountains, Siberia: An alternative view.

Journal of human evolution, 146:102834.

RevDate: 2021-07-21

Leder D, Hermann R, Hüls M, et al (2021)

Publisher Correction: A 51,000-year-old engraved bone reveals Neanderthals' capacity for symbolic behaviour.

RevDate: 2021-07-19
CmpDate: 2021-07-19

Vizzari MT, Benazzo A, Barbujani G, et al (2020)

A Revised Model of Anatomically Modern Human Expansions Out of Africa through a Machine Learning Approximate Bayesian Computation Approach.

Genes, 11(12):.

There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open question whether AMH left Africa through a single process, dispersing almost simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Australo-Melanesia, and later through a northern route crossing the Levant. The development of new methodologies for inferring population history and the availability of worldwide high-coverage whole-genome sequences did not resolve this debate. In this work, we test the two main out-of-Africa hypotheses through an Approximate Bayesian Computation approach, based on the Random-Forest algorithm. We evaluated the ability of the method to discriminate between the alternative models of AMH out-of-Africa, using simulated data. Once assessed that the models are distinguishable, we compared simulated data with real genomic variation, from modern and archaic populations. This analysis showed that a model of multiple dispersals is four-fold as likely as the alternative single-dispersal model. According to our estimates, the two dispersal processes may be placed, respectively, around 74,000 and around 46,000 years ago.

RevDate: 2021-07-17

Schaefer NK, Shapiro B, RE Green (2021)

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.

Science advances, 7(29): pii:7/29/eabc0776.

Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.

RevDate: 2021-07-13

Iasi LNM, Ringbauer H, BM Peter (2021)

An Extended Admixture Pulse Model Reveals the Limitations to Human-Neandertal Introgression Dating.

Molecular biology and evolution pii:6319725 [Epub ahead of print].

Neandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.

RevDate: 2021-07-06

Leder D, Hermann R, Hüls M, et al (2021)

A 51,000-year-old engraved bone reveals Neanderthals' capacity for symbolic behaviour.

Nature ecology & evolution [Epub ahead of print].

While there is substantial evidence for art and symbolic behaviour in early Homo sapiens across Africa and Eurasia, similar evidence connected to Neanderthals is sparse and often contested in scientific debates. Each new discovery is thus crucial for our understanding of Neanderthals' cognitive capacity. Here we report on the discovery of an at least 51,000-year-old engraved giant deer phalanx found at the former cave entrance of Einhornhöhle, northern Germany. The find comes from an apparent Middle Palaeolithic context that is linked to Neanderthals. The engraved bone demonstrates that conceptual imagination, as a prerequisite to compose individual lines into a coherent design, was present in Neanderthals. Therefore, Neanderthal's awareness of symbolic meaning is very likely. Our findings show that Neanderthals were capable of creating symbolic expressions before H. sapiens arrived in Central Europe.

RevDate: 2021-07-06

Bello SM (2021)

Boning up on Neanderthal art.

Nature ecology & evolution [Epub ahead of print].

RevDate: 2021-07-06

Bergmann I, Hublin JJ, Gunz P, et al (2021)

How did modern morphology evolve in the human mandible? The relationship between static adult allometry and mandibular variability in Homo sapiens.

Journal of human evolution, 157:103026 pii:S0047-2484(21)00078-6 [Epub ahead of print].

Key to understanding human origins are early Homo sapiens fossils from Jebel Irhoud, as well as from the early Late Pleistocene sites Tabun, Border Cave, Klasies River Mouth, Skhul, and Qafzeh. While their upper facial shape falls within the recent human range of variation, their mandibles display a mosaic morphology. Here we quantify how mandibular shape covaries with mandible size and how static allometry differs between Neanderthals, early H. sapiens, and modern humans from the Upper Paleolithic/Later Stone Age and Holocene (= later H. sapiens). We use 3D (semi)landmark geometric morphometric methods to visualize allometric trends and to explore how gracilization affects the expression of diagnostic shape features. Early H. sapiens were highly variable in mandible size, exhibiting a unique allometric trajectory that explains aspects of their 'archaic' appearance. At the same time, early H. sapiens share a suite of diagnostic features with later H. sapiens that are not related to mandibular sizes, such as an incipient chin and an anteroposteriorly decreasing corpus height. The mandibular morphology, often referred to as 'modern', can partly be explained by gracilization owing to size reduction. Despite distinct static allometric shape changes in each group studied, bicondylar and bigonial breadth represent important structural constraints for the expression of shape features in most Middle to Late Pleistocene hominin mandibles.

RevDate: 2021-06-24

Schwartz JH, Pantoja-Pérez A, JL Arsuaga (2021)

The nasal region of the ~417 ka Sima de los Huesos (Sierra de Atapuerca, Spain) Hominin: New terminology and implications for later human evolution.

Anatomical record (Hoboken, N.J. : 2007) [Epub ahead of print].

Circum-nasal and nasal cavity morphology add to the picture of the Sima de los Huesos specimens as, at one level, representing a distinct morph and, at another, displaying individual variation. They developed a robust, midline-grooved, three-dimensional spinal ridge lying anteriorly in the nasal cavity floor that was distended posteriorly over the nasal cavity floor, and, typically, an expansive, three-dimensional patch of rugose bone on the nasal cavity wall where a conchal crest would otherwise lie. They vary, for example, in degree of topographic relief of the nasal cavity wall, expression of the spinal ridge, and development of nasal crests and fossae. Lacking an anterior nasal spine, Sima specimens differ from extant and most fossil Homo sapiens, some specimens attributed to H. heidelbergensis, and the Gran Dolina partial face, whose anterior nasal spine is a superoanterior distention of the nasoalveolar clivus, and also from Neanderthals, whose anterior nasal spine projects anteriorly away from the nasoalveolar clivus. Comparison of Neanderthals, the Sima hominin, and specimens regarded as H. heidelbergensis calls for re-evaluating the integrity of "heidelbergensis" and rethinking the phylogenetic relationships of them all. To precisely describe the numerous features and combinations thereof of the nasal region in Sima specimens, and compare them with Neandertals and "H. heidelbergensis", we developed terminology that is applicable not only to hominins, but to mammals in general.

RevDate: 2021-06-24

Zavala EI, Jacobs Z, Vernot B, et al (2021)

Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave.

Nature [Epub ahead of print].

Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1-4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8-11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly-possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.

RevDate: 2021-06-22

Devièse T, Abrams G, Hajdinjak M, et al (2021)

Reply to Van Peer: Direct radiocarbon dating and ancient genomic analysis reveal the true age of the Neanderthals at Spy Cave.

Proceedings of the National Academy of Sciences of the United States of America, 118(26):.

RevDate: 2021-06-22

Van Peer P (2021)

The stratigraphic context of Spy Cave and the timing of Neanderthal disappearance in Northwest Europe.

Proceedings of the National Academy of Sciences of the United States of America, 118(26):.

RevDate: 2021-06-22

Amos W (2021)

Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding.

Royal Society open science, 8(6):201229.

Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/'hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar 'double' trends are observed for the introgression statistic f 4 in a second large dataset published by Qin and Stoneking (Qin & Stoneking 2015 Mol. Biol. Evol. 32, 2665-2674 (doi:10.1093/molbev/msv141)). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two 'out of Africa' events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.

RevDate: 2021-06-20

Jeworutzki E, Tüttelmann F, Rothenberg I, et al (2021)

Can Unlikely Neanderthal Chloride Channel CLC-2 Gene Variants Provide Insights in Modern Human Infertility?.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 55(3):301-310.

BACKGROUND/AIMS: Neanderthals, although well adapted to local environments, were rapidly replaced by anatomically modern humans (AMH) for unknown reasons. Genetic information on Neanderthals is limited restricting applicability of standard population genetics.

METHODS: Here, we apply a novel combination of restricted genetic analyses on preselected physiological key players (ion channels), electrophysiological analyses of gene variants of unclear significance expressed in Xenopus laevis oocytes using two electrode voltage clamp and transfer of results to AMH genetics. Using genetic screening in infertile men identified a loss of CLC-2 associated with sperm deficiency.

RESULTS: Increased genetic variation caused functionally impaired Neanderthals CLC-2 channels.

CONCLUSION: Increased genetic variation could reflect an adaptation to different local salt supplies at the cost of reduced sperm density. Interestingly and consistent with this hypothesis, lack of CLC-2 protein in a patient associates with high blood K+ concentration and azoospermia.

RevDate: 2021-07-02
CmpDate: 2021-07-02

Gibbons A (2021)

Genomes offer rare glimpse of Neanderthal family groups.

Science (New York, N.Y.), 372(6548):1251-1252.

RevDate: 2021-06-16

Levi G, de Lombares C, Giuliani C, et al (2021)

DLX5/6 GABAergic expression affects social vocalization: implications for human evolution.

Molecular biology and evolution pii:6300530 [Epub ahead of print].

DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated to neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioural and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1400 calls/10min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull and brain shape…) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated to Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105y of age), a well-established human model of healthy ageing and longevity, suggesting their involvement in the co-evolution of longevity, sociability and speech.

RevDate: 2021-06-12

Antonio P, Costantino B, Silvia C, et al (2021)

Arothron: An R package for geometric morphometric methods and virtual anthropology applications.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils.

MATERIALS AND METHODS: We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations.

RESULTS: We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain.

CONCLUSIONS: The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens.

RevDate: 2021-06-24
CmpDate: 2021-06-24

Singh PP, Srivastava A, Sultana GNN, et al (2021)

The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations.

Scientific reports, 11(1):12346.

With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India.

RevDate: 2021-06-08

Zhou Y, SR Browning (2021)

Protocol for detecting introgressed archaic variants with SPrime.

STAR protocols, 2(2):100550.

The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population. For complete details on the use and execution of this protocol, please refer to Browning et al. (2018).

RevDate: 2021-07-01

Barras C (2021)

How did Neanderthals and other ancient humans learn to count?.

Nature, 594(7861):22-25.

RevDate: 2021-06-27

Folgerø PO, Johansson C, LH Stokkedal (2021)

The Superior Visual Perception Hypothesis: Neuroaesthetics of Cave Art.

Behavioral sciences (Basel, Switzerland), 11(6):.

Cave Art in the Upper Paleolithic presents a boost of creativity and visual thinking. What can explain these savant-like paintings? The normal brain function in modern man rarely supports the creation of highly detailed paintings, particularly the convincing representation of animal movement, without extensive training and access to modern technology. Differences in neuro-signaling and brain anatomy between modern and archaic Homo sapiens could also cause differences in perception. The brain of archaic Homo sapiens could perceive raw detailed information without using pre-established top-down concepts, as opposed to the common understanding of the normal modern non-savant brain driven by top-down control. Some ancient genes preserved in modern humans may be expressed in rare disorders. Researchers have compared Cave Art with art made by people with autism spectrum disorder. We propose that archaic primary consciousness, as opposed to modern secondary consciousness, included a savant-like perception with a superior richness of details compared to modern man. Modern people with high frequencies of Neanderthal genes, have notable anatomical features such as increased skull width in the occipital and parietal visual areas. We hypothesize that the anatomical differences are functional and may allow a different path to visual perception.

RevDate: 2021-06-14
CmpDate: 2021-06-14

Yamamoto N, Yamamoto R, Ariumi Y, et al (2021)

Does Genetic Predisposition Contribute to the Exacerbation of COVID-19 Symptoms in Individuals with Comorbidities and Explain the Huge Mortality Disparity between the East and the West?.

International journal of molecular sciences, 22(9):.

The elderly and patients with several comorbidities experience more severe cases of coronavirus disease 2019 (COVID-19) than healthy patients without underlying medical conditions. However, it is unclear why these people are prone to developing alveolar pneumonia, rapid exacerbations, and death. Therefore, we hypothesized that people with comorbidities may have a genetic predisposition that makes them more vulnerable to various factors; for example, they are likely to become more severely ill when infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To test this hypothesis, we searched the literature extensively. Polymorphisms of genes, such as those that encode angiotensin-converting enzyme 1 (ACE1), have been associated with numerous comorbidities, such as cardiovascular disease, hypertension, diabetes, chronic kidney disease, and obesity, and there are potential mechanisms to explain these associations (e.g., DD-type carriers have greater ACE1 activity, and patients with a genetic alpha-1 anti-trypsin (AAT) deficiency lack control over inflammatory mediators). Since comorbidities are associated with chronic inflammation and are closely related to the renin-angiotensin-aldosterone system (RAAS), these individuals may already have a mild ACE1/ACE2 imbalance before viral infection, which increases their risk for developing severe cases of COVID-19. However, there is still much debate about the association between ACE1 D/I polymorphism and comorbidities. The best explanation for this discrepancy could be that the D allele and DD subtypes are associated with comorbidities, but the DD genotype alone does not have an exceptionally large effect. This is also expected since the ACE1 D/I polymorphism is only an intron marker. We also discuss how polymorphisms of AAT and other genes are involved in comorbidities and the severity of SARS-CoV-2 infection. Presumably, a combination of multiple genes and non-genetic factors is involved in the establishment of comorbidities and aggravation of COVID-19.

RevDate: 2021-06-18

Salazar-García DC, Power RC, Rudaya N, et al (2021)

Dietary evidence from Central Asian Neanderthals: A combined isotope and plant microremains approach at Chagyrskaya Cave (Altai, Russia).

Journal of human evolution, 156:102985.

Neanderthals are known primarily from their habitation of Western Eurasia, but they also populated large expanses of Northern Asia for thousands of years. Owing to a sparse archaeological record, relatively little is known about these eastern Neanderthal populations. Unlike in their western range, there are limited zooarchaeological and paleobotanical studies that inform us about the nature of their subsistence. Here, we perform a combined analysis of carbon and nitrogen stable isotopes on bone collagen and microbotanical remains in dental calculus to reconstruct the diet of eastern Neanderthals at Chagyrskaya Cave in the Altai Mountains of Southern Siberia, Russia. Stable isotopes identify one individual as possessing a high trophic level due to the hunting of large- and medium-sized ungulates, while the analysis of dental calculus also indicates the presence of plants in the diet of this individual and others from the site. These findings indicate eastern Neanderthals may have had broadly similar subsistence patterns to those elsewhere in their range.

RevDate: 2021-05-24

Ahlquist K, Banuelos M, Funk A, et al (2021)

Our tangled family tree: new genomic methods offer insight into the legacy of archaic admixture.

Genome biology and evolution pii:6283580 [Epub ahead of print].

The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: i) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; ii) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; iii) how these novel methods can detect archaic introgression in modern African populations; and iv) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.

RevDate: 2021-06-18

Spindler L, Comeskey D, Chabai V, et al (2021)

Dating the last Middle Palaeolithic of the Crimean Peninsula: New hydroxyproline AMS dates from the site of Kabazi II.

Journal of human evolution, 156:102996.

Radiocarbon dating of bone and charcoal from sites dating to the Middle and Upper Paleolithic is challenging due to low residual levels of radiocarbon. This means that small amounts of contaminating carbon can wield a great influence over accuracy unless they are fully removed. The site of Kabazi II in the Crimea is important because radiocarbon dates previously obtained from bones in archaeological horizons that date to the Western Crimean Mousterian (WCM) are surprisingly young. We redated the same samples using a single compound dating method that focuses on extracting and dating the amino acid hydroxyproline. We show that single amino acid dates produce significantly older determinations than those that use bulk collagen pretreatment procedures. Our results suggest that instead of dating to 35,000-40,000 cal BP, the bones actually date to >50,000 cal BP. This implies that the WCM at this site is much older than previously thought. In light of these current findings, we considered the dates of other key Crimean sites and concluded that in the absence of reliable pretreatment methods, it would be wise to consider many of them minimum ages. We conclude that there is little robust evidence to suggest Neanderthals were present in the Crimea after 40,000 cal BP.

RevDate: 2021-05-19

Svensson E, Günther T, Hoischen A, et al (2021)

Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.

Current biology : CB pii:S0960-9822(21)00592-3 [Epub ahead of print].

Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.

RevDate: 2021-07-06

Kerner G, Patin E, L Quintana-Murci (2021)

New insights into human immunity from ancient genomics.

Current opinion in immunology, 72:116-125 pii:S0952-7915(21)00045-5 [Epub ahead of print].

Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity.

RevDate: 2021-05-19

Anonymous (2021)

Microbes in Neanderthals' mouths reveal their carb-laden diet.

Nature, 593(7859):316.

RevDate: 2021-05-11

Harvati K (2021)

Katerina Harvati.

Current biology : CB, 31(9):R418-R419.

Interview with paleoanthropologist Katerina Harvati, who studies Neanderthal evolution and modern human origins at the Eberhard Karls University of Tübingen.

RevDate: 2021-05-29

Fellows Yates JA, Velsko IM, Aron F, et al (2021)

The evolution and changing ecology of the African hominid oral microbiome.

Proceedings of the National Academy of Sciences of the United States of America, 118(20):.

The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.

RevDate: 2021-06-24
CmpDate: 2021-06-24

Gopalan S, Atkinson EG, Buck LT, et al (2021)

Inferring archaic introgression from hominin genetic data.

Evolutionary anthropology, 30(3):199-220.

Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.

RevDate: 2021-05-22

Stepanova V, Moczulska KE, Vacano GN, et al (2021)

Reduced purine biosynthesis in humans after their divergence from Neandertals.

eLife, 10:.

We analyze the metabolomes of humans, chimpanzees, and macaques in muscle, kidney and three different regions of the brain. Although several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution contributes to much or all of the reduction of de novo synthesis of purines in humans.

RevDate: 2021-07-02

Mualim K, Theunert C, M Slatkin (2021)

Estimation of coalescence probabilities and population divergence times from SNP data.

Heredity, 127(1):1-9.

We present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.

RevDate: 2021-04-23

Villanea FA, Huerta-Sanchez E, PK Fox (2021)

ABO genetic variation in Neanderthals and Denisovans.

Molecular biology and evolution pii:6248100 [Epub ahead of print].

Variation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We found two Neanderthal variants of the O allele in the Siberian Neanderthals (O1 and O2), one of these variants is shared with an European Neanderthal, who is a heterozygote for this O1 variant and a rare cis-AB variant. The Denisovan individual is heterozygous for two variants of the O1 allele, functionally similar to variants found widely in modern humans. Perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians. Our genetic distance analyses suggest both alleles survive in modern humans due to inbreeding with Neanderthals. We find that the sequence backgrounds of the surviving Neanderthal-like O alleles in modern humans retain a higher sequence divergence than other surviving Neanderthal genome fragments, supporting a view of balancing selection operating in the Neanderthal ABO alleles by retaining highly diverse haplotypes compared to portions of the genome evolving neutrally.

RevDate: 2021-06-25

Weiss CV, Harshman L, Inoue F, et al (2021)

The cis-regulatory effects of modern human-specific variants.

eLife, 10:.

The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.

RevDate: 2021-04-21

Spiegelhalder P, M Bögemann (2021)

[Non-metastatic castration-resistant prostate cancer (M0CRPC) - Apalutamide in high-risk M0CRPC: case reports from the SPARTAN study and the apalutamide compassionate use program].

Aktuelle Urologie [Epub ahead of print].

The occurrence of distant metastases represents a prognostically unfavourable turning point in non-metastatic castration-resistant prostate cancer (M0CRPC). M0CRPC patients with a short PSA doubling time have a particularly high risk of progression. For a long time, there was no further treatment option for these patients apart from watchful waiting while maintaining classic androgen deprivation therapy (ADT). Apalutamide, a next-generation anti-androgen available since January 2019, significantly increased metastasis-free survival compared with placebo in the pivotal SPARTAN trial in patients with high-risk M0CRPC. The presented patient cases from SPARTAN and the apalutamide compassionate use program are examples of the beneficial effects that apalutamide can achieve in the M0CRPC setting.

RevDate: 2021-04-21

Zwir I, Del-Val C, Hintsanen M, et al (2021)

Evolution of genetic networks for human creativity.

Molecular psychiatry [Epub ahead of print].

The genetic basis for the emergence of creativity in modern humans remains a mystery despite sequencing the genomes of chimpanzees and Neanderthals, our closest hominid relatives. Data-driven methods allowed us to uncover networks of genes distinguishing the three major systems of modern human personality and adaptability: emotional reactivity, self-control, and self-awareness. Now we have identified which of these genes are present in chimpanzees and Neanderthals. We replicated our findings in separate analyses of three high-coverage genomes of Neanderthals. We found that Neanderthals had nearly the same genes for emotional reactivity as chimpanzees, and they were intermediate between modern humans and chimpanzees in their numbers of genes for both self-control and self-awareness. 95% of the 267 genes we found only in modern humans were not protein-coding, including many long-non-coding RNAs in the self-awareness network. These genes may have arisen by positive selection for the characteristics of human well-being and behavioral modernity, including creativity, prosocial behavior, and healthy longevity. The genes that cluster in association with those found only in modern humans are over-expressed in brain regions involved in human self-awareness and creativity, including late-myelinating and phylogenetically recent regions of neocortex for autobiographical memory in frontal, parietal, and temporal regions, as well as related components of cortico-thalamo-ponto-cerebellar-cortical and cortico-striato-cortical loops. We conclude that modern humans have more than 200 unique non-protein-coding genes regulating co-expression of many more protein-coding genes in coordinated networks that underlie their capacities for self-awareness, creativity, prosocial behavior, and healthy longevity, which are not found in chimpanzees or Neanderthals.

RevDate: 2021-04-16

Yi Z, Zanolli C, Liao W, et al (2021)

A deep-learning-based workflow to assess taxonomic affinity of hominid teeth with a test on discriminating Pongo and Homo upper molars.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: Convolutional neural network (CNN) is a state-of-art deep learning (DL) method with superior performance in image classification. Here, a CNN-based workflow is proposed to discriminate hominid teeth. Our hope is that this method could help confirm otherwise questionable records of Homo from Pleistocene deposits where there is a standing risk of mis-attributing molars of Pongo to Homo.

METHODS AND MATERIALS: A two-step workflow was designed. The first step is converting the enamel-dentine junction (EDJ) into EDJ card, that is, a two-dimensional image conversion of the three-dimensional EDJ surface. In this step, researchers must carefully orient the teeth according to the cervical plane. The second step is training the CNN learner with labeled EDJ cards. A sample consisting of 53 fossil Pongo and 53 Homo (modern human and Neanderthal) was adopted to generate EDJ cards, which were then separated into training set (n = 84) and validation set (n = 22). To assess the feasibility of this workflow, a Pongo-Homo classifier was trained from the aforementioned EDJ card set, and then the classifier was used to predict the taxonomic affinities of six samples (test set) from von Koenigswald's Chinese Apothecary collection.

RESULTS: Results show that EDJ cards in validation set are classified accurately by the CNN learner. More importantly, taxonomic predictions for six specimens in test set match well with the diagnosis results deduced from multiple lines of evidence, implying the great potential of CNN method.

DISCUSSION: This workflow paves a way for future studies using CNN to address taxonomic complexity (e.g., distinguishing Pongo and Homo teeth from the Pleistocene of Asia). Further improvements include visual interpretation and extending the applicability to moderately worn teeth.

RevDate: 2021-05-03
CmpDate: 2021-05-03

Gibbons A (2021)

DNA from cave dirt traces Neanderthal upheaval.

Science (New York, N.Y.), 372(6539):222-223.

RevDate: 2021-05-21
CmpDate: 2021-05-14

Vernot B, Zavala EI, Gómez-Olivencia A, et al (2021)

Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments.

Science (New York, N.Y.), 372(6542):.

Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.

RevDate: 2021-04-22

Choin J, Mendoza-Revilla J, Arauna LR, et al (2021)

Genomic insights into population history and biological adaptation in Oceania.

Nature, 592(7855):583-589.

The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes1. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago2-4. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.

RevDate: 2021-04-16

Vaesen K, Dusseldorp GL, MJ Brandt (2021)

Author Correction: An emerging consensus in palaeoanthropology: demography was the main factor responsible for the disappearance of Neanderthals.

Scientific reports, 11(1):8450 pii:10.1038/s41598-021-88189-5.

RevDate: 2021-04-27
CmpDate: 2021-04-27

Gibbons A (2021)

When modern humans met Neanderthals.

Science (New York, N.Y.), 372(6538):115-116.

RevDate: 2021-06-09

Hajdinjak M, Mafessoni F, Skov L, et al (2021)

Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry.

Nature, 592(7853):253-257.

Modern humans appeared in Europe by at least 45,000 years ago1-5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

RevDate: 2021-04-14

Callaway E (2021)

Oldest DNA from a Homo sapiens reveals surprisingly recent Neanderthal ancestry.

Nature, 592(7854):339.

RevDate: 2021-06-12
CmpDate: 2021-06-11

Lalueza-Fox C (2021)

Neanderthal assimilation?.

Nature ecology & evolution, 5(6):711-712.

RevDate: 2021-06-19
CmpDate: 2021-06-11

Prüfer K, Posth C, Yu H, et al (2021)

A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia.

Nature ecology & evolution, 5(6):820-825.

Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2-3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000-5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust'-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa.

RevDate: 2021-04-09

Devièse T, Abrams G, Hajdinjak M, et al (2021)

Reevaluating the timing of Neanderthal disappearance in Northwest Europe.

Proceedings of the National Academy of Sciences of the United States of America, 118(12):.

Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.

RevDate: 2021-04-02

Ocobock C, Lacy S, A Niclou (2021)

Between a rock and a cold place: Neanderthal biocultural cold adaptations.

Evolutionary anthropology [Epub ahead of print].

A large body of work focuses on the unique aspects of Neanderthal anatomy, inferred physiology, and behavior to test the assumption that Neanderthals were hyper-adapted to living in cold environments. This research has expanded over the years to include previously unexplored and potentially adaptive features such as brown adipose tissue and fire-usage. Here we review the current state of knowledge of Neanderthal cold adaptations along morphological, physiological, and behavioral lines. While highlighting foundational as well as recent work, we also emphasize key areas for future research. Despite thriving in a variety of climates, it is well-accepted that Neanderthals appear to be the most cold-adapted of known fossil hominin groups; however, there are still many unknowns. There is a great deal yet to be uncovered about the nature and manifestation of Neanderthal adaptation and how the synergy of biology and culture helped buffer them against extreme and variable environments.

RevDate: 2021-04-20

Baab KL, Nesbitt A, Hublin JJ, et al (2021)

Assessing the status of the KNM-ER 42700 fossil using Homo erectus neurocranial development.

Journal of human evolution, 154:102980.

Based on ontogenetic data of endocranial shape, it has been proposed that a younger than previously assumed developmental status of the 1.5-Myr-old KNM-ER 42700 calvaria could explain why the calvaria of this fossil does not conform to the shape of other Homo erectus individuals. Here, we investigate (ecto)neurocranial ontogeny in H. erectus and assess the proposed juvenile status of this fossil using recent Homo sapiens, chimpanzees (Pan troglodytes), and Neanderthals (Homo neanderthalensis) to model and discuss changes in neurocranial shape from the juvenile to adult stages. We show that all four species share common patterns of developmental shape change resulting in a relatively lower cranial vault and expanded supraorbital torus at later developmental stages. This finding suggests that ectoneurocranial data from extant hominids can be used to model the ontogenetic trajectory for H. erectus, for which only one well-preserved very young individual is known. However, our study also reveals differences in the magnitudes and, to a lesser extent, directions of the species-specific trajectories that add to the overall shared pattern of neurocranial shape changes. We demonstrate that the very young H. erectus juvenile from Mojokerto together with subadult and adult H. erectus individuals cannot be accommodated within the pattern of the postnatal neurocranial trajectory for humans. Instead, the chimpanzee pattern might be a better 'fit' for H. erectus despite their more distant phylogenetic relatedness. The data are also compatible with an ontogenetic shape trajectory that is in some regards intermediate between that of recent H. sapiens and chimpanzees, implying a unique trajectory for H. erectus that combines elements of both extant species. Based on this new knowledge, neurocranial shape supports the assessment that KNM-ER 42700 is a young juvenile H. erectus if H. erectus followed an ontogenetic shape trajectory that was more similar to chimpanzees than humans.

RevDate: 2021-04-07

Huffman J, Butler-Laporte G, Khan A, et al (2021)

Alternative splicing of OAS1 alters the risk for severe COVID-19.

medRxiv : the preprint server for health sciences.

A locus containing OAS1/2/3 has been identified as a risk locus for severe COVID-19 among Europeans ancestry individuals, with a protective haplotype of ∼75 kilobases derived from Neanderthals. Here, we show that among several potentially causal variants at this locus, a splice variant of OAS1 occurs in people of African ancestry independently of the Neanderthal haplotype and confers protection against COVID-19 of a magnitude similar to that seen in individuals without African ancestry.

RevDate: 2021-05-23

Yair S, Lee KM, G Coop (2021)

The timing of human adaptation from Neanderthal introgression.

Genetics, 218(1):.

Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.

RevDate: 2021-04-20

Chevalier T, Colard T, Colombo A, et al (2021)

Early ontogeny of humeral trabecular bone in Neandertals and recent modern humans.

Journal of human evolution, 154:102968.

Trabecular bone ontogeny is well known in modern humans and unknown in Neandertals. Yet the bone developmental pattern is useful for interpreting fossils from evolutionary and functional perspectives. Interestingly, microstructure in early ontogeny is supposedly not influenced by high and specific mechanical loading related to the lifestyle of a human group and consequently does not directly depend on the activities of hunter-gatherers. Here, we specifically explored the early growth trajectories of the trabecular bone structure of the humerus and emphasized in particular how bone fraction (bone volume/total volume [BV/TV]) was built up in Neandertals, given the specific modern human bone loss after birth and the use of BV/TV in functional studies. Six Neandertals and 26 recent modern humans ranging from perinates to adolescents were included in this study. Six trabecular parameters were measured within a cubic region of interest extracted from the proximal metaphysis of the humerus. We found that the microstructural changes in Neandertals during early ontogeny (<1 year) fit with modern human growth trajectories for each parameter. The specific bone loss occurring immediately after birth in modern humans also occurred in Neandertals (but not in chimpanzees). However, the early childhood fossil Ferrassie 6 presented unexpectedly high BV/TV, whereas the high BV/TV in the Crouzade I adolescent was predictable. These results suggest that Neandertals and modern humans shared predetermined early growth trajectories and developmental mechanisms. We assume that the close relationship between skeletal characteristics in early ontogeny and adults in modern humans also existed in Neandertals. However, it was difficult to ensure that the high BV/TV in Neandertal early childhood, represented by only one individual, was at the origin of the high BV/TV observed in adults. Consequently, our study does not challenge the mechanical hypothesis that explains the trabecular gracilization of the humerus during the Holocene.

RevDate: 2021-05-19
CmpDate: 2021-05-19

Teixeira JC, Jacobs GS, Stringer C, et al (2021)

Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture.

Nature ecology & evolution, 5(5):616-624.

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

RevDate: 2021-03-16

Mayoral E, Díaz-Martínez I, Duveau J, et al (2021)

Tracking late Pleistocene Neandertals on the Iberian coast.

Scientific reports, 11(1):4103.

Here, we report the recent discovery of 87 Neandertal footprints on the Southwest of the Iberian Peninsula (Doñana shoreline, Spain) located on an upper Pleistocene aeolian littoral setting (about 106 ± 19 kyr). Morphometric comparisons, high resolution digital photogrammetric 3D models and detailed sedimentary analysis have been provided to characterized the footprints and the palaeoenvironment. The footprints were impressed in the shoreline of a hypersaline swamped area related to benthic microbial mats, close to the coastline. They have a rounded heel, a longitudinal arch, relatively short toes, and adducted hallux, and represent the oldest upper Pleistocene record of Neandertal footprints in the world. Among these 87 footprints, 31 are longitudinally complete and measure from 14 to 29 cm. The calculated statures range from 104 to 188 cm, with half of the data between 130 and 150 cm. The wide range of sizes of the footprints suggests the existence of a social group integrated by individuals of different age classes but dominated, however, by non-adult individuals. The footprints, which are outside the flooded area are oriented perpendicular to the shoreline. These 87 footprints reinforce the ecological scenario of Neandertal groups established in coastal areas.

RevDate: 2021-03-12

García-Campos C, Martinén-Torres M, Modesto-Mata M, et al (2021)

Indicators of sexual dimorphism in Homo antecessor permanent canines.

Journal of anthropological sciences = Rivista di antropologia : JASS, 99: [Epub ahead of print].

One of the main concerns of paleoanthropologists is to make a correct interpretation of the variability observed in the fossil record. However, the current knowledge about sexual dimorphism in the human lineage comes mainly from the study of modern human, Neanderthal and pre-Neanderthal populations, whereas information available about the intrapopulation variability of the groups that preceded these taxa is still ambiguous. In this preliminary study, Homo antecessor dental sample was assessed with the aim of trying to evaluate the degree of variability of their permanent canines` dental tissue proportions. Microtomographic techniques were here employed in order to measure and compare the crown volumes and surface areas of their enamel caps and dentine-pulp complexes. Then, the Pearson`s Coefficient of Variation and the Euclidean Distance were assessed to evaluate of intrapopulation variability of Gran Dolina TD6.2 dental sample. The values obtained were also compared with those of the dental samples from Sima de los Huesos site (Spain), the Neanderthal site of Krapina (Croatia), as well as from a broad forensic collection of known sex. Our results showed a marked intrapopulation variability in the dental tissues measurements of the canines of the individuals H1 and H3 from this site. This variability may be interpreted as an indicator of sexual dimorphism. If this is the case, H1 may be considered as a male individual, whereas H3 would be a female. Future discoveries of new fossils in the level TD6.2 of Gran Dolina site might help to confirm or refute this hypothesis.

RevDate: 2021-03-10

Banks WE, Moncel MH, Raynal JP, et al (2021)

An ecological niche shift for Neanderthal populations in Western Europe 70,000 years ago.

Scientific reports, 11(1):5346.

Middle Paleolithic Neanderthal populations occupied Eurasia for at least 250,000 years prior to the arrival of anatomically modern humans. While a considerable body of archaeological research has focused on Neanderthal material culture and subsistence strategies, little attention has been paid to the relationship between regionally specific cultural trajectories and their associated existing fundamental ecological niches, nor to how the latter varied across periods of climatic variability. We examine the Middle Paleolithic archaeological record of a naturally constrained region of Western Europe between 82,000 and 60,000 years ago using ecological niche modeling methods. Evaluations of ecological niche estimations, in both geographic and environmental dimensions, indicate that 70,000 years ago the range of suitable habitats exploited by these Neanderthal populations contracted and shifted. These ecological niche dynamics are the result of groups continuing to occupy habitual territories that were characterized by new environmental conditions during Marine Isotope Stage 4. The development of original cultural adaptations permitted this territorial stability.

RevDate: 2021-05-19
CmpDate: 2021-05-19

Conde-Valverde M, Martínez I, Quam RM, et al (2021)

Neanderthals and Homo sapiens had similar auditory and speech capacities.

Nature ecology & evolution, 5(5):609-615.

The study of audition in fossil hominins is of great interest given its relationship with intraspecific vocal communication. While the auditory capacities have been studied in early hominins and in the Middle Pleistocene Sima de los Huesos hominins, less is known about the hearing abilities of the Neanderthals. Here, we provide a detailed approach to their auditory capacities. Relying on computerized tomography scans and a comprehensive model from the field of auditory bioengineering, we have established sound power transmission through the outer and middle ear and calculated the occupied bandwidth in Neanderthals. The occupied bandwidth is directly related to the efficiency of the vocal communication system of a species. Our results show that the occupied bandwidth of Neanderthals was greater than the Sima de los Huesos hominins and similar to extant humans, implying that Neanderthals evolved the auditory capacities to support a vocal communication system as efficient as modern human speech.

RevDate: 2021-04-16

Vaesen K, Dusseldorp GL, MJ Brandt (2021)

An emerging consensus in palaeoanthropology: demography was the main factor responsible for the disappearance of Neanderthals.

Scientific reports, 11(1):4925.

The causes of Neanderthal disappearance about 40,000 years ago remain highly contested. Over a dozen serious hypotheses are currently endorsed to explain this enigmatic event. Given the relatively large number of contending explanations and the relatively large number of participants in the debate, it is unclear how strongly each contender is supported by the research community. What does the community actually believe about the demise of Neanderthals? To address this question, we conducted a survey among practicing palaeo-anthropologists (total number of respondents = 216). It appears that received wisdom is that demography was the principal cause of the demise of Neanderthals. In contrast, there is no received wisdom about the role that environmental factors and competition with modern humans played in the extinction process; the research community is deeply divided about these issues. Finally, we tested the hypothesis that palaeo-anthropologists' stand in the debate co-varies with their socio-political views and attitudes. We found no evidence for such a correlation.

RevDate: 2021-05-21
CmpDate: 2021-05-21

Richards GD, Guipert G, Jabbour RS, et al (2021)

Neanderthal cranial remains from Baume Moula-Guercy (Soyons, Ardèche, France).

American journal of physical anthropology, 175(1):201-226.

OBJECTIVES: We provide the first comparative description of the Guercy 1 cranium and isolated cranial fragments from Baume Moula-Guercy and examine their affinities to European Preneanderthals, Neanderthals, and Homo sapiens.

MATERIALS AND METHODS: The Moula-Guercy hominins derive from deposits chronostratigraphically and biostratigraphically dated to the Eemian Interglacial (MIS 5e). For comparisons we compiled a sample of European and Southwest Asian subadult-adult Middle-to-Late Pleistocene hominins (≈MIS 14-MIS 2; N = 184). This sample represents a Preneanderthal-Neanderthal group and a H. sapiens group, both of which were further divided into three time-successive subgroups defined by associated marine isotope stages (MIS). Metric and morphological observations were made on the original fossils and a virtual reconstruction of Guercy 1. Developmental age and sex and the minimum-maximum number of individuals were assessed.

RESULTS: Guercy 1 represents the remains of a late stage adolescent (≈15-16.0 years) female. Morphological and metric data combine to associate the total morphological pattern expressed in Guercy 1 with our MIS 7-MIS 5e ("Early Neanderthal") subgroup. Some features, especially those related to the frontal, suggest linkage to a paleodeme comprising the Moula-Guercy, Artenac, La Chaise Abri Suard and, possibly, the Biache-Saint-Vaast samples.

DISCUSSION: Remains of MIS 7-MIS 5e Neanderthals are rare and fragmentary, especially those dated to the Last Interglacial. The Baume Moula-Guercy sample provides new insights into the total morphological pattern expressed in MIS 5e Neanderthals. Further, our results support earlier suggestions that MIS 7-MIS 5e European hominins represent a morphotype that is distinct from both earlier and later members of the Preneanderthal-Neanderthal group.

RevDate: 2021-03-19

Mora-Bermúdez F, Taverna E, WB Huttner (2021)

From stem and progenitor cells to neurons in the developing neocortex: key differences among hominids.

The FEBS journal [Epub ahead of print].

Comparing the biology of humans to that of other primates, and notably other hominids, is a useful path to learn more about what makes us human. Some of the most interesting differences among hominids are closely related to brain development and function, for example behaviour and cognition. This makes it particularly interesting to compare the hominid neural cells of the neocortex, a part of the brain that plays central roles in those processes. However, well-preserved tissue from great apes is usually extremely difficult to obtain. A variety of new alternative tools, for example brain organoids, are now beginning to make it possible to search for such differences and analyse their potential biological and biomedical meaning. Here, we present an overview of recent findings from comparisons of the neural stem and progenitor cells (NSPCs) and neurons of hominids. In addition to differences in proliferation and differentiation of NSPCs, and maturation of neurons, we highlight that the regulation of the timing of these processes is emerging as a general foundational difference in the development of the neocortex of hominids.

RevDate: 2021-04-28
CmpDate: 2021-04-28

Zhou S, Butler-Laporte G, Nakanishi T, et al (2021)

A Neanderthal OAS1 isoform protects individuals of European ancestry against COVID-19 susceptibility and severity.

Nature medicine, 27(4):659-667.

To identify circulating proteins influencing Coronavirus Disease 2019 (COVID-19) susceptibility and severity, we undertook a two-sample Mendelian randomization (MR) study, rapidly scanning hundreds of circulating proteins while reducing bias due to reverse causation and confounding. In up to 14,134 cases and 1.2 million controls, we found that an s.d. increase in OAS1 levels was associated with reduced COVID-19 death or ventilation (odds ratio (OR) = 0.54, P = 7 × 10-8), hospitalization (OR = 0.61, P = 8 × 10-8) and susceptibility (OR = 0.78, P = 8 × 10-6). Measuring OAS1 levels in 504 individuals, we found that higher plasma OAS1 levels in a non-infectious state were associated with reduced COVID-19 susceptibility and severity. Further analyses suggested that a Neanderthal isoform of OAS1 in individuals of European ancestry affords this protection. Thus, evidence from MR and a case-control study support a protective role for OAS1 in COVID-19 adverse outcomes. Available pharmacological agents that increase OAS1 levels could be prioritized for drug development.

RevDate: 2021-03-05

Baldoni M, Al-Hashmi M, Bianchi AE, et al (2021)

Bioarchaeology-related studies in the Arabian Gulf: potentialities and shortcomings.

Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen, 72(1):17-32.

Archaeological studies provide a powerful tool to understand the prehistoric societies, especially when combined to cutting-edge morphological and molecular anthropological analyses, allowing reconstructing past population dynamics, admixture events, and socio-cultural changes. Despite the advances achieved in the last decades by archaeological studies worldwide, several regions of the World have been spared from this scientific improvement due to various reasons. The Arabian Gulf represents a unique ground to investigate, being the passageway for human migrations and one of the hypothesized areas in which Neanderthal introgression occurred. A number of archaeological sites are currently present in the Arabian Gulf and have witnessed the antiquity and the intensiveness of the human settlements in the region. Nevertheless, the archaeological and anthropological investigation in the Gulf is still in its infancy. Data collected through archaeological studies in the area have the potential to help answering adamant questions of human history from the beginning of the structuring of genetic diversity in human species to the Neolithisation process. This review aims at providing an overview of the archaeological studies in the Arabian Gulf with special focus to Qatar, highlighting potentialities and shortcomings.

RevDate: 2021-02-26

Zilio L, Hammond H, Karampaglidis T, et al (2021)

Examining Neanderthal and carnivore occupations of Teixoneres Cave (Moià, Barcelona, Spain) using archaeostratigraphic and intra-site spatial analysis.

Scientific reports, 11(1):4339.

Teixoneres Cave (Moià, Barcelona, Spain) is a reference site for Middle Palaeolithic studies of the Iberian Peninsula. The cave preserves an extensive stratigraphic sequence made up of eight units, which is presented in depth in this work. The main goal of this study is to undertake an initial spatial examination of Unit III, formed during Marine Isotope Stage 3, with the aim of understanding spatial organization and past activities developed by Neanderthals and carnivores (bears, hyenas and smaller carnivores). The total sample analysed includes 38,244 archaeological items and 5888 limestone blocks. The application of GIS tools allows us to clearly distinguish three geologically-defined stratigraphic subunits. Unit III has been previously interpreted as a palimpsest resulting from alternating occupation of the cave by human groups and carnivores. The distribution study shows that faunal specimens, lithic artefacts, hearths and charcoal fragments are significantly concentrated at the entrance of the cave where, it is inferred, hominins carried out different activities, while carnivores preferred the sheltered zones in the inner areas of the cave. The results obtained reveal a spatial pattern characterized by fire use related zones, and show that the site was occupied by Neanderthals in a similar and consistent way throughout the ˃ 7000 years range covered by the analysed subunits. This spatial pattern is interpreted as resulting from repeated short-term human occupations.

RevDate: 2021-02-22

González-Urquijo J, Bailey SE, T Lazuen (2021)

Axlor's level IV human remains are convincingly Neanderthals: A reply to Gómez-Olivencia et al.

RevDate: 2021-05-07
CmpDate: 2021-04-30

Lee JW, Lee IH, Sato T, et al (2021)

Genetic variation analyses indicate conserved SARS-CoV-2-host interaction and varied genetic adaptation in immune response factors in modern human evolution.

Development, growth & differentiation, 63(3):219-227.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pandemic as of early 2020. Upon infection, SARS-CoV-2 attaches to its receptor, that is, angiotensin-converting enzyme 2 (ACE2), on the surface of host cells and is then internalized into host cells via enzymatic machineries. This subsequently stimulates immune response factors. Since the host immune response and severity of COVID-19 vary among individuals, genetic risk factors for severe COVID-19 cases have been investigated. Our research group recently conducted a survey of genetic variants among SARS-CoV-2-interacting molecules across populations, noting near absence of difference in allele frequency spectrum between populations in these genes. Recent genome-wide association studies have identified genetic risk factors for severe COVID-19 cases in a segment of chromosome 3 that involves six genes encoding three immune-regulatory chemokine receptors and another three molecules. The risk haplotype seemed to be inherited from Neanderthals, suggesting genetic adaptation against pathogens in modern human evolution. Therefore, SARS-CoV-2 uses highly conserved molecules as its virion interaction, whereas its immune response appears to be genetically biased in individuals to some extent. We herein review the molecular process of SARS-CoV-2 infection as well as our further survey of genetic variants of its related immune effectors. We also discuss aspects of modern human evolution.

RevDate: 2021-03-12
CmpDate: 2021-02-26

Zeberg H, S Pääbo (2021)

A genomic region associated with protection against severe COVID-19 is inherited from Neandertals.

Proceedings of the National Academy of Sciences of the United States of America, 118(9):.

It was recently shown that the major genetic risk factor associated with becoming severely ill with COVID-19 when infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is inherited from Neandertals. New, larger genetic association studies now allow additional genetic risk factors to be discovered. Using data from the Genetics of Mortality in Critical Care (GenOMICC) consortium, we show that a haplotype at a region on chromosome 12 associated with requiring intensive care when infected with the virus is inherited from Neandertals. This region encodes proteins that activate enzymes that are important during infections with RNA viruses. In contrast to the previously described Neandertal haplotype that increases the risk for severe COVID-19, this Neandertal haplotype is protective against severe disease. It also differs from the risk haplotype in that it has a more moderate effect and occurs at substantial frequencies in all regions of the world outside Africa. Among ancient human genomes in western Eurasia, the frequency of the protective Neandertal haplotype may have increased between 20,000 and 10,000 y ago and again during the past 1,000 y.

RevDate: 2021-02-19

Blinkhorn J, Zanolli C, Compton T, et al (2021)

Nubian Levallois technology associated with southernmost Neanderthals.

Scientific reports, 11(1):2869.

Neanderthals occurred widely across north Eurasian landscapes, but between ~ 70 and 50 thousand years ago (ka) they expanded southwards into the Levant, which had previously been inhabited by Homo sapiens. Palaeoanthropological research in the first half of the twentieth century demonstrated alternate occupations of the Levant by Neanderthal and Homo sapiens populations, yet key early findings have largely been overlooked in later studies. Here, we present the results of new examinations of both the fossil and archaeological collections from Shukbah Cave, located in the Palestinian West Bank, presenting new quantitative analyses of a hominin lower first molar and associated stone tool assemblage. The hominin tooth shows clear Neanderthal affinities, making it the southernmost known fossil specimen of this population/species. The associated Middle Palaeolithic stone tool assemblage is dominated by Levallois reduction methods, including the presence of Nubian Levallois points and cores. This is the first direct association between Neanderthals and Nubian Levallois technology, demonstrating that this stone tool technology should not be considered an exclusive marker of Homo sapiens.

RevDate: 2021-06-28
CmpDate: 2021-06-28

Bach JF (2020)

Revisiting the Hygiene Hypothesis in the Context of Autoimmunity.

Frontiers in immunology, 11:615192.

Initially described for allergic diseases, the hygiene hypothesis was extended to autoimmune diseases in the early 2000s. A historical overview allows appreciation of the development of this concept over the last two decades and its discussion in the context of evolution. While the epidemiological data are convergent, with a few exceptions, the underlying mechanisms are multiple and complex. A major question is to determine what is the respective role of pathogens, bacteria, viruses, and parasites, versus commensals. The role of the intestinal microbiota has elicited much interest, but is it a cause or a consequence of autoimmune-mediated inflammation? Our hypothesis is that both pathogens and commensals intervene. Another question is to dissect what are the underlying cellular and molecular mechanisms. The role of immunoregulatory cytokines, in particular interleukin-10 and TGF beta is probably essential. An important place should also be given to ligands of innate immunity receptors present in bacteria, viruses or parasites acting independently of their immunogenicity. The role of Toll-Like Receptor (TLR) ligands is well documented including via TLR ligand desensitization.

RevDate: 2021-02-19
CmpDate: 2021-02-19

Remmel A (2021)

Neanderthal-like 'mini-brains' created in lab with CRISPR.

Nature, 590(7846):376-377.

RevDate: 2021-05-21
CmpDate: 2021-02-26

Trujillo CA, Rice ES, Schaefer NK, et al (2021)

Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment.

Science (New York, N.Y.), 371(6530):.

The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1 Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.

RevDate: 2021-03-09
CmpDate: 2021-03-09

Bergström A, Stringer C, Hajdinjak M, et al (2021)

Origins of modern human ancestry.

Nature, 590(7845):229-237.

New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories.

RevDate: 2021-02-11

Mortazavi SAR, Kaveh-Ahangar K, Mortazavi SMJ, et al (2021)

How Our Neanderthal Genes Affect the COVID-19 Mortality: Iran and Mongolia, Two Countries with the Same SARS-CoV-2 Mutation Cluster but Different Mortality Rates.

Journal of biomedical physics & engineering, 11(1):109-114.

Neanderthal genes possibly gave modern human protection against viruses. However, a recent study revealed that that a long sequence of DNA that is inherited from our Neanderthal ancestors can be linked to severe COVID-19 infection and hospitalization. Substantial evidence now indicates that our genetic background may be involved in the transmissibility of SARS-CoV-2 and the rapid progress of COVID-19 in some infected individuals. Although both morbidity and mortality of COVID-19 strongly depends on key factors such as age and co-existing health conditions, potential classes of human genomic variants possibly affect the likelihood of SARS-CoV-2 infection and its progress. Despite Iran and Mongolia seem to share the same SARS-CoV-2 mutation cluster, the COVID-19 mortality rates in these two countries are drastically different. While the population in Iran is 25.8 times higher than that of Mongolia, the number of confirmed cases is 1170 times higher. Moreover, the death rate shows a drastic difference. Since Neanderthals interbred with modern humans in Middle East between 47,000 and 65,000 years ago before going extinct 40,000 years ago, some Iranians have much more Neanderthal DNA than other people. Although neither genetic background nor environmental factors alone can determine our risk of developing severe COVID-19, our genes clearly affect both the development and progression of infectious diseases including COVID-19. Given these considerations, we believe that these great differences, at least to some extent, can be due to the proportion of Neanderthal genes among the people of these two countries.

RevDate: 2021-03-10

Reinscheid RK, Mafessoni F, Lüttjohann A, et al (2021)

Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality.

Peptides, 138:170506.

The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human primates, several non-synonymous single-nucleotide polymorphisms (SNPs) occur in both human genes that collectively result in functional attenuation, suggesting adaptive mechanisms in a human context. To investigate historic and geographic origins of these hypomorphic mutations and explore genetic signs of selection, we analyzed ancient genomes and worldwide genotype frequencies of four prototypic SNPs in the NPS system. Neandertal and Denisovan genomes contain exclusively ancestral alleles for NPSR1 while all derived alleles occur in ancient genomes of anatomically modern humans, indicating that they arose in modern Homo sapiens. Worldwide genotype frequencies for three hypomorphic NPSR1 SNPs show significant regional homogeneity but follow a gradient towards increasing derived allele frequencies that supports an out-of-Africa scenario. Increased density of high-frequency polymorphisms around the three NPSR1 loci suggests weak or possibly balancing selection. A hypomorphic mutation in the NPS precursor, however, was detected at high frequency in Eurasian Neandertal genomes and shows genetic signatures indicating that it was introgressed into the human gene pool, particularly in Southern Europe, by interbreeding with Neandertals. We discuss potential evolutionary scenarios including behavior and immune-based natural selection.

RevDate: 2021-02-18

Rampelli S, Turroni S, Mallol C, et al (2021)

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.

Communications biology, 4(1):169.

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

RevDate: 2021-05-03
CmpDate: 2021-05-03

Selig KR, Kupczik K, MT Silcox (2021)

The effect of high wear diets on the relative pulp volume of the lower molars.

American journal of physical anthropology, 174(4):804-811.

OBJECTIVES: One role of dental pulp is in the upkeep and maintenance of dentine. Under wear, odontoblasts in the pulp deposit tertiary dentine to ensure the sensitive internal dental tissues are not exposed and vulnerable to infection. It follows that there may be an adaptive advantage for increasing molar pulp volume in anthropoid primate taxa that are prone to high levels of wear. The relative volume of dental pulp is therefore predicted to covary with dietary abrasiveness (in the sense of including foods that cause high degrees of wear).

MATERIALS AND METHODS: We examined relatively unworn lower second molars in pairs of species of extant hominoids, cebids, and pitheciids that vary in the abrasiveness of their diet (n = 36). Using micro-CT scans, we measured the percent of tooth that is pulp (PTP) as the ratio of pulp volume to that of the total volume of the tooth.

RESULTS: We found that in each pair of species, the taxa that consume a more abrasive diet had a significantly higher PTP than the closely related taxa that consume a softer diet.

CONCLUSIONS: Our results point to an adaptive mechanism in the molars of taxa that consume abrasive diets and are thus subject to higher levels of wear. Our results provide additional understanding of the relationship between dental pulp and diet and may offer insight into the diet of extinct taxa such as Paranthropus boisei or into the adaptive context of the taurodont molars of Neanderthals.

RevDate: 2021-02-24

Lacy SA (2021)

Evidence of dental agenesis in late pleistocene Homo.

International journal of paleopathology, 32:103-110.

OBJECTIVE: Differential diagnosis and tabulation of cases of dental agenesis in Middle and Upper Paleolithic Western Eurasian humans to synthesize this data and to test previous hypotheses about when recent human patterns of third molar agenesis were established.

MATERIALS: 139 Late Pleistocene human remains and 149 individuals from three Epi-Paleolithic/ Holocene non-agricultural comparative collections.

METHODS: All remains were visually and radiographically recorded by the author.

RESULTS: In addition to establishing that third molar agenesis was common during the Late Upper Paleolithic (22,500-10,000 years BP), this study suggests a pattern of increasing prevalence through time.

CONCLUSIONS: An increase in the prevalence of third molar agenesis in the Late Upper Paleolithic could indicate selection for dental size reduction and orthognathy, but also bio-cultural changes from more intensive food preparation techniques.

SIGNIFICANCE: Third molar agenesis, a well-known developmental defect, is often reported for recent human skeletal collections, but the prevalence of the condition for Pleistocene hominins had not been previously quantified in order to consider patterns through time. Hypotheses posited for the high prevalence of third molar agenesis, or hypodontia in general, in some recent human groups require an understanding of the prevalence of these traits in the past.

LIMITATIONS: Paleolithic skeletal remains are incomplete, so these values are under-estimations. Individuals are also separated diachronically and geographically and should not be assumed to represent a single population sample.

Hypotheses on some of the potential selective forces acting on dental size reduction and subsequent agenesis could be tested in recent humans.

RevDate: 2021-03-01

Compton T, Skinner MM, Humphrey L, et al (2021)

The morphology of the Late Pleistocene hominin remains from the site of La Cotte de St Brelade, Jersey (Channel Islands).

Journal of human evolution, 152:102939.

Thirteen permanent fully erupted teeth were excavated at the Paleolithic site of La Cotte de St Brelade in Jersey in 1910 and 1911. These were all found in the same location, on a ledge behind a hearth in a Mousterian occupation level. They were originally identified as being Neanderthal. A fragment of occipital bone was found in a separate locality in a later season. Recent dating of adjacent sediments gives a probable age of <48 ka. The purpose of this article is to provide an updated description of the morphology of this material and consider its likely taxonomic assignment from comparison with Neanderthal and Homo sapiens samples. One of the original teeth has been lost, and we identify one as nonhominin. At least two adult individuals are represented. Cervix shape and the absence of common Neanderthal traits in several teeth suggest affinities with H. sapiens in both individuals, while crown and root dimensions and root morphology of all the teeth are entirely consistent with a Neanderthal attribution, pointing toward a possible shared Neanderthal and H. sapiens ancestry (the likely date of this material corresponds with the time in which both Neanderthals and H. sapiens were present in Europe). The occipital fragment is stratigraphically more recent and does not exhibit any diagnostic Neanderthal features.

RevDate: 2021-04-01

Kliesch S, Schmidt S, Wilborn D, et al (2021)

Management of Germ Cell Tumours of the Testes in Adult Patients: German Clinical Practice Guideline, PART II - Recommendations for the Treatment of Advanced, Recurrent, and Refractory Disease and Extragonadal and Sex Cord/Stromal Tumours and for the Management of Follow-Up, Toxicity, Quality of Life, Palliative Care, and Supportive Therapy.

Urologia internationalis, 105(3-4):181-191.

OBJECTIVES: We developed the first German evidence- and consensus-based clinical guideline on diagnosis, treatment, and follow-up of germ cell tumours (GCT) of the testes in adult patients. We present the guideline content in 2 separate publications. The present second part summarizes therecommendations for the treatment of advanced disease stages and for the management of follow-up and late effects.

MATERIALS AND METHODS: An interdisciplinary panel of 42 experts including 1 patient representative developed the guideline content. Clinical recommendations and statements were based on scientific evidence and expert consensus. For this purpose, evidence tables for several review questions, which were based on systematic literature searches (last search in March 2018), were provided. Thirty-one experts, who were entitled to vote, rated the final clinical recommendations and statements.

RESULTS: Here we present the treatment recommendations separately for patients with metastatic seminoma and non-seminomatous GCT (stages IIA/B and IIC/III), for restaging and treatment of residual masses, and for relapsed and refractory disease stages. The recommendations also cover extragonadal and sex cord/stromal tumours, the management of follow-up and toxicity, quality-of-life aspects, palliative care, and supportive therapy.

CONCLUSION: Physicians and other medical service providers who are involved in the diagnostics, treatment, and follow-up of GCT (all stages, outpatient and inpatient care as well as rehabilitation) are the users of the present guideline. The guideline also comprises quality indicators for measuring the implementation of the guideline recommendations in routine clinical care; these data will be presented in a future publication.

RevDate: 2021-03-11
CmpDate: 2021-03-11

VanSickle C, Cofran Z, D Hunt (2020)

Did Neandertals have large brains? Factors affecting endocranial volume comparisons.

American journal of physical anthropology, 173(4):768-775.

OBJECTIVES: Common wisdom in paleoanthropology is that Neandertals had bigger brains than recent humans. Here we tested the hypothesis that there is no difference in brain size between Neandertals and recent humans while accounting for methodological variation and the makeup of both the Neandertal and recent human samples.

MATERIALS AND METHODS: We examined endocranial volume (ECV) derived from virtually reconstructed endocasts of 11 Neandertals, six of which had associated femoral head diameters (FHD). Our recent human comparative dataset consisted of virtually measured ECV and associated FHD from 94 recent humans from the Robert J. Terry Anatomical Collection (63 male, 31 female). ECV of Neandertals and recent humans was compared using bootstrap resampling, repeating the analysis for two groupings of Neandertals (all and classic) and for three groupings of recent humans (all, males, and females). To examine brain size scaling, we completed an ordinary least squares regression of log (ECV) against log (FHD) for Neandertals and recent humans.

RESULTS: The results of the bootstrap resampling analyses indicated that Neandertals only had significantly larger ECV when compared with recent human females. The regression between ECV and FHD suggested that Neandertals fall within the range of variation for larger humans.

DISCUSSION: Our results demonstrate that Neandertals do not have uniquely large brains when compared with recent humans. Their brain size falls in the large end of the recent human range of variation, but does not exceed it. These results have implications for future research on Neandertal encephalization.

RevDate: 2021-05-21
CmpDate: 2021-05-21

Towle I, C Loch (2021)

Tooth chipping prevalence and patterns in extant primates.

American journal of physical anthropology, 175(1):292-299.

OBJECTIVES: A tooth chip occurs when a hard object forcefully contacts the surface of the tooth, typically removing enamel from the occlusal edge. In this study, chipping patterns in extant primates were compared, and hard-object-feeding assessed alongside other factors (e.g., grit mastication and dental properties), to elucidate dietary and behavioral inferences in archeological and paleontological samples.

MATERIALS AND METHODS: Thirteen species of extant primates were studied, including eight species within the Cercopithecidae, two within the Ceboidea, and three within the Hominoidea. Four additional species were also incorporated from the literature for some of the analyses. The severity (Grade 1-3), position (buccal, lingual, mesial, and distal) and number of tooth fractures were recorded for each specimen.

RESULTS: Species considered hard-object-feeding specialists presented higher rates of chipping, with sakis, mandrills, sooty mangabeys and Raffles' banded langurs having high chipping rates (28.3%, 36.7%, 48.4%, and 34.7% of teeth, respectively). Species that seasonally eat harder foods had intermediate chipping frequencies (e.g., brown woolly monkeys: 18.5%), and those that less commonly consume hard food items had the lowest chipping frequencies (e.g., Kloss gibbon: 7.3%; chimpanzees: 4.4%).

DISCUSSION: The results suggest hard food mastication influences differences in chipping prevalence among the species studied. Although Homo fossil samples show high rates of chipping comparable to hard-object-feeding extant primates, they display a different pattern of chipping, supporting the hypothesis that these fractures are mostly non-food related (e.g., grit mastication in Homo naledi; non-masticatory tooth use in Neanderthals).

RevDate: 2021-01-22

Pederzani S, Aldeias V, Dibble HL, et al (2021)

Reconstructing Late Pleistocene paleoclimate at the scale of human behavior: an example from the Neandertal occupation of La Ferrassie (France).

Scientific reports, 11(1):1419.

Exploring the role of changing climates in human evolution is currently impeded by a scarcity of climatic information at the same temporal scale as the human behaviors documented in archaeological sites. This is mainly caused by high uncertainties in the chronometric dates used to correlate long-term climatic records with archaeological deposits. One solution is to generate climatic data directly from archaeological materials representing human behavior. Here we use oxygen isotope measurements of Bos/Bison tooth enamel to reconstruct summer and winter temperatures in the Late Pleistocene when Neandertals were using the site of La Ferrassie. Our results indicate that, despite the generally cold conditions of the broader period and despite direct evidence for cold features in certain sediments at the site, Neandertals used the site predominantly when climatic conditions were mild, similar to conditions in modern day France. We suggest that due to millennial scale climate variability, the periods of human activity and their climatic characteristics may not be representative of average conditions inferred from chronological correlations with long-term climatic records. These results highlight the importance of using direct routes, such as the high-resolution archives in tooth enamel from anthropogenically accumulated faunal assemblages, to establish climatic conditions at a human scale.

RevDate: 2021-03-16

Dumas G, Malesys S, T Bourgeron (2021)

Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition.

Genome research, 31(3):484-496.

The human brain differs from that of other primates, but the genetic basis of these differences remains unclear. We investigated the evolutionary pressures acting on almost all human protein-coding genes (N = 11,667; 1:1 orthologs in primates) based on their divergence from those of early hominins, such as Neanderthals, and non-human primates. We confirm that genes encoding brain-related proteins are among the most strongly conserved protein-coding genes in the human genome. Combining our evolutionary pressure metrics for the protein-coding genome with recent data sets, we found that this conservation applied to genes functionally associated with the synapse and expressed in brain structures such as the prefrontal cortex and the cerebellum. Conversely, several genes presenting signatures commonly associated with positive selection appear as causing brain diseases or conditions, such as micro/macrocephaly, Joubert syndrome, dyslexia, and autism. Among those, a number of DNA damage response genes associated with microcephaly in humans such as BRCA1, NHEJ1, TOP3A, and RNF168 show strong signs of positive selection and might have played a role in human brain size expansion during primate evolution. We also showed that cerebellum granule neurons express a set of genes also presenting signatures of positive selection and that may have contributed to the emergence of fine motor skills and social cognition in humans. This resource is available online and can be used to estimate evolutionary constraints acting on a set of genes and to explore their relative contributions to human traits.

RevDate: 2021-06-22

McGrath K, Limmer LS, Lockey AL, et al (2021)

3D enamel profilometry reveals faster growth but similar stress severity in Neanderthal versus Homo sapiens teeth.

Scientific reports, 11(1):522.

Early life stress disrupts growth and creates horizontal grooves on the tooth surface in humans and other mammals, yet there is no consensus for their quantitative analysis. Linear defects are considered to be nonspecific stress indicators, but evidence suggests that intermittent, severe stressors create deeper defects than chronic, low-level stressors. However, species-specific growth patterns also influence defect morphology, with faster-growing teeth having shallower defects at the population level. Here we describe a method to measure the depth of linear enamel defects and normal growth increments (i.e., perikymata) from high-resolution 3D topographies using confocal profilometry and apply it to a diverse sample of Homo neanderthalensis and H. sapiens anterior teeth. Debate surrounds whether Neanderthals exhibited modern human-like growth patterns in their teeth and other systems, with some researchers suggesting that they experienced more severe childhood stress. Our results suggest that Neanderthals have shallower features than H. sapiens from the Upper Paleolithic, Neolithic, and medieval eras, mirroring the faster growth rates in Neanderthal anterior teeth. However, when defect depth is scaled by perikymata depth to assess their severity, Neolithic humans have less severe defects, while Neanderthals and the other H. sapiens groups show evidence of more severe early life growth disruptions.

RevDate: 2021-02-15

Heydari M, Guérin G, Zeidi M, et al (2021)

Bayesian luminescence dating at Ghār-e Boof, Iran, provides a new chronology for Middle and Upper Paleolithic in the southern Zagros.

Journal of human evolution, 151:102926.

Ghār-e Boof is a Paleolithic cave site in Iran well known for its rich early Upper Paleolithic Rostamian assemblages. The site is located on the edge of the Dasht-e Rostam plain in the southern Zagros. Recent excavations by the members of the Tübingen-Iranian Stone Age Research Project at Ghār-e Boof also recovered well-stratified Middle Paleolithic assemblages. Here, we provide the first detailed luminescence chronology for the Middle and Upper Paleolithic of the site. More generally, our work is the first luminescence chronology for a Middle and Upper Paleolithic site in the Zagros Mountains region in Iran. The luminescence ages for the Upper Paleolithic of Ghār-e Boof agree with published 14C dates. We applied Bayesian models specifically designed for luminescence dating using the R package 'BayLum' to incorporate the well-established stratigraphic constraints, as well as the published 14C ages with our optically stimulated luminescence (OSL) ages to improve the precision of the chronological framework. The Bayesian chronology shows a significantly improved precision of the OSL ages in particular for the upper part of the sequence where 14C ages were available. The Bayesian OSL ages for the Rostamian horizons, archaeologicalhorizon (AH) III (a-b-c), and AH IV, fall in the range of 37-42 ka (68% credible interval [CI]). Moreover, we determined a series of dates between 45 and 81 ka (68% CI) for the Middle Paleolithic strata from AH IVd to AH VI. Our results point to a demographic shift in the populations responsible for the Middle Paleolithic and the Rostamian within three millennia. This major technological change accompanied by the rise of symbolic artifacts such as personal ornaments, may or may not reflect a replacement of Neanderthals by modern humans. While we are confident that the Rostamian was made by modern humans, available information does not allow us to be sure who made the local Middle Paleolithic.

RevDate: 2021-02-15

Nowaczewska W, Binkowski M, Benazzi S, et al (2021)

New hominin teeth from Stajnia Cave, Poland.

Journal of human evolution, 151:102929.

RevDate: 2021-05-28
CmpDate: 2021-05-28

Greer C, Bhakta H, Ghanem L, et al (2021)

Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans.

Human reproduction (Oxford, England), 36(3):734-755.

STUDY QUESTION: Were Neanderthals and Denisovans (referred here also as extinct hominidae) carrying deleterious variants in genes regulating reproduction?

SUMMARY ANSWER: The majority of extinct hominidae analyzed here, presented a considerable number of deleterious variants per individual in proteins regulating different aspects of reproduction, including gonad and uterine function, and gametogenesis.

WHAT IS KNOWN ALREADY: Neanderthals, Denisovans and extant humans were interfertile and hybridized while occupying geographically overlapping areas in Europe and Asia. This is evidenced by the small archaic genome component (average ∼2%) present in non-African extant humans.

STUDY DESIGN, SIZE, DURATION: The genome of eight extinct hominidae, together with five human genome databases, plus 44 mothers and 48 fathers (fertile controls), were screened to look for deleterious variants in 1734 protein-coding genes regulating reproduction.

Ancient DNA from six Neanderthals and two Denisovans dated between ∼82 000 and 43 000 calibrated years was retrieved from the public European Nucleotide Archive. The hominins analyzed include Altai, Vindija 33.15, 33.19, 33.25 and 33.26, El Sidron 1253, Denisova 3 and 11. Their DNA was analyzed using the CLC Genomics Workbench 12, by mapping overlapping paired-end reads (Illumina, FASTQ files) to the human genome assembly GRCh37 (hg19) (Vindija 33.19, 33.25, 33.26, Denisova 3 and Denisova 11) or by analyzing BAM files (Altai, El Sidron 1253 and Vindija 33.15) (human genome reference, GRCh37 (hg19)). Non-synonymous reproductive variants were classified as deleterious or tolerated (PolyPhen-2 and SIFT analyses) and were compared to deleterious variants obtained from extant human genome databases (Genome Aggregation Database (GnomAD), 1000 Genomes, the Haplotype Map (HapMap), Single Nucleotide Polymorphism Database (dbSNPs)) across different populations. A genetic intersection between extant or extinct DNA variants and other genetic disorders was evaluated by annotating the obtained variants with the Clinical Variant (ClinVar) database.

Among the eight extinct hominidae analyzed, a total of 9650 non-synonymous variants (only coverage ≥20 reads included; frameshift mutations were excluded) in 1734 reproductive protein-coding genes were found, 24% of which were classified as deleterious. The majority (73%) of the deleterious alleles present in extant humans that are shared between extant humans and extinct hominidae were found to be rare (<1%) in extant human populations. A set of 8044 variants were found uniquely in extinct hominidae. At the single-gene level, no extinct individual was found to be homozygous for deleterious variants in genes necessary for gamete recognition and fusion, and no higher chance of embryo-lethality (calculated by Mendelian Genetics) was found upon simulated mating between extant human and extinct hominidae compared to extant human-extant human. However, three of the eight extinct hominidae were found to be homozygous for 48-69 deleterious variants in 55 genes controlling ovarian and uterine functions, or oogenesis (AKAP1, BUB1B, CCDC141, CDC73, DUSP6, ESR1, ESR2, PATL2, PSMC3IP, SEMA3A, WT1 and WNT4). Moreover, we report the distribution of nine Neanderthal variants in genes associated with a human fertility phenotype found in extant human populations, one of which has been associated with polycystic ovarian syndrome and primary congenital glaucoma.

While analyzing archaic DNA, stringent filtering criteria were adopted to screen for deleterious variants in Neanderthals and Denisovans, which could result in missing a number of variants. Such restraints preserve the potential for detection of additional deleterious variants in reproductive proteins in extinct hominidae.

This study provides a comprehensive overview of putatively deleterious variants in extant human populations and extinct individuals occurring in 1734 protein-coding genes controlling reproduction and provides the fundaments for future functional studies of extinct variants in human reproduction.

This study was supported by the Department of Biological Science and by the Office of Research and Sponsored Programs at the University of Tulsa (Faculty Research Grant and Faculty Research Summer Fellowship) to M.A. and the University of Tulsa, Tulsa Undergraduate Research Challenge (TURC) program to E.L.; no conflict of interest to declare.


RevDate: 2021-04-01

Kliesch S, Schmidt S, Wilborn D, et al (2021)

Management of Germ Cell Tumours of the Testis in Adult Patients. German Clinical Practice Guideline Part I: Epidemiology, Classification, Diagnosis, Prognosis, Fertility Preservation, and Treatment Recommendations for Localized Stages.

Urologia internationalis, 105(3-4):169-180.

INTRODUCTION: This is the first German evidence- and consensus-based clinical guideline on diagnosis, treatment, and follow-up on germ cell tumours (GCTs) of the testis in adult patients. We present the guideline content in two publications. Part I covers the topic's background, methods, epidemiology, classification systems, diagnostics, prognosis, and treatment recommendations for the localized stages.

METHODS: An interdisciplinary panel of 42 experts including 1 patient representative developed the guideline content. Clinical recommendations and statements were based on scientific evidence and expert consensus. For this purpose, evidence tables for several review questions, which were based on systematic literature searches (last search was in March 2018) were provided. Thirty-one experts entitled to vote, rated the final clinical recommendations and statements.

RESULTS: We provide 161 clinical recommendations and statements. We present information on the quality of cancer care and epidemiology and give recommendations for staging and classification as well as for diagnostic procedures. The diagnostic recommendations encompass measures for assessing the primary tumour as well as procedures for the detection of metastases. One chapter addresses prognostic factors. In part I, we separately present the treatment recommendations for germ cell neoplasia in situ, and the organ-confined stages (clinical stage I) of both seminoma and nonseminoma.

CONCLUSION: Although GCT is a rare tumour entity with excellent survival rates for the localized stages, its management requires an interdisciplinary approach, including several clinical experts. Quality of care is highly related to institutional expertise and can be reassured by established online-based second-opinion boards. There are very few studies on diagnostics with good level of evidence. Treatment of metastatic GCTs must be tailored to the risk according to the International Germ Cell Cancer Collaboration Group classification after careful diagnostic evaluation. An interdisciplinary approach as well as the referral of selected patients to centres with proven experience can help achieve favourable clinical outcomes.

RevDate: 2021-02-15

Dodat PJ, Tacail T, Albalat E, et al (2021)

Isotopic calcium biogeochemistry of MIS 5 fossil vertebrate bones: application to the study of the dietary reconstruction of Regourdou 1 Neandertal fossil.

Journal of human evolution, 151:102925.

The calcium isotopic composition (δ44/42Ca) of bone and tooth enamel can be used for dietary reconstructions of extant and extinct mammals. In natural conditions, the δ44/42Ca value of bone and teeth varies according to dietary intake with a constant isotopic offset of about -0.6‰. Owing to the poor conservation of collagen, carbon (C), and nitrogen (N) isotopic compositions of the Regourdou Mousterian site (MIS 5, Dordogne, France) previously failed to provide any paleodietary information. Therefore, to reconstruct the trophic chain, we have measured calcium (Ca) isotopes from fossil bone samples of the fauna from the Regourdou site, as well as from three bone samples of the Regourdou 1 Neandertal specimen. The results show a taxon-dependent patterning of the Ca isotopic compositions: herbivores generally have higher δ44/42Ca values than carnivores. All the δ44/42Ca values of Regourdou 1 are low (<-1.6‰), placing this specimen amid carnivores. Using a bone-muscle Ca isotopic offset determined on extant animals, we further show that the δ44/42Ca value of the Regourdou 1 diet, and that of most carnivores, cannot be accounted for by the consumption of meat only, as plants and meat have indistinguishable δ44/42Ca values. Mass balance calculations indicate that the low δ44/42Ca values of the Neandertal's carnivorous diet are explained by the ingestion of bone marrow containing as little as 1% trabecular bone. Our results show that the Regourdou 1 Neanderthal consumed a mixture of various herbivorous prey, as well as trabecular bone, which probably occurred when marrow was ingested, by accident or intentionally.

RevDate: 2021-03-11
CmpDate: 2021-03-11

González-Molina I, Jiménez-García B, Maíllo-Fernández JM, et al (2020)

Distinguishing Discoid and Centripetal Levallois methods through machine learning.

PloS one, 15(12):e0244288.

In this paper, we apply Machine Learning (ML) algorithms to study the differences between Discoid and Centripetal Levallois methods. For this purpose, we have used experimentally knapped flint flakes, measuring several parameters that have been analyzed by seven ML algorithms. From these analyses, it has been possible to demonstrate the existence of statistically significant differences between Discoid products and Centripetal Levallois products, thus contributing with new data and a new method to this traditional debate. The new approach enabled differentiating the blanks created by both knapping methods with an accuracy >80% using only ten typometric variables. The most relevant variables were maximum length, width to the 25%, 50% and 75% of the flake length, external and internal platform angles, maximum width and number of dorsal scars. This study also demonstrates the advantages of the application of multivariate ML methods to lithic studies.

RevDate: 2021-02-15

Adegboyega MT, Stamos PA, Hublin JJ, et al (2021)

Virtual reconstruction of the Kebara 2 Neanderthal pelvis.

Journal of human evolution, 151:102922.

The paucity of well-preserved pelvises in the hominin fossil record has hindered robust analyses of shifts in critical biological processes throughout human evolution. The Kebara 2 pelvis remains one of the best preserved hominin pelvises, providing a rare opportunity to assess Neanderthal pelvic morphology and function. Here, we present two new reconstructions of the Kebara 2 pelvis created from CT scans of the right hip bone and sacrum. For both reconstructions, we proceeded as follows. First, we virtually reconstructed the right hip bone and the sacrum by repositioning the fragments of the hip bone and sacrum. Then, we created a mirrored copy of the right hip bone to act as the left hip bone. Next, we 3D printed the three bones and physically articulated them. Finally, we used fiducial points collected from the physically articulated models to articulate the hip bones and sacrum in virtual space. Our objectives were to (1) reposition misaligned fragments, particularly the ischiopubic ramus; (2) create a 3D model of a complete pelvis; and (3) assess interobserver reconstruction variation. These new reconstructions show that, in comparison with previous measurements, Kebara 2 possessed a higher shape index (maximum anteroposterior length/maximum mediolateral width) for the pelvic inlet and perhaps the outlet and a more anteriorly positioned sacral promontory and pubic symphysis relative to the acetabula. The latter differences result in a lower ratio between the distances anterior and posterior to the anterior margins of the acetabula. Generally, the new reconstructions tend to accentuate features of the Kebara 2 pelvis--the long superior pubic ramus and anteriorly positioned pelvic inlet--that have already been discussed for Kebara 2 and other Neanderthals.

RevDate: 2021-05-19

Higgitt R (2021)

Neanderthal and the fossilization of the Third World.

Social studies of science, 51(3):439-462.

Neanderthal is the quintessential scientific Other. In the late nineteenth century gentlemen-scientists, including business magnates, investment bankers and lawmakers with interest in questions of human and human societal development, framed Europe's Neanderthal and South Asia's indigenous Negritos as close evolutionary kin. Simultaneously, they explained Neanderthal's extinction as the consequence of an inherent backwardness in the face of fair-skinned, steadily-progressing newcomers to ancient Europe who behaved in ways associated with capitalism. This racialization and economization of Neanderthal helped bring meaning and actual legal reality to Negritos via the British Raj's official 'schedules of backward castes and tribes'. It also helped justify the Raj's initiation of market-oriented reforms in order to break a developmental equilibrium deemed created when fair-skinned newcomers to ancient South Asia enslaved Negritos in an enduring caste system. Neanderthal was integral to the scientism behind the British construction of caste, and contributed to India's becoming a principal 'Third World' target of Western structural adjustment policies as continuation of South Asia's 'evolution assistance'.

RevDate: 2020-12-22

Kist NC, Lambert B, Campbell S, et al (2020)

HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification.

Virus evolution, 6(2):veaa085.

Pathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong positive correlation between ethnic diversity in African countries and both human immunodeficiency virus (HIV)-1 p24gag and subtype diversity. We demonstrate that ethnic HLA-allele differences between populations have influenced HIV-1 subtype diversification as the virus adapted to escape common antiviral immune responses. The evolution of HIV Subtype B (HIV-B), which does not appear to be indigenous to Africa, is strongly affected by immune responses associated with Eurasian HLA variants acquired through adaptive introgression from Neanderthals and Denisovans. Furthermore, we show that the increasing and disproportionate number of HIV-infections among African Americans in the USA drive HIV-B evolution towards an Africa-centric HIV-1 state. Similar adaptation of other pathogens to HLA variants common in affected populations is likely.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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The first fossil recognized to be an ancestral human was found in the Neander Valley (thal in German) in 1856. William King suggested Homo neanderthalensis (human from the Neander Valley) as the scientific name for the specimen — hence Neanderthal became the common name by which this early human became known. Now Neanderthal genomes have been sequenced, more is known about their path to extinction, and the existence of Neanderthal culture, including music, has been established. To understand the evolutionary path of the hominid line, one must be familiar with Homo neanderthalensis. These books are highly recommended. R. Robbins

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )