Early history of Neanderthals and Denisovans

Ghosts of extinct apes: genomic insights into African hominid evolution

We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.

The Neanderthal niche space of Western Eurasia 145 ka to 30 ka ago

Neanderthals occupied Western Eurasia between 350 ka and 40 ka ago, during the climatically volatile Pleistocene. A key issue is to what extent Neanderthal populations expanded into areas of Western Eurasia and what conditions facilitated such range expansions. The range extent of Neanderthals is generally based on the distribution of Neanderthal material, but the land-altering nature of glacial periods has erased much of the already sparse material evidence of Neanderthals, particularly in the northern latitudes. To overcome this obstacle species distribution models can estimate past distributions of Neanderthals, however, most implementations are generally constrained spatially and temporally and may be artificially truncating the Neanderthal niche space. Using dated contexts from Neanderthal sites from across Western Eurasia, millennial-scale paleoclimate reconstructions, and a spatiotemporal species distribution model, we infer the fundamental climatic niche space of Neanderthals and estimate the extent of Neanderthal occupation. We find that (a.) despite the long timeframe, Neanderthals occupy a relatively narrow fundamental climatic niche space, (b.) the estimated projected potential Neanderthal niche space suggests a larger geographic range than the material record suggests, and (c.) that there was a general decline in the size of the projected potential Neanderthal niche from 145 ka ago onward, possibly contributing to their extinction.

Creating frames of reference for chert exploitation during the Late Pleistocene in Southwesternmost Iberia

Southwestern Iberia has played a key role in characterizing Late Pleistocene human ecodynamics. Among other aspects of human behavior, chert procurement and management studies in this region have received increasing attention in the past two decades, especially focusing on the sites showing repeated human occupation, such as the case of Vale Boi (Southern Portugal). However, these studies have been very limited in their geographical scope, and mostly focused on brief macroscopic descriptions of the raw materials. To further our knowledge of the relationship between regional availability of raw materials and its impact on human adaptations and mobility, a more detailed approach to characterizing geological sources is needed. This paper characterizes chert raw materials location, diversity, and availability in a geologically well-defined region of southern Portugal - the Algarve. Through macroscopic and petrographic approaches, we provide a detailed characterization of geological chert sources to build a frame of reference for chert exploitation in the region. Our results show that there are four main chert formations in Algarve, and that despite the within-source variability, sufficient differences at macroscopic and petrographic levels are present to allow clear source attribution. These results provide a baseline for raw material studies in archaeological assemblages across southwestern Iberia, that will be essential to further characterize the dynamics of human behavior in some of the most important eco-cultural niches.

Midfacial Morphology and Neandertal-Modern Human Interbreeding

Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages.

Oxytocin and vasotocin receptor variation and the evolution of human prosociality

Modern human lifestyle strongly depends on complex social traits like empathy, tolerance and cooperation. These diverse facets of social cognition have been associated with variation in the oxytocin receptor (OTR) and its sister genes, the vasotocin/vasopressin receptors (VTR1A/AVPR1A and AVPR1B/VTR1B). Here, we compared the available genomic sequences of these receptors between modern humans, archaic humans, and 12 non-human primate species, and identified sites that show heterozygous variation in modern humans and archaic humans distinct from variation in other primates, and for which we could find association studies with clinical implications. On these sites, we performed a range of analyses (variant clustering, pathogenicity prediction, regulation, linkage disequilibrium frequency), and reviewed the literature on selection data in different modern-human populations. We found five sites with modern human specific variation, where the modern human allele is the major allele in the global population (OTR: rs1042778, rs237885, rs6770632; VTR1A: rs10877969; VTR1B: rs33985287). Among them, variation in the OTR-rs6770632 site was predicted to be the most functional. Two alleles (OTR: rs59190448 and rs237888) present only in modern humans and archaic humans were putatively under positive selection in modern humans, with rs237888 predicted to be a highly functional site. Three sites showed convergent evolution between modern humans and bonobos (OTR: rs2228485 and rs237897; VTR1A: rs1042615), with OTR-rs2228485 ranking highly in terms of functionality and reported to be under balancing selection in modern humans (Schaschl, 2015) [1]. Our findings have implications for understanding hominid prosociality, as well as the similarities between modern human and bonobo social behavior.

Estimating divergence times from DNA sequences

The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the "Two-Two (TT)" and the "Two-Two-outgroup (TTo)" methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.

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

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.

Reconstructing cranial evolution in an extinct hominin

Homo erectus is the first hominin species with a truly cosmopolitan distribution and resembles recent humans in its broad spatial distribution. The microevolutionary events associated with dispersal and local adaptation may have produced similar population structure in both species. Understanding the evolutionary population dynamics of H. erectus has larger implications for the emergence of later Homo lineages in the Middle Pleistocene. Quantitative genetics models provide a means of interrogating aspects of long-standing H. erectus population history narratives. For the current study, cranial fossils were sorted into six major palaeodemes from sites across Africa and Asia spanning 1.8-0.1 Ma. Three-dimensional shape data from the occipital and frontal bones were used to compare intraspecific variation and test evolutionary hypotheses. Results indicate that H. erectus had higher individual and group variation than Homo sapiens, probably reflecting different levels of genetic diversity and population history in these spatially disperse species. This study also revealed distinct evolutionary histories for frontal and occipital bone shape in H. erectus, with a larger role for natural selection in the former. One scenario consistent with these findings is climate-driven facial adaptation in H. erectus, which is reflected in the frontal bone through integration with the orbits.

Thr92Ala polymorphism in the type 2 deiodinase gene: an evolutionary perspective

PURPOSE

In the past, a role of thyroid hormones in human evolution has been hypothesized. T3, the metabolically active form, derives from extrathyroidal conversion of T4 by deionidase 2 (D2) enzyme encoded by DIO2 gene. In thyroid-deficient patients, decreased levels of free T3 have been associated with the polymorphism rs225014 A/G in DIO2, which causes the substitution of Threonine with Alanine (p.Thr92Ala) at protein level.

METHODS

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

RESULTS

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

CONCLUSION

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

Reconstructing Denisovan Anatomy Using DNA Methylation Maps

Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.

What have the revelations about Neanderthal DNA revealed about Homo sapiens?

Genetic studies have presented increasing indications about the complexity of the interactions between Homo sapiens, Neanderthals and Denisovans, during Pleistocene. The results indicate potential replacement or admixture of the groups of hominins that lived in the same region at different times. Recently, the time of separation among these hominins in relation to the Last Common Ancestor – LCA has been reasonably well established. Events of mixing with emphasis on the Neanderthal gene flow into H. sapiens outside Africa, Denisovans into H. sapiens ancestors in Oceania and continental Asia, Neanderthals into Denisovans, as well as the origin of some phenotypic features in specific populations such as the color of the skin, eyes, hair and predisposition to develop certain kinds of diseases have also been found. The current information supports the existence of both replacement and interbreeding events, and indicates the need to revise the two main explanatory models, the Multiregional and the Out-of-Africa hypotheses, about the origin and evolution of H. sapiens and its co-relatives. There is definitely no longer the possibility of justifying only one model over the other. This paper aims to provide a brief review and update on the debate around this issue, considering the advances brought about by the recent genetic as well as morphological traits analyses.

Early Levallois core technology between Marine Isotope Stage 12 and 9 in Western Europe

Early Levallois core technology is usually dated in Europe to the end of Marine Isotope Stage (MIS) 9 and particularly from the beginning of MIS 8 to MIS 6. This technology is considered as one of the markers of the transition from lower to Middle Paleolithic or from Mode 2 to Mode 3. Recent discoveries show that some lithic innovations actually appeared earlier in western Europe, from MIS 12 to MIS 9, contemporaneous with changes in subsistence strategies and the first appearance of early Neanderthal anatomical features. Among these discoveries, there is the iconic Levallois core technology. A selection of well-dated assemblages in the United Kingdom, France, and Italy dated from MIS 12 to 9, which include both cores and flakes with Levallois features, has been described and compared with the aim of characterizing this technology. The conclusion supports the interpretation that several technical features may be attributed to a Levallois technology similar to those observed in younger Middle Paleolithic sites, distinct from the main associated core technologies in each level. Some features in the sample of sites suggest a gradual transformation of existing core technologies. The small evidence of Levallois could indicate occasional local innovations from different technological backgrounds and would explain the diversity of Levallois methods that is observed from MIS 12. The technological roots of Levallois technology in the Middle Pleistocene would suggest a multiregional origin and diffusion in Europe and early evidence of regionalization of local traditions through Europe from MIS 12 to 9. The relationships of Levallois technology with new needs and behaviors are discussed, such as flake preference, functional reasons related to hunting and hafting, an increase in the use of mental templates in European populations, and changes in the structure of hominin groups adapting to climatic and environmental changes.

Neanderthal-Denisovan ancestors interbred with a distantly related hominin

Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans.

Inbreeding, Allee effects and stochasticity might be sufficient to account for Neanderthal extinction

The replacement of Neanderthals by Anatomically Modern Humans has typically been attributed to environmental pressure or a superiority of modern humans with respect to competition for resources. Here we present two independent models that suggest that no such heatedly debated factors might be needed to account for the demise of Neanderthals. Starting from the observation that Neanderthal populations already were small before the arrival of modern humans, the models implement three factors that conservation biology identifies as critical for a small population's persistence, namely inbreeding, Allee effects and stochasticity. Our results indicate that the disappearance of Neanderthals might have resided in the smallness of their population(s) alone: even if they had been identical to modern humans in their cognitive, social and cultural traits, and even in the absence of inter-specific competition, Neanderthals faced a considerable risk of extinction. Furthermore, we suggest that if modern humans contributed to the demise of Neanderthals, that contribution might have had nothing to do with resource competition, but rather with how the incoming populations geographically restructured the resident populations, in a way that reinforced Allee effects, and the effects of inbreeding and stochasticity.

Archaic hominin introgression into modern human genomes

Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?

Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals

Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia.

Modern humans and Neanderthals coexisted in the Levant for tens of thousands of years before modern humans spread and replaced Neanderthals. Here, Greenbaum et al. develop a model showing that transmission of disease and genes can explain the maintenance and then collapse of this contact zone.

Legofit: estimating population history from genetic data

BACKGROUND

Our current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these biases, it is necessary to estimate these parameters simultaneously with those describing admixture. Genetic estimates of population histories also confront problems of statistical identifiability: different models or different combinations of parameter values may fit the data equally well. To deal with this problem, we need methods of model selection and model averaging, which are lacking from most existing software.

RESULTS

The Legofit software package allows simultaneous estimation of parameters describing admixture, and the sizes and separation times of ancestral populations. It includes facilities for data manipulation, estimation, analysis of residuals, model selection, and model averaging.

CONCLUSIONS

Legofit uses genetic data to study the history of a subdivided population. It is unaffected by recent history and can therefore focus on the deep history of population size, subdivision, and admixture. It outperforms several statistical methods that have been widely used to study population history and should be useful in any species for which DNA sequence data is available from several populations.

Complex Phenotypes: Mechanisms Underlying Variation in Human Stature

PURPOSE OF REVIEW

The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature.

RECENT FINDINGS

Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.

Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals

A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.

Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians

Indigenous Australians are particularly affected by type 2 diabetes mellitus (T2D) due to both their genetic susceptibility and a range of environmental and lifestyle risk factors. Recent genetic studies link predisposition to some diseases, including T2D, to alleles acquired from archaic hominins, such as Neanderthals and Denisovans, which persist in the genomes of modern humans today. Indo-Pacific human populations, including Indigenous Australians, remain extremely underrepresented in genomic research with a paucity of data examining the impact of Denisovan or Neanderthal lineages on human phenotypes in Oceania. The few genetic studies undertaken emphasize the uniqueness and antiquity of Indigenous Australian genomes, with possibly the largest proportion of Denisovan ancestry of any population in the world. In this review, we focus on the potential contributions of ancient genes/pathways to modern human phenotypes, while also highlighting the evolutionary roles of genetic adaptation to dietary and environmental changes associated with an adopted Western lifestyle. We discuss the role of genetic and epigenetic factors in the pathogenesis of T2D in understudied Indigenous Australians, including the potential impact of archaic gene lineages on this disease. Finally, we propose that greater understanding of the underlying genetic predisposition may contribute to the clinical efficacy of diabetes management in Indigenous Australians. We suggest that improved identification of T2D risk variants in Oceania is needed. Such studies promise to clarify how genetic and phenotypic differences vary between populations and, crucially, provide novel targets for personalised medical therapies in currently marginalized groups.

Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions?

Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.

Impact and Evolutionary Determinants of Neanderthal Introgression on Transcriptional and Post-Transcriptional Regulation

Archaic admixture is increasingly recognized as an important source of diversity in modern humans, and Neanderthal haplotypes cover 1%-3% of the genome of present-day Eurasians. Recent work has shown that archaic introgression has contributed to human phenotypic diversity, mostly through the regulation of gene expression. Yet the mechanisms through which archaic variants alter gene expression and the forces driving the introgression landscape at regulatory regions remain elusive. Here, we explored the impact of archaic introgression on transcriptional and post-transcriptional regulation. We focused on promoters and enhancers across 127 different tissues as well as on microRNA (miRNA)-mediated regulation. Although miRNAs themselves harbor few archaic variants, we found that some of these variants may have a strong impact on miRNA-mediated gene regulation. Enhancers were by far the regulatory elements most affected by archaic introgression: up to one-third of the tissues we tested presented significant enrichments. Specifically, we found strong enrichments of archaic variants in adipose-related tissues and primary T cells, even after accounting for various genomic and evolutionary confounders such as recombination rate and background selection. Interestingly, we identified signatures of adaptive introgression at enhancers of some key regulators of adipogenesis, raising the interesting hypothesis of a possible adaptation of early Eurasians to colder climates. Collectively, this study sheds new light on the mechanisms through which archaic admixture has impacted gene regulation in Eurasians and, more generally, increases our understanding of the contribution of Neanderthals to the regulation of acquired immunity and adipose homeostasis in modern humans.

Living on the edge: Was demographic weakness the cause of Neanderthal demise?

The causes of disappearance of the Neanderthals, the only human population living in Europe before the arrival of Homo sapiens, have been debated for decades by the scientific community. Different hypotheses have been advanced to explain this demise, such as cognitive, adaptive and cultural inferiority of Neanderthals. Here, we investigate the disappearance of Neanderthals by examining the extent of demographic changes needed over a period of 10,000 years (yrs) to lead to their extinction. In regard to such fossil populations, we inferred demographic parameters from present day and past hunter-gatherer populations, and from bio-anthropological rules. We used demographic modeling and simulations to identify the set of plausible demographic parameters of the Neanderthal population compatible with the observed dynamics, and to explore the circumstances under which they might have led to the disappearance of Neanderthals. A slight (<4%) but continuous decrease in the fertility rate of younger Neanderthal women could have had a significant impact on these dynamics, and could have precipitated their demise. Our results open the way to non-catastrophic events as plausible explanations for Neanderthal extinction.

Mosaic dental morphology in a terminal Pleistocene hominin from Dushan Cave in southern China

Recent studies reveal high degrees of morphological diversity in Late Pleistocene humans from East Asia. This variability was interpreted as complex demographic patterns with several migrations and possible survival of archaic groups. However, lack of well-described, reliably classified and accurately dated sites has seriously limited understanding of human evolution in terminal Pleistocene. Here we report a 15,000 years-old H. sapiens (Dushan 1) in South China with unusual mosaic features, such as large dental dimensions, cingulum-like structures at the dentine level in the posterior dentition and expression of a "crown buccal vertical groove complex", all of which are uncommon in modern humans and more typically found in Middle Pleistocene archaic humans. They could represent the late survival of one of the earliest modern humans to settle in an isolated region of southern China and, hence, the retention of primitive-like traits. They could also represent a particularity of this group and, hence, reflect a high degree of regional variation. Alternatively, these features may be the result of introgression from some late-surviving archaic population in the region. Our study demonstrates the extreme variability of terminal Pleistocene populations in China and the possibility of a complex demographic story in the region.

Multiple episodes of interbreeding between Neanderthal and modern humans

Neanderthals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neanderthal ancestry is ~12-20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population, and the hypothesis that reduced Neanderthal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neanderthal ancestry component (the 'dilution' hypothesis). To summarize the asymmetric pattern of Neanderthal allele frequencies, we compiled the joint fragment frequency spectrum of European and East Asian Neanderthal fragments and compared it with both analytical theory and data simulated under various models of admixture. Using maximum-likelihood and machine learning, we found that a simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.

The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure

In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362-371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T₂ (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.

The Middle Pleistocene (MIS 12) human dental remains from Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), Italy. A comparative high resolution endostructural assessment

The penecontemporaneous Middle Pleistocene sites of Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), set c. 450 km apart in central and northeastern Italy, respectively, have yielded some among the oldest human fossil remains testifying to a peopling phase of the Italian Peninsula broadly during the glacial MIS 12, a stage associated with one among the harshest climatic conditions in the Northern hemisphere during the entire Quaternary period. Together with the large samples from Atapuerca Sima de los Huesos, Spain, and Caune de l’Arago at Tautavel, France, the remains from Fontana Ranuccio and Visogliano are among the few mid-Middle Pleistocene dental assemblages from Western Europe available for investigating the presence of an early Neanderthal signature in their inner structure. We applied two- three-dimensional techniques of virtual imaging and geometric morphometrics to the high-resolution X-ray microtomography record of the dental remains from these two Italian sites and compared the results to the evidence from a selected number of Pleistocene and extant human specimens/samples from Europe and North Africa. Depending on their preservation quality and on the degree of occlusal wear, we comparatively assessed: (i) the crown enamel and radicular dentine thickness topographic variation of a uniquely represented lower incisor; (ii) the lateral crown tissue proportions of premolars and molars; (iii) the enamel-dentine junction, and (iv) the pulp cavity morphology of all available specimens. Our analyses reveal in both samples a Neanderthal-like inner structural signal, for some aspects also resembling the condition shown by the contemporary assemblage from Atapuerca SH, and clearly distinct from the recent human figures. This study provides additional evidence indicating that an overall Neanderthal morphological dental template was preconfigured in Western Europe at least 430 to 450 ka ago.

[A biological anthropology of the disappearance of the Neandertal Man: recent data]

What could have been the causes of the disappearance of Neanderthals? We will try here to make a synthesis between one of the fundamental questions of biological anthropology relating to human evolution (hypotheses on the causes of the extinction of Neanderthals) and evolutionary bio-medical concepts, some of which have recently been reformulated thanks to the progress of paleogenomics (ancestral inheritance of the current human immune system, paleo-microbiology, host-pathogen relationship…).

Neanderthal and Denisovan ancestry in Papuans: A functional study

Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan alleles. Here, we have shown that the Papuan genomes contain different gene functional groups inherited from each of the ancient people. The Papuan genomes demonstrate a relative prevalence of Neanderthal alleles in genes responsible for the regulation of transcription and neurogenesis. The enrichment of specific functional groups with Denisovan alleles is less pronounced; these groups are responsible for bone and tissue remodeling. This analysis shows that introgression of alleles from Neanderthals and Denisovans to Papuans occurred independently and retention of these alleles may carry specific adaptive advantages.