Culture, population structure, and low genetic diversity in Pleistocene hominins

Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples

Archaeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the non-random association of genetic variants at different loci (i.e., linkage disequilibrium, LD). This may be in part because basic properties of LD in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: 1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; 2) The product of the LD coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and 3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.

Middle Pleistocene fire use: The first signal of widespread cultural diffusion in human evolution

Control of fire is one of the most important technological innovations within the evolution of humankind. The archaeological signal of fire use becomes very visible from around 400,000 y ago onward. Interestingly, this occurs at a geologically similar time over major parts of the Old World, in Africa, as well as in western Eurasia, and in different subpopulations of the wider hominin metapopulation. We interpret this spatiotemporal pattern as the result of cultural diffusion, and as representing the earliest clear-cut case of widespread cultural change resulting from diffusion in human evolution. This fire-use pattern is followed slightly later by a similar spatiotemporal distribution of Levallois technology, at the beginning of the African Middle Stone Age and the western Eurasian Middle Paleolithic. These archaeological data, as well as studies of ancient genomes, lead us to hypothesize that at the latest by 400,000 y ago, hominin subpopulations encountered one another often enough and were sufficiently tolerant toward one another to transmit ideas and techniques over large regions within relatively short time periods. Furthermore, it is likely that the large-scale social networks necessary to transmit complicated skills were also in place. Most importantly, this suggests a form of cultural behavior significantly more similar to that of extant Homo sapiens than to our great ape relatives.

Tracking behavioral persistence and innovations during the Middle Pleistocene in Western Europe. Shift in occupations between 700 and 450 ka at la Noira site (Centre, France)

Some areas in Western Europe indicate hiatuses in human occupations, which cannot be systematically attributed to taphonomic factors and poor site preservation. The site of la Noira in the center of France records two occupation phases with a significant time gap. The older one is dated to around 700 ka (stratum a) with an Acheulean assemblage, among the earliest in Western Europe, and the upper phase of the sequence (stratum c) is dated to ca. 450 ka. Humans left the area at around 670 ka, at the beginning of the marine isotope stage (MIS) 16 glacial stage, when cold conditions became too severe. No sites between 650 and 450 ka have yet been discovered in the center region despite systematic surveys over the past three decades. The archaeological evidence indicates that populations returned to the area, at the end of MIS 12 or the beginning of the long interglacial MIS 11. Here, we use technological behaviors common to the two levels of la Noira-strata a and c to evaluate their differences. Compared to other key European sequences, this site can be used to address the evolution of the behavioral strategies in Europe between MIS 17 and 11. We formulate two hypotheses concerning the human settlement of this area: (1) local behavioral evolution over time of populations occasionally occupying the region when the climate was favorable or (2) dispersal and arrival of new populations from other areas. The results focus on (1) changes in land-use patterns with the extension of the territory used by hominins in the upper level, (2) the introduction of new core technologies, including some evidence of early Levallois debitage, and (3) more intensive shaping of bifaces and bifacial tools. Results attest that the la Noira archaeological assemblages record similar regional behavioral evolution as observed at a larger scale in Europe.

Population structure drives cultural diversity in finite populations: A hypothesis for localized community patterns on Rapa Nui (Easter Island, Chile)

Understanding how and why cultural diversity changes in human populations remains a central topic of debate in cultural evolutionary studies. Due to the effects of drift, small and isolated populations face evolutionary challenges in the retention of richness and diversity of cultural information. Such variation, however, can have significant fitness consequences, particularly when environmental conditions change unpredictably, such that knowledge about past environments may be key to long-term persistence. Factors that can shape the outcomes of drift within a population include the semantics of the traits as well as spatially structured social networks. Here, we use cultural transmission simulations to explore how social network structure and interaction affect the rate of trait retention and extinction. Using Rapa Nui (Easter Island, Chile) as an example, we develop a model-based hypothesis for how the structural constraints of communities living in small, isolated populations had dramatic effects and likely led to preventing the loss of cultural information in both community patterning and technology.

Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean

Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here, we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mitochondrial DNA (mtDNA) haplotype-one that is rare in the western Indian Ocean-thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in the sperm whale social group: 13 first-degree and 27 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e. vocal clans) is the next step in our research programme to elucidate and better apprehend the complex organization of sperm whale social groups.

The ripples of modernity: How we can extend paleoanthropology with the extended evolutionary synthesis

Contemporary understandings of paleoanthropological data illustrate that the search for a line defining, or a specific point designating, "modern human" is problematic. Here we lend support to the argument for the need to look for patterns in the paleoanthropological record that indicate how multiple evolutionary processes intersected to form the human niche, a concept critical to assessing the development and processes involved in the emergence of a contemporary human phenotype. We suggest that incorporating key elements of the Extended Evolutionary Synthesis (EES) into our endeavors offers a better and more integrative toolkit for modeling and assessing the evolution of the genus Homo. To illustrate our points, we highlight how aspects of the genetic exchanges, morphology, and material culture of the later Pleistocene complicate the concept of "modern" human behavior and suggest that multiple evolutionary patterns, processes, and pathways intersected to form the human niche.

The Impact of Ancient Genome Studies in Archaeology

The study of ancient genomes has burgeoned at an incredible rate in the last decade. The result is a shift in archaeological narratives, bringing with it a fierce debate on the place of genetics in anthropological research. Archaeogenomics has challenged and scrutinized fundamental themes of anthropological research, including human origins, movement of ancient and modern populations, the role of social organization in shaping material culture, and the relationship between culture, language, and ancestry. Moreover, the discussion has inevitably invoked new debates on indigenous rights, ownership of ancient materials, inclusion in the scientific process, and even the meaning of what it is to be a human. We argue that the broad and seemingly daunting ethical, methodological, and theoretical challenges posed by archaeogenomics, in fact, represent the very cutting edge of social science research. Here, we provide a general review of the field by introducing the contemporary discussion points and summarizing methodological and ethical concerns, while highlighting the exciting possibilities of ancient genome studies in archaeology from an anthropological perspective.

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.

Cultural specialization and genetic diversity: Killer whales and beyond

Culturally-transmitted ecological specialization can reduce niche breadths with demographic and ecological consequences. I use agent-based models, grounded in killer whale biology, to investigate the potential consequences of cultural specialization for genetic diversity. In these models, cultural specialization typically reduces the number of mitochondrial haplotypes, mitochondrial haplotype diversity, mitochondrial nucleotide diversity, and heterozygosity at nuclear loci. The causal route of this decline is mostly indirect, being ascribed to a reduction in absolute population size resulting from cultural specialization. However, small group size exacerbates the decline in genetic diversity, presumably because of increased founder effects at the initiation of each cultural ecotype. These results are concordant with measures of low genetic diversity in the killer whale, although culturally-transmitted ecological specialization alone might not be sufficient to fully account for the species' very low mitochondrial diversity. The process may also operate in other species.

A biface production older than 600 ka ago at Notarchirico (Southern Italy) contribution to understanding early Acheulean cognition and skills in Europe

For the past decade, debates on the earliest evidence of bifacial shaping in Western Europe have focused on several key issues, such as its origin (i.e., local or introduced), or on what should define the Acheulean culture. Whatever hypotheses are proposed for its origin, the onset and technological strategies for making Large Cutting Tools (LCTs), including biface production, are key issues and are often associated with other behavioural changes, such as increased core technology complexity. Current archaeological patterns do not support the existence of transitional industries. Rather, the scant evidence suggests that biface production associated with the management of bifacial volume was widespread around 700 ka. Among the earliest sites, the site of Notarchirico in Southern Italy stands out as one of the most significant examples. 40Ar/39Ar ages and ESR dates recently provided a revised chronology for the whole sedimentary sequence and constrained the archaeological levels between ca. 610 and 670 ka. Five archaeosurfaces (A, A1, B, D and F) yielded LCTs, including bifaces, during Marcello Piperno's excavations from 1980 to 1995. In light of this new chronological framework, which is much shorter than previously thought, we propose in this contribution a revision of the bifaces by applying the "chaine opératoire" method for the first time (analysis of reduction processes). Our goals are to assess biface production in this early Western European locality and to characterize the strategies applied at the site throughout the sequence. A corpus of 32 tools was selected from the A-A1, B, D and F archaeosurfaces. The technological analysis shows that hominins had the capacity to manage bifacial volumes, when raw material quality was adequate. Clear differences do not emerge between the different levels in terms of shaping modes or final forms. However, we demonstrate that the oldest level (level F), with the richest corpus, lacks flint and displays a higher diversity of bifaces. This ability to manage bifacial and bilateral equilibrium, as well as the diversity of the morphological results, is observed in a few penecontemporaneous sites (700-600 ka), both in the north-western and southern parts of Western Europe. These patterns suggest that hominins mastered well-controlled and diversified biface production, combining intense shaping and minimal shaping, and shared a common technological background regardless of the geographical area, and applied this technology regardless of the available raw materials. The degree of skill complexity of hominins in Western Europe between 700 and 600 ka, the current lack of evidence suggesting "gradual industries" between core-and-flake series and Acheulean techno-complexes, raise numerous questions on the origin of new behaviours in Western Europe, their mode of diffusion, and their association with Homo heidelbergensis or other Middle Pleistocene populations.

The reach of gene-culture coevolution in animals

Culture (behaviour based on socially transmitted information) is present in diverse animal species, yet how it interacts with genetic evolution remains largely unexplored. Here, we review the evidence for gene-culture coevolution in animals, especially birds, cetaceans and primates. We describe how culture can relax or intensify selection under different circumstances, create new selection pressures by changing ecology or behaviour, and favour adaptations, including in other species. Finally, we illustrate how, through culturally mediated migration and assortative mating, culture can shape population genetic structure and diversity. This evidence suggests strongly that animal culture plays an important evolutionary role, and we encourage explicit analyses of gene-culture coevolution in nature.

Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions.

The view that Homo sapiens evolved from a single region/population within Africa has been given primacy in studies of human evolution.

However, developments across multiple fields show that relevant data are no longer consistent with this view.

We argue instead that Homo sapiens evolved within a set of interlinked groups living across Africa, whose connectivity changed through time.

Genetic models therefore need to incorporate a more complex view of ancient migration and divergence in Africa.

We summarize this new framework emphasizing population structure, outline how this changes our understanding of human evolution, and identify new research directions.

Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

A population bottleneck 5000-7000 years ago in human males, but not females, has been inferred across several African, European and Asian populations. Here, Zeng and colleagues synthesize theory and data to suggest that competition among patrilineal kin groups produced the bottleneck pattern.

Gene-culture coevolution in whales and dolphins

Whales and dolphins (Cetacea) have excellent social learning skills as well as a long and strong mother-calf bond. These features produce stable cultures, and, in some species, sympatric groups with different cultures. There is evidence and speculation that this cultural transmission of behavior has affected gene distributions. Culture seems to have driven killer whales into distinct ecotypes, which may be incipient species or subspecies. There are ecotype-specific signals of selection in functional genes that correspond to cultural foraging behavior and habitat use by the different ecotypes. The five species of whale with matrilineal social systems have remarkably low diversity of mtDNA. Cultural hitchhiking, the transmission of functionally neutral genes in parallel with selective cultural traits, is a plausible hypothesis for this low diversity, especially in sperm whales. In killer whales the ecotype divisions, together with founding bottlenecks, selection, and cultural hitchhiking, likely explain the low mtDNA diversity. Several cetacean species show habitat-specific distributions of mtDNA haplotypes, probably the result of mother-offspring cultural transmission of migration routes or destinations. In bottlenose dolphins, remarkable small-scale differences in haplotype distribution result from maternal cultural transmission of foraging methods, and large-scale redistributions of sperm whale cultural clans in the Pacific have likely changed mitochondrial genetic geography. With the acceleration of genomics new results should come fast, but understanding gene-culture coevolution will be hampered by the measured pace of research on the socio-cultural side of cetacean biology.

Technological variability during the Early Middle Palaeolithic in Western Europe. Reduction systems and predetermined products at the Bau de l'Aubesier and Payre (South-East France)

The study of the lithic assemblages of two French sites, the Bau de l’Aubesier and Payre, contributes new knowledge of the earliest Neanderthal techno-cultural variability. In this paper we present the results of a detailed technological analysis of Early Middle Palaeolithic lithic assemblages of MIS 8 and 7 age from the two sites, which are located on opposite sides of the Rhône Valley in the south-east of France. The MIS 9–7 period is considered in Europe to be a time of new behaviours, especially concerning lithic strategies. The shift from the Lower Palaeolithic to the Early Middle Palaeolithic is “classically” defined by an increase in the number of core technologies, including standardized ones, which are stabilized in the full Middle Palaeolithic (MIS 5–3), associated with the decline of the “Acheulean” biface. Applying a common technological approach to the analysis of the two assemblages highlights their technological variability with respect to reduction systems and end products. Differences between Payre and the Bau de l’Aubesier concerning raw material procurement and faunal exploitation only partially explain this multifaceted technological variability, which in our opinion also reflects the existence of distinct technological strategies within the same restricted geographic area, which are related to distinct traditions, site uses, and/or as yet unknown parameters.

Cultural Hitchhiking in the Matrilineal Whales

Five species of whale with matrilineal social systems (daughters remain with mothers) have remarkably low levels of mitochondrial DNA diversity. Non-heritable matriline-level demography could reduce genetic diversity but the required conditions are not consistent with the natural histories of the matrilineal whales. The diversity of nuclear microsatellites is little reduced in the matrilineal whales arguing against bottlenecks. Selective sweeps of the mitochondrial genome are feasible causes but it is not clear why these only occurred in the matrilineal species. Cultural hitchhiking (cultural selection reducing diversity at neutral genetic loci transmitted in parallel to the culture) is supported in sperm whales which possess suitable matrilineal socio-cultural groups (coda clans). Killer whales are delineated into ecotypes which likely originated culturally. Culture, bottlenecks and selection, as well as their interactions, operating between- or within-ecotypes, may have reduced their mitochondrial diversity. The societies, cultures and genetics of false killer and two pilot whale species are insufficiently known to assess drivers of low mitochondrial diversity.

Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia

Archaeology, linguistics, and increasingly genetics are clarifying how populations moved from mainland Asia, through Island Southeast Asia, and out into the Pacific during the farming revolution. Yet key features of this process remain poorly understood, particularly how social behaviors intersected with demographic drivers to create the patterns of genomic diversity observed across Island Southeast Asia today. Such questions are ripe for computer modeling. Here, we construct an agent-based model to simulate human mobility across Island Southeast Asia from the Neolithic period to the present, with a special focus on interactions between individuals with Asian, Papuan, and mixed Asian-Papuan ancestry. Incorporating key features of the region, including its complex geography (islands and sea), demographic drivers (fecundity and migration), and social behaviors (marriage preferences), the model simultaneously tracks a full suite of genomic markers (autosomes, X chromosome, mitochondrial DNA, and Y chromosome). Using Bayesian inference, model parameters were determined that produce simulations that closely resemble the admixture profiles of 2299 individuals from 84 populations across Island Southeast Asia. The results highlight that greater propensity to migrate and elevated birth rates are related drivers behind the expansion of individuals with Asian ancestry relative to individuals with Papuan ancestry, that offspring preferentially resulted from marriages between Asian women and Papuan men, and that in contrast to current thinking, individuals with Asian ancestry were likely distributed across large parts of western Island Southeast Asia before the Neolithic expansion.

Early evidence of Acheulean settlement in northwestern Europe--la Noira site, a 700,000 year-old occupation in the center of France

The human settlement of Europe during Pleistocene times was sporadic and several stages have been recognized, both from paleaoanthropological and archaeological records. If the first phase of hominin occupation (as early as 1.4 Ma) seems mainly restricted to the southern part of the continent, the second phase, characterized by specific lithic tools (handaxes), is linked to Acheulean settlements and to the emergence of Homo heidelbergensis, the ancestor of Neanderthals. This phase reached northwestern Europe and is documented in numerous sites in Germany, Great Britain and northern France, generally after 600 ka. At la Noira (Brinay, Central France), the Middle Pleistocene alluvial formation of the Cher River covers an archaeological level associated with a slope deposit (diamicton). The lithic assemblage from this level includes Large Cutting Tools (LCTs), flakes and cores, associated with numerous millstone slabs. The lithic series is classified as Acheulean on the basis of both technological and typological analyses. Cryoturbation features indicate that the slope deposits and associated archaeological level were strongly frozen and disturbed after hominin occupation and before fluvial deposition. Eight sediment samples were dated by the electron spin resonance (ESR) method and the weighted average age obtained for the fluvial sands overlying the slope deposits is 665±55 ka. This age is older than previous chronological data placing the first European Acheulean assemblages north of 45(th) parallel north at around 500 ka and modifies our current vision of the initial peopling of northern Europe. Acheulean settlements are older than previously assumed and the oldest evidences are not only located in southern Europe. La Noira is the oldest evidence of Acheulean presence in north-western Europe and attests to the possibility of pioneering phases of Acheulean settlement which would have taken place on a Mode 1-type substratum as early as 700 ka. The lithic assemblage from la Noira thus provides behavioral and technological data on early Acheulean occupation in Europe and contributes to our understanding of the diffusion of this tradition.

San Bernardino Cave (Italy) and the appearance of Levallois technology in Europe: results of a radiometric and technological reassessment

The introduction of Levallois technology in Europe marked the transition from the Lower to the early Middle Paleolithic. This new method of flake production was accompanied by significant behavioral changes in hominin populations. The emergence of this technological advance is considered homogeneous in the European archaeological record at the Marine isotopic stage (MIS) 9/MIS 8 boundary. In this paper we report a series of combined electron spin resonance/U-series dates on mammal bones and teeth recovered from the lower units of San Bernardino Cave (Italy) and the technological analyses of the lithic assemblages. The San Bernardino Cave has yielded the earliest evidence of Levallois production on the Italian Peninsula recovered to date. In addition to our results and the review of the archaeological record, we describe the chronological and geographical differences between European territories and diversities in terms of technological developments. The belated emergence of Levallois technology in Italy compared to western Europe corresponds to the late Italian Neanderthal speciation event. The new radiometric dates and the technological analyses of San Bernardino Cave raise the issue of the different roles of glacial refugia in the peopling and the spread of innovative flaking strategies in Europe during the late Middle Pleistocene.

Ash from the Toba supereruption in Lake Malawi shows no volcanic winter in East Africa at 75 ka

The most explosive volcanic event of the Quaternary was the eruption of Mt. Toba, Sumatra, 75,000 y ago, which produced voluminous ash deposits found across much of the Indian Ocean, Indian Peninsula, and South China Sea. A major climatic downturn observed within the Greenland ice cores has been attributed to the cooling effects of the ash and aerosols ejected during the eruption of the Youngest Toba Tuff (YTT). These events coincided roughly with a hypothesized human genetic bottleneck, when the number of our species in Africa may have been reduced to near extinction. Some have speculated that the demise of early modern humans at that time was due in part to a dramatic climate shift triggered by the supereruption. Others have argued that environmental conditions would not have been so severe to have such an impact on our ancestors, and furthermore, that modern humans may have already expanded beyond Africa by this time. We report an observation of the YTT in Africa, recovered as a cryptotephra layer in Lake Malawi sediments, >7,000 km west of the source volcano. The YTT isochron provides an accurate and precise age estimate for the Lake Malawi paleoclimate record, which revises the chronology of past climatic events in East Africa. The YTT in Lake Malawi is not accompanied by a major change in sediment composition or evidence for substantial temperature change, implying that the eruption did not significantly impact the climate of East Africa and was not the cause of a human genetic bottleneck at that time.

Transmission coupling mechanisms: cultural group selection

The application of phylogenetic methods to cultural variation raises questions about how cultural adaption works and how it is coupled to cultural transmission. Cultural group selection is of particular interest in this context because it depends on the same kinds of mechanisms that lead to tree-like patterns of cultural variation. Here, we review ideas about cultural group selection relevant to cultural phylogenetics. We discuss why group selection among multiple equilibria is not subject to the usual criticisms directed at group selection, why multiple equilibria are a common phenomena, and why selection among multiple equilibria is not likely to be an important force in genetic evolution. We also discuss three forms of group competition and the processes that cause populations to shift from one equilibrium to another and create a mutation-like process at the group level.

Predictions of native American population structure using linguistic covariates in a hidden regression framework

BACKGROUND

The mainland of the Americas is home to a remarkable diversity of languages, and the relationships between genes and languages have attracted considerable attention in the past. Here we investigate to which extent geography and languages can predict the genetic structure of Native American populations.

METHODOLOGY/PRINCIPAL FINDINGS

Our approach is based on a Bayesian latent cluster regression model in which cluster membership is explained by geographic and linguistic covariates. After correcting for geographic effects, we find that the inclusion of linguistic information improves the prediction of individual membership to genetic clusters. We further compare the predictive power of Greenberg's and The Ethnologue classifications of Amerindian languages. We report that The Ethnologue classification provides a better genetic proxy than Greenberg's classification at the stock and at the group levels. Although high predictive values can be achieved from The Ethnologue classification, we nevertheless emphasize that Choco, Chibchan and Tupi linguistic families do not exhibit a univocal correspondence with genetic clusters.

CONCLUSIONS/SIGNIFICANCE

The Bayesian latent class regression model described here is efficient at predicting population genetic structure using geographic and linguistic information in Native American populations.

Nonadaptive processes in primate and human evolution

Evolutionary biology has tended to focus on adaptive evolution by positive selection as the primum mobile of evolutionary trajectories in species while underestimating the importance of nonadaptive evolutionary processes. In this review, I describe evidence that suggests that primate and human evolution has been strongly influenced by nonadaptive processes, particularly random genetic drift and mutation. This is evidenced by three fundamental effects: a relative relaxation of selective constraints (i.e., purifying selection), a relative increase in the fixation of slightly deleterious mutations, and a general reduction in the efficacy of positive selection. These effects are observed in protein-coding, regulatory regions, and in gene expression data, as well as in an augmentation of fixation of large-scale mutations, including duplicated genes, mobile genetic elements, and nuclear mitochondrial DNA. The evidence suggests a general population-level explanation such as a reduction in effective population size (N(e)). This would have tipped the balance between the evolutionary forces of natural selection and random genetic drift toward genetic drift for variants having small selective effects. After describing these proximate effects, I describe the potential consequences of these effects for primate and human evolution. For example, an increase in the fixation of slightly deleterious mutations could potentially have led to an increase in the fixation rate of compensatory mutations that act to suppress the effects of slightly deleterious substitutions. The potential consequences of compensatory evolution for the evolution of novel gene functions and in potentially confounding the detection of positively selected genes are explored. The consequences of the passive accumulation of large-scale genomic mutations by genetic drift are unclear, though evidence suggests that new gene copies as well as insertions of transposable elements into genes can potentially lead to adaptive phenotypes. Finally, because a decrease in selective constraint at the genetic level is expected to have effects at the morphological level, I review studies that compare rates of morphological change in various mammalian and island populations where N(e) is reduced. Furthermore, I discuss evidence that suggests that craniofacial morphology in the Homo lineage has shifted from an evolutionary rate constrained by purifying selection toward a neutral evolutionary rate.

An X-linked haplotype of Neandertal origin is present among all non-African populations

Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of Homo sapiens who left Africa between 80 and 50 Kya (thousand years ago) to colonize the rest of the world. Here, we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6,092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.

Genome digging: insight into the mitochondrial genome of Homo

BACKGROUND

A fraction of the Neanderthal mitochondrial genome sequence has a similarity with a 5,839-bp nuclear DNA sequence of mitochondrial origin (numt) on the human chromosome 1. This fact has never been interpreted. Although this phenomenon may be attributed to contamination and mosaic assembly of Neanderthal mtDNA from short sequencing reads, we explain the mysterious similarity by integration of this numt (mtAncestor-1) into the nuclear genome of the common ancestor of Neanderthals and modern humans not long before their reproductive split.

PRINCIPAL FINDINGS

Exploiting bioinformatics, we uncovered an additional numt (mtAncestor-2) with a high similarity to the Neanderthal mtDNA and indicated that both numts represent almost identical replicas of the mtDNA sequences ancestral to the mitochondrial genomes of Neanderthals and modern humans. In the proteins, encoded by mtDNA, the majority of amino acids distinguishing chimpanzees from humans and Neanderthals were acquired by the ancestral hominins. The overall rate of nonsynonymous evolution in Neanderthal mitochondrial protein-coding genes is not higher than in other lineages. The model incorporating the ancestral hominin mtDNA sequences estimates the average divergence age of the mtDNAs of Neanderthals and modern humans to be 450,000-485,000 years. The mtAncestor-1 and mtAncestor-2 sequences were incorporated into the nuclear genome approximately 620,000 years and 2,885,000 years ago, respectively.

CONCLUSIONS

This study provides the first insight into the evolution of the mitochondrial DNA in hominins ancestral to Neanderthals and humans. We hypothesize that mtAncestor-1 and mtAncestor-2 are likely to be molecular fossils of the mtDNAs of Homo heidelbergensis and a stem Homo lineage. The d(N)/d(S) dynamics suggests that the effective population size of extinct hominins was low. However, the hominin lineage ancestral to humans, Neanderthals and H. heidelbergensis, had a larger effective population size and possessed genetic diversity comparable with those of chimpanzee and gorilla.

From molecular mechanisms of cardiac development to genetic substrate of congenital heart diseases

Congenital heart disease is one of the most important chapters in medicine because its incidence is increasing and nowadays it is close to 1.2%. Most congenital heart disorders are the result of defects during embryogenesis, which implies that they are due to alterations in genes involved in cardiac development. This review summarizes current knowledge regarding the molecular mechanisms involved in cardiac development in order to clarify the genetic basis of congenital heart disease.

The evolution of human genetic and phenotypic variation in Africa

Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations.

Out of Africa: modern human origins special feature: the origin of Neandertals

Western Eurasia yielded a rich Middle (MP) and Late Pleistocene (LP) fossil record documenting the evolution of the Neandertals that can be analyzed in light of recently acquired paleogenetical data, an abundance of archeological evidence, and a well-known environmental context. Their origin likely relates to an episode of recolonization of Western Eurasia by hominins of African origin carrying the Acheulean technology into Europe around 600 ka. An enhancement of both glacial and interglacial phases may have played a crucial role in this event, as well as in the subsequent evolutionary history of the Western Eurasian populations. In addition to climatic adaptations and an increase in encephalization, genetic drift seems to have played a major role in their evolution. To date, a clear speciation event is not documented, and the most likely scenario for the fixation of Neandertal characteristics seems to be an accretion of features along the second half of the MP. Although a separation time for the African and Eurasian populations is difficult to determine, it certainly predates OIS 11 as phenotypic Neandertal features are documented as far back as and possibly before this time. It is proposed to use the term "Homo rhodesiensis" to designate the large-brained hominins ancestral to H. sapiens in Africa and at the root of the Neandertals in Europe, and to use the term "Homo neanderthalensis" to designate all of the specimens carrying derived metrical or non-metrical features used in the definition of the LP Neandertals.