Recovering signals of ghost archaic introgression in African populations

Characterizing selection on complex traits through conditional frequency spectra

Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). The power to detect a trait-associated variant in GWAS is a function of its frequency and effect size - but for traits under selection, the effect size of a variant determines the strength of selection against it, constraining its frequency. Recognizing the biases inherent to GWAS ascertainment, we propose studying the joint distribution of allele frequencies across populations, conditional on the frequencies in the GWAS cohort. Before considering these conditional frequency spectra, we first characterized the impact of selection and non-equilibrium demography on allele frequency dynamics forwards and backwards in time. We then used these results to understand conditional frequency spectra under realistic human demography. Finally, we investigated empirical conditional frequency spectra for GWAS variants associated with 106 complex traits, finding compelling evidence for either stabilizing or purifying selection. Our results provide insights into polygenic score portability and other properties of variants ascertained with GWAS, highlighting the utility of conditional frequency spectra.

A structured coalescent model reveals deep ancestral structure shared by all modern humans

Understanding the history of admixture events and population size changes leading to modern humans is central to human evolutionary genetics. Here we introduce a coalescence-based hidden Markov model, cobraa, that explicitly represents an ancestral population split and rejoin, and demonstrate its application on simulated and real data across multiple species. Using cobraa, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ~1.5 million years ago came together in an admixture event ~300 thousand years ago, in a ratio of ~80:20%. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human-Neanderthal or human-Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.

Mapping a complex evolutionary history

Tracking the geographic origins of genetic ancestors reveals past human migrations.

Insufficient Evidence for a Severe Bottleneck in Humans During the Early to Middle Pleistocene Transition

A recently proposed model suggests a severe bottleneck in the panmictic ancestral population of modern humans during the Early to Middle Pleistocene transition. Here, we show this model provides a worse fit to the data than a panmictic model without the bottleneck.

Dentition of the Mugharet El'Aliya Fossil Human Maxilla, Morocco

OBJECTIVE

This study follows up on our recent morphological analysis of the juvenile maxilla from Mugharet el'Aliya, Morocco. Although this specimen shows a reportedly archaic morphology, likely due to its large size, 3D shape analyses indicated affinities with early Homo sapiens. Here, we conducted an in-depth comparative investigation of the associated dentition to further clarify this individual's phylogenetic and taxonomic affinities.

MATERIALS AND METHODS

Our analyses were based on three kinds of data: (a) external crown dimensions and non-metric features, analyzed via summary statistics; (b) CT scan data enabling the study of internal structures (enamel-dentine junction) via geometric morphometrics; and (c) high-resolution replicas of the external surface of the upper canine enabling the study of perikymata numbers via probability functions. The comparative samples included Middle Pleistocene (Chibanian) Europeans and Africans, Neanderthals, and early and later H. sapiens.

RESULTS

Mugharet el'Aliya showed the greatest similarities in external and internal tooth morphology with early and later H. sapiens. Perikymata counts cluster the upper canine with H. sapiens. However, its canine and fourth premolar are megadont at a level generally atypical for H. sapiens.

DISCUSSION

Our analyses of the dentition of the Mugharet el'Aliya individual support our previous findings on the morphological analysis of the maxilla, placing this fossil closest to H. sapiens. Our study further strengthens the evidence connecting fossils from the North African Aterian to those from Western Asia, especially Qafzeh. We also provide the first comparative analysis of a permanent upper canine from the Aterian fossil record.

Archaic hominin admixture and its consequences for modern humans

As anatomically modern humans dispersed out of Africa, they encountered and mated with now extinct hominins, including Neanderthals and Denisovans. It is now well established that all non-African individuals derive approximately 2% of their genome from Neanderthal ancestors and individuals of Melanesian and Australian aboriginal ancestry inherited an additional 2%-5% of their genomes from Denisovan ancestors. Attention has started to shift from documenting amounts of archaic admixture and identifying introgressed segments to understanding their molecular, phenotypic, and evolutionary consequences and refining models of human history. Here, we review recent insights into admixture between modern and archaic humans, emphasizing methodological innovations and the functional and phenotypic effects Neanderthal and Denisovan sequences have in contemporary individuals.

Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events

Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events-such as ancient bottlenecks or admixture-is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation.

Computational Genomics and Its Applications to Anthropological Questions

The advent of affordable genome sequencing and the development of new computational tools have established a new era of genomic knowledge. Sequenced human genomes number in the tens of thousands, including thousands of ancient human genomes. The abundance of data has been met with new analysis tools that can be used to understand populations' demographic and evolutionary histories. Thus, a variety of computational methods now exist that can be leveraged to answer anthropological questions. This includes novel likelihood and Bayesian methods, machine learning techniques, and a vast array of population simulators. These computational tools provide powerful insights gained from genomic datasets, although they are generally inaccessible to those with less computational experience. Here, we outline the theoretical workings behind computational genomics methods, limitations and other considerations when applying these computational methods, and examples of how computational methods have already been applied to anthropological questions. We hope this review will empower other anthropologists to utilize these powerful tools in their own research.

Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings

Homo sapiens and Neanderthals underwent hybridization during the Middle/Upper Paleolithic age, culminating in retention of small amounts of Neanderthal-derived DNA in the modern human genome. In the current study, we address the potential roles Neanderthal single nucleotide polymorphisms (SNP) may be playing in autism susceptibility in samples of black non-Hispanic, white Hispanic, and white non-Hispanic people using data from the Simons Foundation Powering Autism Research (SPARK), Genotype-Tissue Expression (GTEx), and 1000 Genomes (1000G) databases. We have discovered that rare variants are significantly enriched in autistic probands compared to race-matched controls. In addition, we have identified 25 rare and common SNPs that are significantly enriched in autism on different ethnic backgrounds, some of which show significant clinical associations. We have also identified other SNPs that share more specific genotype-phenotype correlations but which are not necessarily enriched in autism and yet may nevertheless play roles in comorbid phenotype expression (e.g., intellectual disability, epilepsy, and language regression). These results strongly suggest Neanderthal-derived DNA is playing a significant role in autism susceptibility across major populations in the United States.

Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies

Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.

Conditional frequency spectra as a tool for studying selection on complex traits in biobanks

Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). The power to detect a trait-associated variant in GWAS is a function of frequency and effect size - but for traits under selection, the effect size of a variant determines the strength of selection against it, constraining its frequency. To account for GWAS ascertainment, we propose studying the joint distribution of allele frequencies across populations, conditional on the frequencies in the GWAS cohort. Before considering these conditional frequency spectra, we first characterized the impact of selection and non-equilibrium demography on allele frequency dynamics forwards and backwards in time. We then used these results to understand conditional frequency spectra under realistic human demography. Finally, we investigated empirical conditional frequency spectra for GWAS variants associated with 106 complex traits, finding compelling evidence for either stabilizing or purifying selection. Our results provide insight into polygenic score portability and other properties of variants ascertained with GWAS, highlighting the utility of conditional frequency spectra.

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.

Two new Later Stone Age sites from the Final Pleistocene in the Falémé Valley, eastern Senegal

The understanding of cultural dynamics at work at the end of the Final Pleistocene in West Africa suffers from a significant lack of excavated and dated sites, particularly in the Sahelian and Sudanian ecozones. While the Later Stone Age shows varied behavioral developments in different parts of the continent, the chrono-cultural framework of this period remains largely unknown in West Africa. We report on archaeological, geomorphological, and chronological research on two Final Pleistocene Later Stone Age sites in the Falémé Valley, eastern Senegal. Optically stimulated luminescence ages place the site of Toumboura I-2017 between 17 ± 1 and 16 ± 1 ka and the Ravin de Sansandé site between 13 ± 1 ka and 12 ± 1.1 ka. The excavated lithics show typical Later Stone Age industries, characterized by chaînes opératoires of core reduction mainly producing flakes and bladelets as well as blades and laminar flakes. Segments dominate the toolkits but a few backed bladelets and end-scrapers on flake blanks were recognized. Local raw materials were used, with a preference for chert and quartz, as well as greywacke. These Later Stone Age lithic assemblages are the oldest known in Senegal so far and add to the small number of sites known in West Africa for this period, which are mainly located farther south, in sub-tropical ecozones. The Later Stone Age sites of the Falémé Valley are contemporaneous with typical Middle Stone Age technologies in Senegal dated to at least the Pleistocene/Holocene transition. Our results thus provide new archaeological evidence highlighting the complex cultural processes at work during the Final Pleistocene in West Africa.

Biogeographic Perspectives on Human Genetic Diversification

Modern humans originated in Africa 300,000 yr ago, and before leaving their continent of origin, they underwent a process of intense diversification involving complex demographic dynamics. Upon exiting Africa, different populations emerged on the four other inhabited continents, shaped by the interplay of various evolutionary processes, such as migrations, founder effects, and natural selection. Within each region, continental populations, in turn, diversified and evolved almost independently for millennia. As a backdrop to this diversification, introgressions from archaic species contributed to establishing different patterns of genetic diversity in different geographic regions, reshaping our understanding of our species' variability. With the increasing availability of genomic data, it has become possible to delineate the subcontinental human population structure precisely. However, the bias toward the genomic research focused on populations from the global North has limited our understanding of the real diversity of our species and the processes and events that guided different human groups throughout their evolutionary history. This perspective is part of a series of articles celebrating 40 yr since our journal, Molecular Biology and Evolution, was founded (Russo et al. 2024). The perspective is accompanied by virtual issues, a selection of papers on human diversification published by Genome Biology and Evolution and Molecular Biology and Evolution.

Demogenomic inference from spatially and temporally heterogeneous samples

Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected from different places and at different times. This heterogeneous sampling can be an issue for demographic inferences and results in biased demographic parameters and incorrect model choice if not properly considered. When explicitly accounted for, it can result in very complex models and high data dimensionality that are difficult to analyse. In this paper, we formally study the impact of such spatial and temporal sampling heterogeneity on demographic inference, and we introduce a way to circumvent this problem. To deal with structured samples without increasing the dimensionality of the site frequency spectrum (SFS), we introduce a new structured approach to the existing program fastsimcoal2. We assess the efficiency and relevance of this methodological update with simulated and modern human genomic data. We particularly focus on spatial and temporal heterogeneities to evidence the interest of this new SFS-based approach, which can be especially useful when handling scattered and ancient DNA samples, as in conservation genetics or archaeogenetics.

Speciation-by-Extinction

Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.

Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications

Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.

Are vipers prototypic fear-evoking snakes? A cross-cultural comparison of Somalis and Czechs

Snakes are known as highly fear-evoking animals, eliciting preferential attention and fast detection in humans. We examined the human fear response to snakes in the context of both current and evolutionary experiences, conducting our research in the cradle of humankind, the Horn of Africa. This region is characterized by the frequent occurrence of various snake species, including deadly venomous viperids (adders) and elapids (cobras and mambas). We conducted experiments in Somaliland and compared the results with data from Czech respondents to address the still unresolved questions: To which extent is human fear of snakes affected by evolutionary or current experience and local culture? Can people of both nationalities recognize venomous snakes as a category, or are they only afraid of certain species that are most dangerous in a given area? Are respondents of both nationalities equally afraid of deadly snakes from both families (Viperidae, Elapidae)? We employed a well-established picture-sorting approach, consisting of 48 snake species belonging to four distinct groups. Our results revealed significant agreement among Somali as well as Czech respondents. We found a highly significant effect of the stimulus on perceived fear in both populations. Vipers appeared to be the most salient stimuli in both populations, as they occupied the highest positions according to the reported level of subjectively perceived fear. The position of vipers strongly contrasts with the fear ranking of deadly venomous elapids, which were in lower positions. Fear scores of vipers were significantly higher in both populations, and their best predictor was the body width of the snake. The evolutionary, cultural, and cognitive aspects of this phenomenon are discussed.

Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition

Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.

Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes

f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.

Ghost admixture in eastern gorillas

Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.

Multiple Sources of Uncertainty Confound Inference of Historical Human Generation Times

Wang et al. (2023) recently proposed an approach to infer the history of human generation intervals from changes in mutation profiles over time. As the relative proportions of different mutation types depend on the ages of parents, binning variants by the time they arose allows for the inference of changes in average paternal and maternal generation intervals. Applying this approach to published allele age estimates, Wang et al. (2023) inferred long-lasting sex differences in average generation times and surprisingly found that ancestral generation times of West African populations remained substantially higher than those of Eurasian populations extending tens of thousands of generations into the past. Here, we argue that the results and interpretations in Wang et al. (2023) are primarily driven by noise and biases in input data and a lack of validation using independent approaches for estimating allele ages. With the recent development of methods to reconstruct genome-wide gene genealogies, coalescence times, and allele ages, we caution that downstream analyses may be strongly influenced by uncharacterized biases in their output.

Longstanding behavioural stability in West Africa extends to the Middle Pleistocene at Bargny, coastal Senegal

Middle Stone Age (MSA) technologies first appear in the archaeological records of northern, eastern and southern Africa during the Middle Pleistocene epoch. The absence of MSA sites from West Africa limits evaluation of shared behaviours across the continent during the late Middle Pleistocene and the diversity of subsequent regionalized trajectories. Here we present evidence for the late Middle Pleistocene MSA occupation of the West African littoral at Bargny, Senegal, dating to 150 thousand years ago. Palaeoecological evidence suggests that Bargny was a hydrological refugium during the MSA occupation, supporting estuarine conditions during Middle Pleistocene arid phases. The stone tool technology at Bargny presents characteristics widely shared across Africa in the late Middle Pleistocene but which remain uniquely stable in West Africa to the onset of the Holocene. We explore how the persistent habitability of West African environments, including mangroves, contributes to distinctly West African trajectories of behavioural stability.

A weakly structured stem for human origins in Africa

Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent1. Progress is hampered by a shortage of fossil and genomic data, as well as variability in previous estimates of divergence times1. Here we seek to discriminate among such models by considering linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference2. We infer detailed demographic models for populations across Africa, including eastern and western representatives, and newly sequenced whole genomes from 44 Nama (Khoe-San) individuals from southern Africa. We infer a reticulated African population history in which present-day population structure dates back to Marine Isotope Stage 5. The earliest population divergence among contemporary populations occurred 120,000 to 135,000 years ago and was preceded by links between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years. Such weakly structured stem models explain patterns of polymorphism that had previously been attributed to contributions from archaic hominins in Africa2-7. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be genetically and morphologically similar, and that only an inferred 1-4% of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations. We show that model misspecification explains the variation in previous estimates of divergence times, and argue that studying a range of models is key to making robust inferences about deep history.

Evolutionary Genetics and Admixture in African Populations

As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: They contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of genetic variation in Africa and examine deep population structure within Africa, including the evidence of ancient introgression from archaic "ghost" populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of population structure in Africa on health and disease and call for more ethically conducted studies of genetic variation in Africa.

Leveraging our common African origins to understand human evolution and health

In the March 2023 issue of Cell, Fan et al.¹ report whole-genome sequencing across 12 indigenous African populations and analyze local adaptation and evolutionary history. Here, Wonkam and Adeyemo highlight their findings and how this contributes to African and global genomic research.

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation

We conduct high coverage (>30×) whole-genome sequencing of 180 individuals from 12 indigenous African populations. We identify millions of unreported variants, many predicted to be functionally important. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression events from "ghost" populations with highly diverged genetic lineages. Although currently geographically isolated, we observe evidence for gene flow between eastern and southern Khoesan-speaking hunter-gatherer populations lasting until ∼12 kya. We identify signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes. We identify a positively selected variant in the lightly pigmented San that influences pigmentation in vitro by regulating the enhancer activity and gene expression of PDPK1.

Modeling of African population history using f -statistics can be highly biased and is not addressed by previously suggested SNP ascertainment schemes

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

MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations

Adaptive introgression (AI) facilitates local adaptation in a wide range of species. Many state-of-the-art methods detect AI with ad-hoc approaches that identify summary statistic outliers or intersect scans for positive selection with scans for introgressed genomic regions. Although widely used, approaches intersecting outliers are vulnerable to a high false-negative rate as the power of different methods varies, especially for complex introgression events. Moreover, population genetic processes unrelated to AI, such as background selection or heterosis, may create similar genomic signals to AI, compromising the reliability of methods that rely on neutral null distributions. In recent years, machine learning (ML) methods have been increasingly applied to population genetic questions. Here, we present a ML-based method called MaLAdapt for identifying AI loci from genome-wide sequencing data. Using an Extra-Trees Classifier algorithm, our method combines information from a large number of biologically meaningful summary statistics to capture a powerful composite signature of AI across the genome. In contrast to existing methods, MaLAdapt is especially well-powered to detect AI with mild beneficial effects, including selection on standing archaic variation, and is robust to non-AI selective sweeps, heterosis from deleterious mutations, and demographic misspecification. Furthermore, MaLAdapt outperforms existing methods for detecting AI based on the analysis of simulated data and the validation of empirical signals through visual inspection of haplotype patterns. We apply MaLAdapt to the 1000 Genomes Project human genomic data and discover novel AI candidate regions in non-African populations, including genes that are enriched in functionally important biological pathways regulating metabolism and immune responses.

A Pleistocene assemblage of near-modern Papio hamadryas from the Middle Awash study area, Afar Rift, Ethiopia

OBJECTIVES

The aim of this study is to assess a new assemblage of papionin fossils (n = 143) recovered from later Pleistocene sediments in the Middle Awash study area in the Afar Rift of Ethiopia.

MATERIALS AND METHODS

We collected metric and qualitative data to compare the craniodental and postcranial anatomy of the papionin fossils with subspecies of modern Papio hamadryas and with Plio-Pleistocene African papionins. We also estimated sex and ontogenetic age.

RESULTS

The new fossils fit well within the range of morphological variation observed for extant P. hamadryas, overlapping most closely in dental size and proportions with the P. h. cynocephalus individuals in our extant samples, and well within the ranges of P. h. anubis and P. h. hamadryas. The considerable overlap in craniodental anatomy with multiple subspecies precludes subspecific diagnosis. We therefore referred 143 individuals to P. hamadryas ssp. The majority of the individuals assessed for ontogenetic age fell into middle- and old-adult age categories based on the degree of dental wear. Males (26%) were better represented than females (12%) among individuals preserving the canine-premolar honing complex.

DISCUSSION

These new near-modern P. hamadryas fossils provide a window into population-level variation in the later Pleistocene. Our findings echo previous suggestions from genomic studies that the papionin family tree may have included a ghost population and provide a basis for future testing of hypotheses regarding hybridization in the recent evolutionary history of this taxon.

Moving beyond the adaptationist paradigm for human evolution, and why it matters

The Journal of Human Evolution (JHE) was founded 50 years ago when much of the foundation for how we think about human evolution was in place or being put in place, providing the main framework for how we consider our origins today. Here, we will explore historical developments, including early JHE outputs, as they relate to our understanding of the relationship between phenotypic variation and evolutionary process, and use that as a springboard for considering our current understanding of these links as applied to human evolution. We will focus specifically on how the study of variation itself has shifted us away from taxonomic and adaptationist perspectives toward a richer understanding of the processes shaping human evolutionary history, using literature searches and specific test cases to highlight this. We argue that natural selection, gene exchange, genetic drift, and mutation should not be considered individually when considering the production of hominin diversity. In this context, we offer suggestions for future research directions and reflect on this more complex understanding of human evolution and its broader relevance to society. Finally, we end by considering authorship demographics and practices in the last 50 years within JHE and how a shift in these demographics has the potential to reshape the science of human evolution going forward.

Evolution of Homo in the Middle and Late Pleistocene

The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.

Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast

Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.

Including diverse and admixed populations in genetic epidemiology research

The inclusion of ancestrally diverse participants in genetic studies can lead to new discoveries and is important to ensure equitable health care benefit from research advances. Here, members of the Ethical, Legal, Social, Implications (ELSI) committee of the International Genetic Epidemiology Society (IGES) offer perspectives on methods and analysis tools for the conduct of inclusive genetic epidemiology research, with a focus on admixed and ancestrally diverse populations in support of reproducible research practices. We emphasize the importance of distinguishing socially defined population categorizations from genetic ancestry in the design, analysis, reporting, and interpretation of genetic epidemiology research findings. Finally, we discuss the current state of genomic resources used in genetic association studies, functional interpretation, and clinical and public health translation of genomic findings with respect to diverse populations.

Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins

Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.

The contribution of Neanderthal introgression to modern human traits

Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.

Chronology of natural selection in Oceanian genomes

As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul.

Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

The species studied in any evolutionary investigation generally constitute a small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has rarely been studied and is poorly understood. Here, we use mathematical analysis and simulations to examine the robustness of species tree methods based on the multispecies coalescent model to introgression from a ghost or extant lineage. We found that many results originally obtained for introgression between extant species can easily be extended to ghost introgression, such as the strongly interactive effects of incomplete lineage sorting (ILS) and introgression on the occurrence of anomalous gene trees (AGTs). The relative performance of the summary species tree method (ASTRAL) and the full-likelihood method (*BEAST) varies under different introgression scenarios, with the former being more robust to gene flow between non-sister species whereas the latter performing better under certain conditions of ghost introgression. When an outgroup ghost (defined as a lineage that diverged before the most basal species under investigation) acts as the donor of the introgressed genes, the time of root divergence among the investigated species generally was overestimated, whereas ingroup introgression, as commonly perceived, can only lead to underestimation. In many cases of ingroup introgression that may or may not involve ghost lineages, the stronger the ILS, the higher the accuracy achieved in estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

Pan-Africanism vs. single-origin of Homo sapiens: Putting the debate in the light of evolutionary biology

The scenario of Homo sapiens origin/s within Africa has become increasingly complex, with a pan-African perspective currently challenging the long-established single-origin hypothesis. In this paper, we review the lines of evidence employed in support of each model, highlighting inferential limitations and possible terminological misunderstandings. We argue that the metapopulation scenario envisaged by pan-African proponents well describes a mosaic diversification among late Middle Pleistocene groups. However, this does not rule out a major contribution that emerged from a single population where crucial derived features-notably, a globular braincase-appeared as the result of a punctuated, cladogenetic event. Thus, we suggest that a synthesis is possible and propose a scenario that, in our view, better reconciles with consolidated expectations in evolutionary theory. These indicate cladogenesis in allopatry as an ordinary pattern for the origin of a new species, particularly during phases of marked climatic and environmental instability.

Temporal mapping of derived high-frequency gene variants supports the mosaic nature of the evolution of Homo sapiens

Large-scale estimations of the time of emergence of variants are essential to examine hypotheses concerning human evolution with precision. Using an open repository of genetic variant age estimations, we offer here a temporal evaluation of various evolutionarily relevant datasets, such as Homo sapiens-specific variants, high-frequency variants found in genetic windows under positive selection, introgressed variants from extinct human species, as well as putative regulatory variants specific to various brain regions. We find a recurrent bimodal distribution of high-frequency variants, but also evidence for specific enrichments of gene categories in distinct time windows, pointing to different periods of phenotypic changes, resulting in a mosaic. With a temporal classification of genetic mutations in hand, we then applied a machine learning tool to predict what genes have changed more in certain time windows, and which tissues these genes may have impacted more. Overall, we provide a fine-grained temporal mapping of derived variants in Homo sapiens that helps to illuminate the intricate evolutionary history of our species.

Five Priorities of African Genomics Research: The Next Frontier

To embrace the prospects of accurately diagnosing thousands of monogenic conditions, predicting disease risks for complex traits or diseases, tailoring treatment to individuals' pharmacogenetic profiles, and potentially curing some diseases, research into African genomic variation is a scientific imperative. African genomes harbor millions of uncaptured variants accumulated over 300,000 years of modern humans' evolutionary history, with successive waves of admixture, migration, and natural selection combining with extensive ecological diversity to create a broad and exceptional genomic complexity. Harnessing African genomic complexity, therefore, will require sustained commitment and equitable collaboration from the scientific community and funding agencies. African governments must support academic public research and industrial partnerships that build the necessary genetic medicine workforce, utilize the emerging genomic big data to develop expertise in computer science and bioinformatics, and evolve national and global governance frameworks that recognize the ethical implications of data-driven genomic research and empower its application in African social, cultural, economic, and religious contexts. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors

The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA ("NUMTs"). NUMTs are considered "mtDNA fossils" as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior. This large divergence suggests a distant interspecies hybridization. Additionally, analysis of two other NUMTs suggests that such events occur repeatedly. Our findings suggest a complex pattern of speciation in primate/human ancestors and provide one potential explanation for the mosaic nature of fossil morphology found at the emergence of the hominin lineage. A preliminary version of this manuscript was uploaded to the preprint server BioRxiv in 2017 (10.1101/134502).

Apportioning archaic variants among modern populations

The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution of archaic ancestry in modern populations can be leveraged to better understand the interaction between our species and its archaic relatives. Resolving the interactions between modern and archaic human populations can be difficult, as archaic variants in modern populations have been shaped by genetic drift, bottlenecks and gene flow. Here, we investigate the distribution of archaic variation in Eurasian populations. We find that archaic ancestry coverage at the individual- and population-level present distinct patterns in modern human populations: South Asians have nearly twice the number of population-unique archaic alleles compared with Europeans or East Asians, indicating that these populations experienced differing demographic and archaic admixture events. We confirm previous observations that East Asian individuals have more Neanderthal ancestry than European individuals, but surprisingly, when we compare the number of single nucleotide polymorphisms with archaic alleles found across a population, Europeans have more Neanderthal ancestry than East Asians. We compare these results to simulated models and conclude that these patterns are consistent with multiple admixture events between modern humans and Neanderthals.

This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.

African climate and geomorphology drive evolution and ghost introgression in sable antelope

The evolutionary history of African ungulates has been largely explained in the light of Pleistocene climatic oscillations and the way these influenced the distribution of vegetation types, leading to range expansions and/or isolation in refugia. In contrast, comparatively fewer studies have addressed the continent's environmental heterogeneity and the role played by its geomorphological barriers. In this study, we performed a range-wide analysis of complete mitogenomes of sable antelope (Hippotragus niger) to explore how these different factors may have contributed as drivers of evolution in South-Central Africa. Our results supported two sympatric and deeply divergent mitochondrial lineages in west Tanzanian sables, which can be explained as the result of introgressive hybridization of a mitochondrial ghost lineage from an archaic, as-yet-undefined, congener. Phylogeographic subdivisions into three main lineages suggest that sable diversification may not have been solely driven by climatic events affecting populations differently across a continental scale. Often in interplay with climate, geomorphological features have also clearly shaped the species' patterns of vicariance, where the East Africa Rift System and the Eastern Arc Mountains acted as geological barriers. Subsequent splits among southern populations may be linked to rearrangements in the Zambezi system, possibly framing the most recent time when the river attained its current drainage profile. This work underscores how the use of comprehensive mitogenomic datasets on a model species with a wide geographic distribution can contribute to a much-enhanced understanding of environmental, geomorphological, and evolutionary patterns in Africa throughout the Quaternary.

Disrupting Essentialism in Medical Genetics Education

Many traditional practices in medical genetics education need review to counteract messages of essentialism, or the belief in an underlying natural structure differentiating social categories. While genomics research increasingly disproves a genetic foundation for race, research from educational scholars demonstrates that current medical genetics instruction may actually reinforce racial bias in learners. In this monograph, we outline seven recommendations for medical educators to actively counteract essentialism, racial, and otherwise, in the genetics classroom. In particular, we emphasize the importance of engaging learners in nuanced discussions around stereotyping and its negative consequences for both accurate diagnoses and promoting health equity.

The origins of human cumulative culture: from the foraging niche to collective intelligence

Various studies have investigated cognitive mechanisms underlying culture in humans and other great apes. However, the adaptive reasons for the evolution of uniquely sophisticated cumulative culture in our species remain unclear. We propose that the cultural capabilities of humans are the evolutionary result of a stepwise transition from the ape-like lifestyle of earlier hominins to the foraging niche still observed in extant hunter-gatherers. Recent ethnographic, archaeological and genetic studies have provided compelling evidence that the components of the foraging niche (social egalitarianism, sexual and social division of labour, extensive co-residence and cooperation with unrelated individuals, multilocality, fluid sociality and high between-camp mobility) engendered a unique multilevel social structure where the cognitive mechanisms underlying cultural evolution (high-fidelity transmission, innovation, teaching, recombination, ratcheting) evolved as adaptations. Therefore, multilevel sociality underlies a 'social ratchet' or irreversible task specialization splitting the burden of cultural knowledge across individuals, which may explain why human collective intelligence is uniquely able to produce sophisticated cumulative culture. The foraging niche perspective may explain why a complex gene-culture dual inheritance system evolved uniquely in humans and interprets the cultural, morphological and genetic origins of Homo sapiens as a process of recombination of innovations appearing in differentiated but interconnected populations. This article is part of a discussion meeting issue 'The emergence of collective knowledge and cumulative culture in animals, humans and machines'.

Widespread introgression across a phylogeny of 155 Drosophila genomes

Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here, we leverage 155 genome assemblies from 149 species to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred across most of the 9 clades that we examined. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the tree of life.

The dynamics of introgression across an avian radiation

Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.

Revisiting the out of Africa event with a deep-learning approach

Anatomically modern humans evolved around 300 thousand years ago in Africa. They started to appear in the fossil record outside of Africa as early as 100 thousand years ago, although other hominins existed throughout Eurasia much earlier. Recently, several studies argued in favor of a single out of Africa event for modern humans on the basis of whole-genome sequence analyses. However, the single out of Africa model is in contrast with some of the findings from fossil records, which support two out of Africa events, and uniparental data, which propose a back to Africa movement. Here, we used a deep-learning approach coupled with approximate Bayesian computation and sequential Monte Carlo to revisit these hypotheses from the whole-genome sequence perspective. Our results support the back to Africa model over other alternatives. We estimated that there are two sequential separations between Africa and out of African populations happening around 60-90 thousand years ago and separated by 13-15 thousand years. One of the populations resulting from the more recent split has replaced the older West African population to a large extent, while the other one has founded the out of Africa populations.