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

Although Neanderthals are extinct, fragments of their genomes persist in contemporary humans. Here we show that while the genome-wide frequency of Neanderthal-like sites is approximately constant across all contemporary out-of-Africa populations, genes involved in lipid catabolism contain more than threefold excess of such sites in contemporary humans of European descent. Evolutionally, these genes show significant association with signatures of recent positive selection in the contemporary European, but not Asian or African populations. Functionally, the excess of Neanderthal-like sites in lipid catabolism genes can be linked with a greater divergence of lipid concentrations and enzyme expression levels within this pathway, seen in contemporary Europeans, but not in the other populations. We conclude that sequence variants that evolved in Neanderthals may have given a selective advantage to anatomically modern humans that settled in the same geographical areas.

One of the enduring questions in the evolution of our species surrounds the fate of 'archaic' forms of Homo. Did Neanderthals go extinct without interbreeding with modern humans 25-40 thousand years ago or are their genes present among modern-day Europeans? Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively. Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years.

Variation in human skin and hair color is one of the most striking aspects of human variability, and explaining this diversity is one of the central questions of human biology. Only in the last decade or so has it been realistically possible to address this question experimentally using population genetic approaches. On the basis of earlier studies in mice, and on studies in humans with various Mendelian disorders, many of the genes underpinning population variation in skin color have been identified. More recently, genome-wide approaches have identified other loci that appear to contribute to pigmentary variation. The ability to study sequence diversity from world populations has allowed examination of whether the observed variability is due to random genetic drift or is a result of natural selection. The genetic evidence taken as a whole provides strong evidence for natural selection, functioning so as to increase pigment diversity across the world's populations. Future larger studies are likely to provide more details of this process and may provide evidence for exactly which mechanistic pathways have mediated selection.

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

Abstract Admixture has been a pervasive phenomenon in human history, shaping extensively the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as adaptive admixture . However, the role of adaptive admixture in human evolution and the power to detect it are poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, accounting for background selection and assuming different admixture scenarios. We show that two statistics based on admixture proportions, F adm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas iHS and F ST falsely detect neutral mutations that have been selected in the source populations only. By combining F adm and LAD into a single statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africa and in Madagascar, North Africa and South Asia, respectively. Our approach also uncovers new cases of adaptive admixture, including the APOL1 / MYH9 locus in the Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides new evidence that adaptive admixture has occurred in multiple human populations, whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow. Author summary Adaptive introgression, i.e., the acquisition of adaptive traits through hybridization with another species, is a well-documented phenomenon in evolution. Conversely, adaptive admixture, i.e., the acquisition of adaptive traits through admixture between populations of the same species, is poorly described. In this study, we evaluate the importance of adaptive admixture in human recent evolutionary history. We first determine the expected signatures of adaptive admixture on patterns of genomic diversity, using realistic simulations. We then identify the methods that are the most powerful to detect such molecular signatures. Finally, by using the methods identified as the most powerful, we search for cases of adaptive admixture in the genomes of 15 admixed populations from around the globe. We find evidence that adaptive admixture has occurred in several populations from Northeast Africa, Southeast Asia and Oceania. This study suggests that admixture has indeed facilitated human genetic adaptation, particularly at genes involved in metabolism and resistance against pathogens.

ABSTRACT Scans for positive selection in human populations have identified hundreds of sites across the genome with evidence of recent adaptation. These signatures often overlap across populations, but the question of how often these overlaps represent a single ancestral event remains unresolved. If a single positive selection event spread across many populations, the same sweeping haplotype should appear in each population and the selective pressure could be common across diverse populations and environments. Identifying such shared selective events would be of fundamental interest, pointing to genomic loci and human traits important in recent history across the globe. Additionally, genomic annotations that recently became available could help attach these signatures to a potential gene and molecular phenotype that may have been selected across multiple populations. We performed a scan for positive selection using the integrated haplotype score on 20 populations, and compared sweeping haplotypes using the haplotype-clustering capability of fastPHASE to create a catalog of shared and unshared overlapping selective sweeps in these populations. Using additional genomic annotations, we connect these multi-population sweep overlaps with potential biological mechanisms at several loci, including potential new sites of adaptive introgression, the glycophorin locus associated with malarial resistance, and the alcohol dehydrogenase cluster associated with alcohol dependency.

Recent human evolution refers to evolutionary adaptation, sexual and natural selection, and genetic drift within Homo sapiens populations, since their Recent human evolution refers to evolutionary adaptation, sexual and natural selection, and genetic drift within Homo sapiens populations, since their separation and dispersal in the Middle Paleolithic about 50,000 years ago. Contrary to popular belief, not only are humans still evolving, their evolution since the dawn of agriculture is faster than ever before. It has been proposed that human cult Resistan…

Natural selection is the differential survival and reproduction of individuals due to differences in the relative fitness endowed on them by their own Natural selection is the differential survival and reproduction of individuals due to differences in the relative fitness endowed on them by their own particular complement of observable characteristics. It is a key law or mechanism of evolution which changes the heritable traits characteristic of a population or species over generations. Charles Darwin popularised the term "natural selection", co Without phenotypic variation, there would be no evolution by natural selection. A prerequisite for natural selection to result in adaptive evolution, novel traits and speciation is the presence of heritable genetic variation that affects phenotypic fitness differences. Genetic variation is the result of mutations, genetic recombinations and alterations in the karyotype (the number, shape, size and internal arrangement of the chromosomes). Any of these changes might have an effect that is highly advantageous or highly disadvantageous for phenotypic variations, but large effects on phenotypes are rare. In the past, most changes in the genetic material were considered neutral or close to neutral because they occurred in noncoding DNA or resulted in a synonymous substitution. However, many mutations in non-coding DNA have deleterious effects. Although both mutation rates and average fitness effects of mutations are dependent on the organism, a majority of mutations in humans are slightly deleterious. Some mutations occur in "toolkit" or regulatory genes. Changes in these often have large effects on the phenotype of the individual because they regulate the function of many other genes. Most, but not all, mutations in regulatory genes result in non-viable embryos. Some nonlethal regulatory mutations occur in HOX genes in humans, which can result in a cervical rib or polydactyly, an increase in the number of fingers or toes. When such mutations result in a higher fitness, natural selection favours these phenotypes and the novel trait spreads in the population. Established traits are not immutable; traits that have high fitness in one environmental context may be much less fit if environmental conditions change. In the absence of natural selection to preserve such a trait, it becomes more variable and deteriorate over time, possibly resulting in a vestigial manifestation of the trait, also called evolutionary baggage. In many circumstances, the apparently vestigial structure may retain a limited functionality, or may be co-opted for other advantageous traits in a phenomenon known as preadaptation. A famous example of a vestigial structure, the eye of the blind…