Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin’s finches, suggesting that similar features are important for evolution across diverse taxa.

Our results are consistent with a history of gene flow between the Levant and southern Arabia. Consideration of genetic, archaeological, and paleoclimate data provide a slight edge for the SDR but, ultimately, more data are needed to definitively identify which dispersal route out of Africa was used.

Objectives: Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history. Materials and Methods:We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f 4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes.Results: We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes.Discussion: We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations. K E Y W O R D Sarchaic humans, dispersal, Neanderthal introgression, Near East, out of Africa, Yemen

Anatomically modern humans (AMHs) left Africa ~60,000 years ago, marking the first of multiple dispersal events by AMH between Africa and the Arabian Peninsula. The southern dispersal route (SDR) out of Africa (OOA) posits that early AMHs crossed the Bab el-Mandeb strait from the Horn of Africa into what is now Yemen and followed the coast of the Indian Ocean into eastern Eurasia. If AMHs followed the SDR and left modern descendants in situ, Yemeni populations should retain old autochthonous mitogenome lineages. Alternatively, if AMHs did not follow the SDR or did not leave modern descendants in the region, only young autochthonous lineages will remain as evidence of more recent dispersals. We sequenced 113 whole mitogenomes from multiple Yemeni regions with a focus on haplogroups M, N, and L3(xM,N) as they are considered markers of the initial OOA migrations. We performed Bayesian evolutionary analyses to generate time-measured phylogenies calibrated by Neanderthal and Denisovan mitogenome sequences in order to determine the age of Yemeni-specific clades in our dataset. Our results indicate that the M1, N1, and L3(xM,N) sequences in Yemen are the product of recent migration from Africa and western Eurasia. Although these data suggest that modern Yemeni mitogenomes are not markers of the original OOA migrants, we hypothesize that recent population dynamics may obscure any genetic signature of an ancient SDR migration.

Yemeni mitogenomes are largely the product of Holocene migration, and subsequent in situ evolution, from Africa and western Eurasia. However, we hypothesize that recent population movements may obscure the genetic signature of more ancient migrations. Additional research, e.g., analyses of Yemeni nuclear genetic data, is needed to better reconstruct the complex population and migration histories associated with Out of Africa.

ObjectivesModern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabian depending on which dispersal route out of Africa was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history.Materials and MethodsWe analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared those data to populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes.ResultsWe find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes.DiscussionWe infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.

As the collapse of the Western Roman Empire accelerated during the 4th and 5th centuries, arriving "barbarian" groups began to establish new communities in the border provinces of the declining (and eventually former) empire. This was a time of significant cultural and political change throughout not only these border regions but Europe as a whole. To better understand post-Roman community formation in one of these key frontier zones after the collapse of the Hunnic movement, we generated new paleogenomic data for a set of 38 burials from a time series of three 5th century cemeteries at Lake Balaton, Hungary. We utilized a comprehensive sampling approach to characterize these cemeteries, and analyzed them within a careful interdisciplinary framework along with data from 38 additional burials from a previously published mid-6th century site. Despite many commonalities in burial representation and demography, we find striking differences in how close genealogical relationships were recognized and expressed in burial customs amongst these small, rural communities. In addition, each site demonstrated a unique genomic ancestry profile, though interestingly a significant relationship was inferred between genetic variation and the presence of a 5th century "female package" of dress accessories and grave goods. Notably, the range of genetic diversity in all four of these local burial communities is extensive and wider ranging than contemporaneous Europeans sequenced to date. Our analysis shows that the formation of early Medieval communities was a multifarious process even at a local level, consisting of genetically heterogeneous groups demonstrating a variety of social systems. Significance: The decline of the Western Roman Empire resulted in a significant cultural and political transformation of Europe during the early Medieval, and many modern nations claim to trace their origins to this period. We conducted an interdisciplinary paleogenomic study using a novel comprehensive, time-series approach, studying three mid-to-late 5th century sites and one mid 6th century site all from a localized region south of Lake Balaton (Hungary). We find very high levels of genetic diversity in this small region as well as significant variability in how genealogical relationships were reflected in cemetery organization. By carefully combining genetic, archaeological, and historical data, we demonstrate that post-Roman communities were formed by not only culturally, but also genetically diverse groups.