Highlights d Bronze Age (BA) Helladic, Cycladic, and Minoan genomes from the Aegean were sequenced d 3,000 BCE Aegeans are homogeneous and derive ancestry mainly from Neolithic farmers d Neolithic Caucasus-like and BA Pontic-Caspian Steppe-like gene flow shaped the Aegean d Present-day Greeks are genetically similar to 2,000 BCE Aegeans from Northern Greece

The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century.Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at the Agouti locus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from eleven sites along a transect spanning the Sand Hills at 660,000 SNPs across the genome.

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Hybridization is frequent in the wild but it is unclear when admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation rapidly after admixture in 3 hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.

Effective conservation actions to counteract the current decline of populations and species require a deep knowledge on their genetic structure. We used Single Nucleotide Polymorphisms (SNPs) to infer the population structure of the highly threatened freshwater pearl mussel Margaritifera margaritifera in the Iberian Peninsula. A total of 130 individuals were collected from 26 locations belonging to 16 basins. We obtained 31,692 SNPs through Genotyping by Sequencing (GBS) and used this dataset to infer population structure. Genetic diversity given as observed heterozygosity was low. Pairwise FST comparisons revealed low levels of genetic differentiation among geographically close populations. Up to 3 major genetic lineages were determined: Atlantic, Cantabrian and Douro. This structure suggests a close co-evolutionary process with brown trout (Salmo trutta), the primordial fish host of this mussel in the studied area. Some sub-basins showed some genetic structuring, whereas in others no intrapopulation differentiation was found. Our results confirm that genetic conservation units do not match individual basins, and that knowledge about the genetic structure is necessary before planning recovery plans that may involve relocation or restocking. The same reasoning should be applied to strictly freshwater species that are sessile or have restricted dispersal abilities and are currently imperiled worldwide.

Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we analyze 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-yearold (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of "Ancient North Siberians" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry related to present-day East Asians, giving rise to ancestral Native Americans and "Ancient Paleosiberians" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the "Neosiberians" from which many contemporary Siberians derive. We detect gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic throughout the Late Pleistocene and Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia. Northeastern Siberia (the modern Russian Far East) is one of the most remote and extreme environments colonized by humans. Extending from the Taimyr Peninsula in the west to the Pacific Ocean in the east, and from the China/Russia border north to the Arctic Ocean, the region is home to dozens of diverse ethnolinguistic groups. Recent genetic studies of the

11In freshwater fish, processes of population divergence and speciation are often linked 12 to the geomorphology of rivers and lakes that create barriers isolating populations. 13However, current geographical isolation does not necessarily imply total absence of 14 gene flow during the divergence process. Here, we focused on four species of the 15 genus Squalius in Portuguese rivers: S. carolitertii, S. pyrenaicus, S. aradensis and S. 16 torgalensis. Previous studies based on eight nuclear and mitochondrial markers 17 revealed incongruent patterns, with nuclear loci suggesting that S. pyrenaicus was a 18 paraphyletic group, since its northern populations were genetically closer to S. 19 carolitertii than to other southern populations. Here, for the first time, we successfully 20 applied a genomic approach to the study of the relationship between these species, 21 using a Genotyping by Sequencing approach to obtain single nucleotide 22 polymorphisms (SNPs). Our results revealed a species tree with two main lineages: (i) 23 S. carolitertii and S. pyrenaicus; (ii) S. torgalensis and S. aradensis. Moreover, 24 regarding S. carolitertii and S. pyrenaicus, we found evidence for past introgression 25 between these two species in the northern part of S. pyrenaicus distribution. This 26 introgression reconciles previous mitochondrial and nuclear incongruent results and 27 explains the apparent paraphyly of S. pyrenaicus. Although we cannot distinguish a 28 scenario of hybrid speciation from secondary contact, our estimates are consistent 29 across models, suggesting that the northern populations of S. pyrenaicus received 30 approximately 80% from S. carolitertii and 20% from southern S. pyrenaicus. This 31 illustrates that even in freshwater species currently found in isolated river drainages, 32we are able to detect past gene flow events in present-day genomes, suggesting that 33 speciation is more complex than simply allopatric. 34 35 3

Experimental evolution is a powerful tool to understand the adaptive potential of populations under environmental change. Here, we study the importance of the historical genetic background in the outcome of evolution at the genome-wide level. Using the natural clinal variation of Drosophila subobscura, we sampled populations from two contrasting latitudes (Adraga, Portugal and Groningen, Netherlands) and introduced them in a new common environment in the laboratory. We characterized the genome-wide temporal changes underlying the evolutionary dynamics of these populations, which had previously shown fast convergence at the phenotypic level, but not at chromosomal inversion frequencies. We found that initially differentiated populations did not converge either at genome-wide level or at candidate SNPs with signs of selection. In contrast, populations from Portugal showed convergence to the control population that derived from the same geographical origin and had been long-established in the laboratory. Candidate SNPs showed a variety of different allele frequency change patterns across generations, indicative of an underlying polygenic basis. We did not detect strong linkage around candidate SNPs, but rather a small but long-ranging effect. In conclusion, we found that history played a major role in genomic variation and evolution, with initially differentiated populations reaching the same adaptive outcome through different genetic routes.