To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human and archaic admixture. These results support models in which ancestry from the minor parental species is more likely to persist when rapidly uncoupled from alleles that are deleterious in hybrids. Our analyses further indicate that selection on the swordtail hybrids stems predominantly from deleterious combinations of epistatically-interacting alleles.

Over the past 20 y, many studies have examined the history of the plant ecological and molecular model, Arabidopsis thaliana, in Europe and North America. Although these studies informed us about the recent history of the species, the early history has remained elusive. In a large-scale genomic analysis of African A. thaliana, we sequenced the genomes of 78 modern and herbarium samples from Africa and analyzed these together with over 1,000 previously sequenced Eurasian samples. In striking contrast to expectations, we find that all African individuals sampled are native to this continent, including those from sub-Saharan Africa. Moreover, we show that Africa harbors the greatest variation and represents the deepest history in the A. thaliana lineage. Our results also reveal evidence that selfing, a major defining characteristic of the species, evolved in a single geographic region, best represented today within Africa. Demographic inference supports a model in which the ancestral A. thaliana population began to split by 120-90 kya, during the last interglacial and Abbassia pluvial, and Eurasian populations subsequently separated from one another at around 40 kya. This bears striking similarities to the patterns observed for diverse species, including humans, implying a key role for climatic events during interglacial and pluvial periods in shaping the histories and current distributions of a wide range of species.he plant Arabidopsis thaliana is the principal plant model species, and as such has been useful not only to examine basic biological mechanisms but also to elucidate evolutionary processes. The exceptional resources available in this species, including seed stocks collected from throughout Eurasia for over 75 y, have been a valuable tool for learning about the natural history of A. thaliana on this continent (1, 2). Previous studies have shown that current variation in Eurasia is mainly a result of expansions and mixing from refugia in Iberia, Central Asia, and Italy/Balkans after the end of the last glacial period ∼10 kya (3-8). The main finding of the recent analysis of 1,135 sequenced genomes was that a few Eurasian samples represent divergent relict lineages, whereas the vast majority derived from the recent expansion of a single clade (4). Given the large number of studies that examine the natural history of A. thaliana, one would expect that this history would by now be described rather completely and there would be no major surprises left to uncover. However, there are still many open questions about the ancient history of the species.Several features differentiate A. thaliana from its closest relatives. Although most members of the Arabidopsis genus are obligate outcrossing perennials with large flowers and genome sizes of over 230 Mb and 8 chromosomes, A. thaliana is a predominantly selfing annual with reduced floral morphology and a reduced genome size of ∼150 Mb and 5 chromosomes. The transition to predominant selfing in A. thaliana was likely the catalyst for these derived morphological and...

The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Re-cent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to inconsistency and duplication of effort. This situation presents a major barrier to empirical researchers seeking to use simulations for power analyses of upcoming studies or sanity checks on existing genomic data. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a growing catalog of published simulation models from a range of organisms and supports multiple simulation engine backends. This resource is available as a well-documented python library with a simple command-line interface. We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage a broader community of developers to contribute to this growing resource.