Mapping migration and adaptation in genomes

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Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species

Publication . Mendes, Sofia L.; Machado, Miguel P.; MM, Coelho; Sousa, Vitor C

Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers—Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis—using a population genomics dataset of 23,562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well-differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage, we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes.

2021-08Journal article

Open access

Reply to "Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin"

Publication . Berner, Daniel; Lucek, Kay; Sousa, Vitor C; Excoffier, Laurent; Seehausen, Ole

A Matters Arising article1 raised concerns about the interpretation of our findings reported in our recent publication on admixture-facilitated ecological speciation in Lake Constance stickleback2. After careful consideration of the criticism, including additional analyses testing the proposed alternative hypotheses, we can confirm our confidence in the inference of secondary contact between a West European and an East European stickleback lineage in the catchment of Lake Constance, and that this admixture facilitated the ecological divergence between lake and stream ecotypes within Lake Constance2. In particular, Berner1 (i) questioned whether West and East European stickleback populations should be considered as divergent lineages, (ii) suggested that Lake Constance stickleback originated from the upper Danube instead of East Europe, (iii) questioned the suitability of our demographic modelling approach to reject an ‘ecological vicariance’ scenario, (iv) proposed that divergent selection within Lake Constance biased our inference of a secondary contact and admixture scenario, and (v) criticized our conclusion on admixture-facilitation of ecological speciation as premature. We address each of these concerns in this sequence.

2021-05Journal article

Open access