Data from: Late Pleistocene range expansion of North American topminnows accompanied by admixture and introgression

Aim: We used genome-scale sampling to assess the phylogeography of a group of topminnows in the Fundulus notatus species complex. Two of the species have undergone extensive range expansions resulting in broadly overlapping distributions, and sympatry within drainages has provided opportunities for hybridization and introgression. We assess the timing and pattern of range expansion in the context of late-Pleistocene-Holocene drainage events, and evaluate the evidence for introgressive hybridization between species. Location: Central and southern United States including drainages of the Gulf of Mexico Coastal Plain and portions of the Mississippi River drainage in and around the Central Highlands. Taxon: Topminnows, Genus Fundulus, subgenus Zygonectes - Fundulus notatus, Fundulus olivaceus, Fundulus euryzonus Methods: We sampled members of the F. notatus species complex throughout their respective ranges, including numerous drainage systems where species co-occur. We collected genome-wide Single Nucleotide Polymorphisms (SNPs) using the Genotype by Sequencing (GBS) method, and subjected data to population genetic analyses to infer the population histories of both species, including explicit tests for admixture and introgression. The methods employed included STRUCTURE, Principle Coordinates Analysis, TreeMix and Approximate Bayesian Computation. Results: Genetic data are presented for 749 individuals sampled from 14 F. notatus, 20 F. olivaceus, and two F. euryzonus populations. Members of the species complex differed in phylogeographic structure, with F. notatus exhibiting geographic clusters corresponding to Pleistocene coastal drainages, and F. olivaceus comparatively lacking in phylogeographic structure. Evidence for interspecific introgression varied by drainage. Main Conclusions: Populations of F. notatus and F. olivaceus exhibited contrasting patterns of lineage diversity among coastal drainages, indicating inter-specific differences in their Pleistocene southern refugia. Phylogeographic patterns in both species indicated that range expansions into the northern limits of contemporary distributions coincided with and continued subsequent to the Last Glacial Maximum. There was evidence of introgression between species in some, but not all drainages where the species co-occur, in a pattern that is correlated with previous estimates of hybridization rates.