History of speciation inferred from genomic analysis of a species complex of north temperate fishes

Comparative biogeographic analyses have provided key insights into the history of divergence among closely-related species. We collected genomic data across much of the range of two salmonid fishes, Arctic char (AC, Salvelinus alpinus) and Dolly Varden (DV, S. malma) that comprise a complex of lineages whose relationships and evolutionary interactions have remained uncertain. A time-calibrated phylogeny indicated reciprocal monophyly of AC and DV, that the species diverged an estimated ~1.4 million years ago, and that eastern Pacific southern Dolly Varden (S. m. lordi) is the basal lineage within DV. Historical and contemporary gene flow was detected between species and regional groups within species. We found strong evidence for a model of divergence without gene flow between AC and DV followed by secondary contact about 14,500 years ago with subsequent gene flow. Our geographic and genomic investigation within the AC-DV complex clarifies the origin and inter-relationships of the species and further highlight the North Pacific and Arctic as dynamic areas of evolution of regional faunas

Methods
Genotyping by sequencing analysis using Pst1 enzyme. It has been aligned to the Salvelinus sp. reference genome and consists of a variant call format file (vcf) with 350 samples that contains biallelic single nucelotide polymorphims that have a heterozygosity of less than 0.6 (N = 6,601,213).