Comparative Analysis of Genomic Differentiation and Outcomes of Contact Between Taxa Within a Species Complex of North Temperate Fishes.

The outcomes of contact between closely-related species provide insights into the processes that influence divergence along the speciation continuum. We conducted a comparative genomic analysis of divergence between several taxa of Salvelinus fishes from the North Pacific that vary in estimated divergence times from 0.8 to 5.2 million years ago. We found a general increase in the extent of reproductive isolation, as assessed by the presence and kinds of hybrids produced in sympatry, and estimated divergence time. There was evidence of less effective gene flow between Salvelinus confluentus (bull trout) and S. malma lordi (Southern Dolly Varden) in sympatry than between the more recently diverged S. alpinus (Arctic char) and S. m. malma (Northern Dolly Varden) in sympatry. By contrast, although S. m. malma and S. m. lordi are estimated to have diverged from each other only slightly more recently than S. alpinus and S. malma (1.3-1.4 million years ago, respectively), the former produced hybrid swarms upon contact in two lakes while the latter pair showed pronounced, but incomplete, reproductive isolation while sympatric in three lakes. Genome wide assessments of divergence between pairs of taxa suggested that restriction of gene flow between each pair is widespread across the genome, consistent with advanced reproductive isolation between S. confluentus and S. m. lordi and S. alpinus and S. m. malma, but contrasts with an apparent lack of reproductive isolation between S. m. malma and S. m. lordi. We suggest that differences in reproductive ecology (or lack thereof) between pairs of taxa in sympatry likely contribute to variation in their position along the speciation continuum.