The Phylogeography of Westslope Cutthroat Trout Based on Whole-Mitome Sequences and Nuclear SNP Markers

Despite that westslope cutthroat trout are a species of conservation concern in the interior West, we know little about the phylogeographic structure of this taxon. To address this issue, we sequenced the mitome of 96 westslope cutthroat trout from throughout the historical range in four major river basins—the Columbia, Missouri, Saskatchewan, and Fraser—in the U.S. and Canada, and analyzed a panel of variable single nucleotide polymorphisms from the nuclear genome for fish from a subset of this range. These data indicate pronounced divergence between lineages at the scale of large river basins. In general, Idaho and Oregon basins south of the extent of glaciation during the Last Glacial Maximum reflect a suite of diverse lineages to which fish in the John Day basin are basal. A less variable northern lineage consists of fish from the Washington Cascades and the remainder of the U.S. and Canadian range. However, populations from the Clearwater River basin appear in nearly all clades. Hydrological connections that would explain these patterns are unclear. Stocked populations appear to be recognizable with either mitochondrial or nuclear markers.