Mitochondrial phylogeny
The COI phylogenetic tree has two major lineages, a northern and southern clade with divergence time of 0.52 million years ago, and both clades contain individuals from the intermediate morphotype (Figure 2 ). There is clear geographical structure, with populations from the same drainage belonging to the same clades and even the same haplotype. For example, there is a distinct subclade in the northern clade that includes samples from the Tuolumne and Merced drainages, and excludes other haplotypes found in the northern clade. Similarly, several clades in the southern lineage consist of samples only from the Kern or Kern/Kaweah drainage. The TCS network shows that the two distinct haplogroups are separated by eight substitutions (Figure S2 ). Haplotypes assigned to the northern clade are widely distributed, although many are unique and occur locally. These haplotypes are found in the Tuolumne (N. riversi ), San Joaquin (intermediate morphotype), Kings, and Kern (N. ingens ) drainages, including 13 out of the 21 populations of intermediate and N. ingens sample sites, as far as the southernmost population (site27). On the other hand, the southern clade consists only of samples from San Joaquin (intermediate morphotype), Kings, Kern, and Kaweah (N. ingens ), and no southern clade haplotypes are observed in northern populations of N. riversi . (Table S1 ).