Nuclear Phylogeny
The species tree inferred using SNAPP, based on individuals from eight sample sites, also shows two major clades. However, a northern clade includes only samples from the Tuolumne, Merced, and San Joaquin drainages, whereas a southern clade only includes samples from Kings, Kaweah, and Kern drainages (Figure 3 ). The species tree topology has strong posterior branch support for all nodes, and suggests that morphologically intermediate populations from the San Joaquin watershed are genetically closer to the northern N. riversiindividuals. In contrast, the concatenated Maximum likelihood analysis using IQtree does not show two major clades, but instead represents the evolutionary divergence as hierarchically nested branches of populations that reflect geographical proximity (Figure 4 ). Bootstrap support is high for populations, though weak for a few branches joining different populations. It is also worthwhile to note that the tree topology largely supports a clear geographical subdivision by drainage system (Figure 4 ).