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 ).