Population Structure and Ancestry Coefficients
The clustering of individuals into ancestral populations was estimated
with sNMF using cluster numbers from 1 to 20. The optimal number of
clusters was unclear as the cross-entropy continuously decreases up to
K=11, although the relative change in cross-entropy values is smaller
after K=6 (Figure S3 ). In the K=3 model, clusters are
consistent with morphotypes (N. riversi , intermediate, andN. ingens ), but with some populations showing some admixture
among these major lineages. These admixed populations are located in a
geographical transition zone where separate lineages could have
experienced historical gene flow (Figure S1 ). In the K=4 model,
the southern cluster splits into two clusters, revealing a distinct
ancestral subpopulation located in the Kings drainage. In the K=5 model,
the southernmost cluster further subdivides into west (Kaweah) and east
(Kern) ancestral populations. In the K=6 model, the northern sample
sites (sites 3 and 4) split from other northern populations and thus
subdivide N. riversi (sites 1 to 6) into two clusters. From K=7
to K=11, new clusters mostly emerge around the contact zones of major
drainages (Figure S1 ).