Fig. 6: Whole-genome phylogenetic analyses.
Panel (a) shows a map of the sampling localities in the western United States; Dubois is included for reference but was not sampled for whole-genome phylogenetics. The Jackson Hole ancestry cline (i.e., the range of the ancient Jackson Hole hybrids) is shown for reference as well (red zone). Panel b shows the midpoint-rooted maximum likelihood phylogram inferred from the whole-genome SNP set (2,013,201 autosomal SNPs). Panels (c–e) show three common unrooted tree topologies inferred from 1000 SNP windows. The tree in panel (c) is the most common topology and matches the whole-genome tree in b. Trees in panels d and e differ by grouping the Warner Mts. population with L. melissa or the Sierra Nevada population, respectively. Panels (f–h) show the proportion of 1000 SNP topologies matching the trees in c–e for autosomal windows, Z-chromosome windows, and the 1000 SNP windows that contain the candidate barrier loci (see main text). There is a significant deficit of the topology in d on the Z chromosome and among the barrier loci (x-fold = 0.10, one-sided P < 0.001, and x-fold = 0.43, one-sided P = 0.047, respectively), and a significant excess of topology (e) on the Z chromosome and among the barrier loci (x-fold = 5.36, P < 0.001, and x-fold = 3.62, P = 0.008). See Supplementary Fig. 25 for the full set of tree topologies recovered. Source data are provided as a Source Data file.
