Genomic differentiation
Mitochondrial and nuclear phylogenies (Fig. 2d) show strong support for two reciprocally monophyletic species: M. americana and M. caurina. Both trees also show support for an insular M. caurinaclade (QCI, ADM). The placement of continental M. caurina (COL, PNW) differed in the two phylogenies, but with strong support indicating their distinctiveness from the insular M. caurina . Two individuals (KUI, MTX) exhibited cytonuclear discordance. PCA results (Fig. 2a-c) were consistent with our nuclear phylogeny, demonstrating substantial divergence between New World Martes species (PC1 = 46%; Fig. 2b) and also between insular and continental populations ofM. caurina (PC1 = 39%; Fig. 2c). Within M. caurina, PC2 separates mainland M. caurina populations (COL, PNW) and accounts for 34% of the variation. PCA plots (Fig. 2a-c) highlight the intermediacy of putative hybrid individuals (KUI, MTX) and also their distinction from each other.
The inbreeding coefficient, FIS, is highest for insularM. caurina : 0.89 for ADM and 0.77 for QCI (Supplemental Information 4). Mainland M. caurina also exhibit high FIS, 0.65 for PNW and 0.62 for COL, followed by populations of M. americana. CHI has the lowest FIS of all M. americana populations and the two putative hybrid individuals have an FIS of essentially zero. FST was 0.438 between pooled M. americanaand pooled M. caurina . Contrasting pooled M. americanaagainst pooled (insular and mainland) populations of M. caurinafound similar, high FST estimates (mean = 0.44-0.45, weighted mean = 0.68-0.70) with only moderate FSTestimates between insular and continental populations of M. caurina (mean = 0.01, weighted mean = 0.11; Supplemental Information5).F2- statistics (Supplemental Information 6) and FS(local inbreeding or relatedness2, Supplemental Information 7) demonstrate similar patterns of genetic differentiation, highlighting divergence within M. caurina . Nucleotide diversity (π) was similar across species, but analyses of insular and mainland M. caurina populations separately produced elevated estimates of π, with the highest values for insular M. caurina (Supplemental Information 8). Insular M. caurina had the highest positiveD value, with mainland M. caurina exhibiting only negative and the lowest median D values (Supplemental Information 8).