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).