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 the two continental M. caurina(COL, PNW) differed in the two phylogenies, but they were strongly
supported as distinct from the insular M. caurina , suggesting
substantial genomic divergence between continental and insular M.
caurina . Two individuals (KUI, MTX) exhibited cytonuclear discordance.
PCA results (Fig. 2a-c) are consistent with our nuclear phylogeny,
demonstrating substantial divergence not only between New WorldMartes species (PC1 = 46%; Fig. 2b), but also between insular
and continental populations of M. caurina (PC1 = 39%; Fig. 2c).
Within M. caurina, PC2 also separates mainland M. caurinapopulations (COL, PNW) and accounts for a notable 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 2
putative hybrid individuals have an FIS of essentially
0. FST was 0.438 between pooled M. americana and
pooled M. caurina . Contrasting pooled M. americana against
pooled (insular and mainland) populations of M. caurina found
similar, high FST estimates (mean = 0.44-0.45, weighted
mean = 0.68-0.70) with only moderate FST estimates
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 between
individuals and species, highlighting divergence within M.
caurina . Nucleotide diversity (π) was similar across species, but
analysis of insular and mainland M. caurina populations
separately produced elevated π estimates, with the highest values for
insular M. caurina (Supplemental Information 8). Insular M.
caurina also exhibited the highest positive D value, with
mainland M. caurina exhibiting only negative and the lowest
median D value (Supplemental Information 8).