Species delimitation and introgression analyses
Of the five species models tested in BFD*, the “4 species” model
(S. zerene, S. atlantis, northern S. hesperis , and
southern S. hesperis ) had the highest marginal likelihood
estimate (MLE) and the most strongly negative Bayes Factor (BF),
indicating that this model was the best supported by the data (Table 1).
The maximum clade credibility (MCC) tree indicated strong support for
the northern S. hesperis and S. atlantis clade (posterior
probability of 1), but the clade containing S. zerene and
southern S. hesperis was less supported with a posterior
probability of 0.87 (Fig. 3a, left panel). The MCC tree additionally
indicated that the southern S. hesperis/S. zerene clade diverged
slightly earlier than the clade containing S. atlantis and
northern S. hesperis .
DensiTree visualization of the BFD* results indicated discordance in the
relationship between S. zerene and the remaining three species on
the tree. The major recovered topology, which accounted for 87.4% of
the sampled trees (shown in blue in Fig. 3a, right panel), was the same
as the topology presented in the MCC tree, however the second most
common topology (7.1% of the sampled trees, shown in purple) depictedS. zerene as basal to the other three species. A third
topology accounting for the remaining 5.4% of the sampled trees (shown
in orange) depicted S. zerene as the sister taxon to the S.
atlantis/ northern S. hesperis clade. The S.
atlantis /northern S. hesperis sister relationship was
consistently recovered in each sampled topology.
Given the discordant relationship between S. zerene and S.
atlantis/S. hesperis in our phylogenetic and BFD* analyses, we used
TreeMix to test for introgression between these species. The unrooted
maximum likelihood phylogeny produced in TreeMix (Fig. 3b, Fig. S2) was
largely consistent with the SNP phylogeny in Fig. 1. Heatmaps containing
the pairwise population residuals for each migration model generally
indicated improved fit with the addition of migration events (Fig. S2),
but this seemed to plateau for models m 3-5; the residual plots
for three, four, and five migration events were highly similar,
suggesting that continued addition of migration events past this point
did not greatly improve fit. The m 3 model indicated a substantial
migration event from the interior of the branch containing S.
zerene to the central S. hesperis population (Fig. 3b; migration
weight = 0.41, p = 0); a migration edge plotted along the interior of
the branch rather than the terminus may indicate historical admixture or
admixture from unsampled populations (Pickrell & Pritchard 2012). This
model also indicated two less substantial, but still statistically
significant, migration events between S. zerene and the clade
containing the central and New Mexico/Arizona S. hesperispopulations (migration weight = 0.07, p = 0.037), and betweenS. zerene and S. atlantis (migration weight = 0.07,p = 0.017). Though models m 4 and m 5 had similar
residuals (Fig. S2), they indicated non-significant migration weights
between some populations: in m 4 the migration edge between the
New Mexico/Arizona S. hesperis population and S. atlantiswas non-significant (migration weight: 0.02, p = 0.169), and inm 5 the edges between S. zerene and the clade containing
the New Mexico/Arizona and central S. hesperis populations
(migration weight = 0.09, p = 0.058), between the New
Mexico/Arizona S. hesperis populations and S. atlantis(migration weight = 0.02, p = 0.092), and between the central and
northern S. hesperis populations (migration weight = 0.01,p = 0.345) were non-significant.
Of the 61 f 3 tests for introgression that we computed, only three
were significant (Table S2); one indicated admixture from S.
zerene and the southern Utah population of S. hesperis into the
central S. hesperis population (p = 0), and another fromS. zerene and the New Mexico/Arizona population of S.
hesperis into the central S. hesperis population (p =
0.003). The third test suggested gene flow from the New Mexico/Arizona
and northern S. hesperis populations into the central S.
hesperis population (p = 0.035).