Phylogenetic relationships
Maximum likelihood phylogenetic inference using whole mitochondrial
genomes (15,268 nucleotides) showed that the Xerces Blue specimens form
a monophyletic clade, as do the Silvery Blue specimens (Fig. 1A). We
inferred a time-calibrated Bayesian phylogenetic tree from
protein-coding genes (11,028 nucleotides) of the mitochondrial DNA
genomes of Xerces Blue, Silvery Blue, and 12 related butterflies in
Polyommatinae. The Xerces Blue and the Silvery Blue are recovered as
sister taxa with high support (posterior probability=1). Because there
are no known fossils to calibrate the time since divergence, we first
used a molecular clock that spanned the range of rates frequently used
for arthropod mitochondrial genes (1.5-2.3% divergence/Ma). This
yielded an origin of this subgroup of Polyommatinae at 10.26 Ma
(7.16-13.76 Ma 95% HPD interval) and divergence of the Xerces Blue from
the Silvery Blue at 849,000 years ago (560,895-1,159,512 years 95% HPD
interval, Fig. 1B). A second estimate based on larger-scale fossil-based
calibrations (7) placed the origin of the subgroup at ca. 33 Ma (8) with
the subsequent divergence of the Xerces Blue and Silvery Blue at 2.60 Ma
(2.14-3.08 Ma 95% HPD interval, Figure 1B). The recent speciation of
Xerces and Silvery blue is not obviously due to infection with theWolbachia , as no evidence of infection of the sampled specimens
with this alpha-proteobacterium is detected in the raw read data.