whole
genome shotgun sequences were available were then
added. Multiple sequences for each gene were aligned
and trimmed in MEGA4 (Tamura et al., 2007); refer to
Supplementary Table S2 for lengths of multiple alignments.
For this analysis, substitution saturation was tested
with DAMBE (Xia & Lemey, 2009). Models of evolution for
each gene were identified using the Akaike significance
criterion in ModelTest3.8