Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy

Herein, we evaluated the concordance of population inferences and
conclusions resulting from the analysis of short mitochondrial fragments
(i.e., partial or complete D-Loop nucleotide sequences) versus complete
mitogenome sequences for 53 bobwhites representing six ecoregions across
TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that
analyses performed using small mitochondrial fragments were insufficient
for estimating the true (i.e., complete) mitogenome haplotype structure,
corresponding levels of divergence, and maternal population history of our
samples. Notably, discordant demographic inferences were observed when
mismatch distributions of partial (i.e., partial D-Loop) versus complete
mitogenome sequences were compared, with the reduction in mitochondrial
genomic information content observed to encourage spurious inferences in
our samples. A probabilistic approach to variant prediction for the
complete bobwhite mitogenomes revealed 344 segregating sites corresponding
to 347 total mutations, including 49 putative nonsynonymous single
nucleotide variants (SNVs) distributed across 12 protein coding genes.
Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of
the 13 heteroplasmies involving one moderate to high frequency SNV.
Haplotype network and phylogenetic analyses for the complete bobwhite
mitogenome sequences revealed two divergent maternal lineages (dXY =
0.00731; FST = 0.849; P < 0.05), thereby supporting the potential
for two putative subspecies. However, the diverged lineage (n = 103
variants) almost exclusively involved bobwhites geographically classified
as Colinus virginianus texanus, which is discordant with the expectations
of previous geographic subspecies designations. Tests of adaptive
evolution for functional divergence (MKT), frequency distribution tests
(D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive
selection or hybridization with the sympatric scaled quail (Callipepla
squamata) as being explanatory factors for the two bobwhite maternal
lineages observed. Instead, our analyses support the supposition that two
diverged maternal lineages have survived from pre-expansion to
post-expansion population(s), with the segregation of some slightly
deleterious nonsynonymous mutations.