DOI: 10.5061/dryad.t39q6
title: Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy

description: 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 &lt; 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.
description: Bobwhite Mitogenome
 Reads-Illumina_PEIllumina mitogenome PE
 reads (Part 1; split due to size; before extracting the contents of this
 zipped archive file, download the Part 1 and Part 2 files and combine them
 from a Linux/OSX command line by using cat, for example: cat
 Bobwhites_Illumina*.tar.gz &gt; allBobwhites_Illumina.tar.gz). Bird
 ID's appear on subdirectories and fastq filesBobwhites_Illumina1.tar.gzBobwhite Mitogenome Reads-Illumina_PEIllumina mitogenome PE reads (Part 2; split due to size; before extracting the contents of this zipped archive file, download the Part 1 and Part 2 files and combine them from a Linux/OSX command line by using cat, for example: cat Bobwhites_Illumina*.tar.gz &gt; allBobwhites_Illumina.tar.gz). Bird ID's appear on subdirectories and fastq filesBobwhites_Illumina2.tar.gzScaled Quail Mitogenome Reads-Illumina_PEIllumina mitogenome PE reads for one wild scaled quail.ScaledQuail_Illumina.tar.gzQuail Mitogenome Alignment For RAxML TreeQuail Mitogenome Alignment For RAxML Tree (nexus)tree_alignment.nexBobwhite Mitogenome Alignment_IDsBobwhite mitogenome alignment (nexus file) with individual IDs that match the RAxML tree and alignment file.Group1_Group2.nex