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.本研究针对美国德克萨斯州（TX）与俄克拉荷马州（OK）6个生态区的53只山齿鹑（bobwhites），分别基于短线粒体片段（即部分或完整D环核苷酸序列）与完整线粒体基因组（mitogenome）序列开展分析，评估二者所得种群推断结果与结论的一致性。中位连接（Median Joining, MJ）单倍型网络分析显示，使用短线粒体片段开展的分析，无法准确估算本研究样本的真实（即完整）线粒体基因组单倍型结构、对应的遗传分化水平以及母系种群历史。值得注意的是，对比部分序列（即部分D环序列）与完整线粒体基因组序列的错配分布时，可观察到种群历史推断结果不一致的情况，且线粒体基因组信息含量的缺失会导致本研究样本产生虚假推断。针对完整山齿鹑线粒体基因组的变异预测概率分析显示，共存在344个分离位点，对应总计347个突变，其中包含分布于12个蛋白质编码基因上的49个推定非同义单核苷酸变异（single nucleotide variants, SNVs）。13只山齿鹑被检测出存在明显的异质性现象，其中10例异质性事件涉及1个中等到高频的单核苷酸变异。对完整山齿鹑线粒体基因组序列开展的单倍型网络与系统发育分析显示，存在两个分化的母系支系（核苷酸分歧度dXY=0.00731；固定指数FST=0.849；P<0.05），由此支持存在两个推定亚种的可能性。然而，该分化支系（n=103个变异位点）几乎仅包含地理归类为德克萨斯山齿鹑（Colinus virginianus texanus）的个体，这与以往地理亚种划分的预期结果不一致。针对功能分化的适应性进化检验（McDonald-Kreitman检验, MKT）、频率分布检验（D、FS）以及系统发育分析软件RAxML的分析结果均未发现，正选择或与同域分布的鳞斑鹑（Callipepla squamata）的杂交可作为本研究观察到的两个山齿鹑母系支系的解释因素。相反，本研究的分析结果支持如下假说：两个分化的母系支系从种群扩张前存续至扩张后，且伴随部分轻微有害的非同义突变的分离。