Explaining large mitochondrial sequence differences within a population sample

Mitochondrial DNA sequence is frequently used to infer species' boundaries, as divergence is relatively rapid when populations are reproductively isolated. However, the shared history of a non-recombining gene naturally leads to correlation of pairwise differences, resulting in mtDNA clusters that might be mistaken for evidence of multiple species. There are four distinct processes that can explain high levels of mtDNA sequence difference within a single sample. Here, we examine one case in detail as an exemplar to distinguish among competing hypotheses. Within our sample of tree wētā (Hemideina crassidens; Orthoptera), we found multiple mtDNA haplotypes for a protein-coding region (cytb/ND1) that differed by a maximum of 7.9%. From sequencing the whole mitochondrial genome of two representative individuals, we found evidence of constraining selection. Heterozygotes were as common as expected under random mating at five nuclear loci. Morphological traits and nuclear markers did not reso...线粒体DNA（mitochondrial DNA, mtDNA）序列常被用于推断物种边界，这是因为当种群出现生殖隔离时，其遗传分化速度相对较快。然而，非重组基因的共同演化历史会自然导致两两序列差异之间出现相关性，进而形成线粒体DNA簇，此类簇可能被误判为存在多个物种的佐证。目前存在四种不同的演化过程，可解释单一样本中线粒体DNA序列差异程度偏高的现象。本研究选取其中一例进行详细剖析，作为区分各类竞争假说的典范。在本次研究采集的树沙螽（tree wētā，*Hemideina crassidens*；直翅目Orthoptera）样本中，我们在一处蛋白质编码区域（cytb/ND1）内发现了多种线粒体DNA单倍型（haplotype），单倍型间的最大序列差异可达7.9%。通过对两名代表性个体的全线粒体基因组进行测序，我们检测到了约束选择（constraining selection）的相关证据。在5个核基因座（nuclear loci）上，杂合子（heterozygote）的出现频率符合随机交配条件下的预期分布。形态学性状与核标记未能（原文此处内容截断）