Data from: 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 resolve the mtDNA groupings of individuals. We concluded that the large differences found among our sample of mtDNA sequences were simply owing to a large population size over an extended period of time allowing an equilibrium between mutation and drift to retain a great deal of genetic diversity within a single species.

线粒体DNA（Mitochondrial DNA）序列常被用于物种边界的推断，因种群发生生殖隔离时，其序列分化速率相对较快。然而，不重组基因的共同演化历史会自然引发两两序列差异的相关性，进而形成可能被误判为多物种存在证据的线粒体DNA簇。目前已有四类明确的过程可解释单一样本中线粒体DNA序列的高分化水平。本研究选取一例作为典型例证，通过详细剖析以区分各类竞争性假说。在本次研究的树沙螽（Hemideina crassidens；直翅目Orthoptera）样本中，研究人员于蛋白编码区域（cytb/ND1）内发现多个线粒体DNA单倍型，彼此间最大序列差异达7.9%。通过对两名代表性个体的完整线粒体基因组进行测序，我们找到了纯化选择的相关证据。在五个核基因座上，杂合子的出现频率符合随机交配下的预期水平。形态性状与核标记均未能解析出个体的线粒体DNA类群划分。本研究最终得出结论：本次样本中线粒体DNA序列间的显著差异，仅源于种群长期维持较大有效规模，使得突变与遗传漂变间达到动态平衡，从而在单一物种种群内保留了大量遗传多样性。