Data from: Incongruence of mitochondrial and nuclear gene trees in the carabid beetles Ohomopterus

We studied the molecular phylogeny of the carabid subgenus Ohomopterus (genus Carabus) using two mtDNA regions (16SrRNA and ND5) and three nuclear DNA regions (wingless, phosphoenolpyruvate carboxykinase, and an anonymous locus). We revisited the previously reported incongruence between the distribution of mtDNA markers and morphologically defined species (Su et al., 1996, J. Mol. Evol., 43:662-671) which they attributed to "type switching", a concerted change in many morphological characters that results in the repeated evolution of a particular morphological type. Our mtDNA gene tree obtained from 44 individuals representing all 15 currently recognized species of Ohomopterus revealed that haplotypes isolated from individuals of a single "species" were frequently separated into distant clades, confirming the previous report. The three nuclear markers generally conformed better with the morphologically defined species. The phylogenetic signal in mtDNA and nuclear DNA data differed strongly and these two partitions were significantly incongruent with each other according to Farris et al.'s (1994) ILD test, although the three nuclear partitions were not homogeneous either. Our results did not support the type switching hypothesis which was proposed to fit the morphological data to the mitochondrial gene tree: incongruence of the mtDNA tree with other nuclear markers indicates that the mtDNA-based tree does not reflect species history any better than the morphological data. Incongruence of gene trees in Ohomopterus may have been promoted by the complex processes of geographic isolation and hybridization in the Japanese Archipelago that led to occasional gene flow and recombination between separated entities. It is intriguing that reticulate patterns occurred in this group, as species of Ohomopterus exhibit extremely divergent genitalic structures that represent a highly efficient reproductive isolation mechanism.

本研究针对步甲属（Carabus）下的奥摩步甲亚属（Ohomopterus）开展分子系统发育研究，选用两个线粒体DNA（mitochondrial DNA, mtDNA）区域（16S核糖体RNA（16SrRNA）与烟酰胺腺嘌呤二核苷酸脱氢酶亚基5（ND5））以及三个核DNA区域（无翅基因（wingless）、磷酸烯醇式丙酮酸羧激酶（phosphoenolpyruvate carboxykinase）与一个匿名基因座（anonymous locus））进行分析。我们重新验证了此前报道的线粒体DNA标记分布与形态学界定物种间的不一致性（Su等，1996，《分子进化杂志》，43:662-671），该研究将此现象归因于“类型转换（type switching）”——即多组形态性状协同演化，反复产生特定形态类型的过程。我们对代表奥摩步甲亚属当前全部15个已确认物种的44个个体进行测序分析，得到的线粒体基因树结果显示，同一“物种”个体所携带的单倍型常被归入相距较远的演化支，这一发现证实了此前的研究结论。三个核基因标记的聚类结果总体上与形态学界定的物种分类更为吻合。线粒体DNA与核DNA数据的系统发育信号存在显著差异，依据Farris等人1994年提出的间隔长度不一致性检验（Incongruence Length Difference test, ILD test），这两类数据分区之间存在显著的不一致性；即便三个核基因分区之间也并非完全同质。本研究结果不支持“类型转换”假说——该假说旨在使形态学数据匹配线粒体基因树。线粒体基因树与核基因标记的不一致性表明，基于线粒体DNA构建的基因树并不比形态学数据更能反映物种的真实演化历史。奥摩步甲亚属内基因树的不一致性，可能源于日本列岛复杂的地理隔离与杂交过程——这一过程导致隔离类群间偶尔发生基因流与遗传重组。值得关注的是，该类群存在网状演化模式，而奥摩步甲亚属物种的生殖器结构高度分化，这代表了一种高效的生殖隔离机制。