A recent phylogenetic study based only on chloroplast DNA (cpDNA) variation revealed that populations of an Isodon species are frequently embedded paraphyletically among other Isodon species. This phylogenetic discrepancy between species taxonomy and molecular phylogeny was considered to have resulted from chloroplast DNA captures and/or incomplete lineage sorting. To elucidate which of these factors was mainly responsible for the observed phylogenetic pattern, we performed phylogenetic analyses of multiple populations of Isodon species in Japan using cpDNA variation, three single‐copy nuclear genes, and double‐digest restriction‐site‐associated DNA sequencing (ddRAD‐seq). Although a species often shared chlorotypes with other species, our phylogenetical analyses based on variation in the three single‐copy nuclear genes and the ddRAD‐seq data showed that most populations belonging to the same species were monophyletic at the species level, suggesting that chloroplast capture may have frequently occurred between Isodon species. Some populations of an intraspecific taxon were embedded paraphyletically within the species, regardless of the large amount of phylogenetic information in nuclear DNA; this incongruity may have resulted from incomplete lineage sorting.

中文翻译：

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基于叶绿体和核 DNA 变异的系统发育揭示了日本等齿 (唇形科) 物种中频繁的叶绿体捕获

最近一项仅基于叶绿体 DNA (cpDNA) 变异的系统发育研究表明，等齿龙属物种的种群经常与其他等齿龙属物种并列嵌入。物种分类学和分子系统发育之间的这种系统发育差异被认为是由叶绿体 DNA 捕获和/或不完整的谱系分类造成的。为了阐明这些因素中的哪一个主要负责观察到的系统发育模式，我们使用 cpDNA 变异、三个单拷贝核基因和双酶切限制位点相关 DNA 测序对日本的多个 Isodon 物种进行了系统发育分析。 ddRAD-seq)。虽然一个物种经常与其他物种共享氯型，我们基于三个单拷贝核基因变异和 ddRAD-seq 数据的系统发育分析表明，属于同一物种的大多数种群在物种水平上是单系的，这表明叶绿体捕获可能经常发生在 Isodon 物种之间。一些种内分类群的种群被并系地嵌入物种内，而不管核 DNA 中的大量系统发育信息；这种不一致可能是由于谱系分类不完整造成的。不管核 DNA 中有大量的系统发育信息；这种不一致可能是由于谱系分类不完整造成的。不管核 DNA 中有大量的系统发育信息；这种不一致可能是由于谱系分类不完整造成的。