Data from: A multilocus sequencing approach reveals the cryptic phylogeographical history of Phyllodoce nipponica Makino (Ericaceae)

Discordant phylogeographical patterns among species with similar distributions may not only denote specific biogeographical histories of different species, but also could represent stochastic variance of genealogies in applied genetic markers. A multilocus investigation representing different genomes can be used to address the latter concern, allowing robust inference to biogeographical history. In the present study, we conducted a multilocus phylogeographical analysis to re-examine the genetic structuring of Phyllodoce nipponica, in which chloroplast (cp)DNA markers exhibited a discordant pattern compared to those of other alpine plants. The geographical structure of sequence variation at five nuclear loci was not consistent with that of cpDNA and showed differentiation between the northern and southern parts of the range of this species. Its demographic history inferred from the isolation-with-migration model suggests that the north–south divergence originated from Pleistocene vicariance. In addition, the demographic parameters showed a lack of chloroplast-specific gene flow, suggesting that stochastic variance in genealogy resulted in the discordant geographical structure. Thus, P. nipponica probably experienced Pleistocene vicariance between its southern and northern range parts in concordance with other alpine plants in the Japanese archipelago. The findings of the present study demonstrates the importance of using a multilocus approach for inferring population dynamics, as well as for reconciling discordant phylogeographical patterns among species.

分布格局相似的物种间出现不一致的系统地理学（phylogeographical）格局，不仅可能反映不同物种各自独特的生物地理历史，也可能源于所使用的遗传标记的基因谱系随机方差。采用覆盖不同基因组的多位点研究可解决后者这一问题，从而实现对生物地理历史的可靠推断。本研究开展了多位点系统地理学分析，以重新审视日本松毛翠（Phyllodoce nipponica）的遗传结构——该物种的叶绿体（cp）DNA标记所呈现的格局与其他高山植物（alpine plants）不一致。本研究中5个核基因座的序列变异地理格局与叶绿体DNA不符，且显示该物种分布区南北两部分存在遗传分化。基于隔离与迁移模型（isolation-with-migration model）推断的种群历史表明，其南北分化起源于更新世（Pleistocene）隔离分化事件。此外，种群参数显示不存在叶绿体特有的基因流（gene flow），这表明基因谱系的随机方差是导致不一致地理格局的原因。因此，日本松毛翠的分布区南北两部分大概率经历了更新世隔离分化，这与日本群岛内其他高山植物的情况一致。本研究结果证实，采用多位点方法不仅有助于推断种群动态，也能协调不同物种间不一致的系统地理学格局。