Different processes shape the patterns of divergence in the nuclear and chloroplast genomes of a relict tree species in East Asia

Isolation by spatial distance (IBD), environment (IBE), and historical climatic stability (IBI) are three common processes assessed in phylogeographic and/or landscape genetic studies. However, the relative contributions of these three processes with respect to spatial genetic patterns have seldom been compared. Moreover, whether the relative contribution differ in different regions or when assessed using different genetic markers has rarely been reported. Lindera obtusiloba has been found to have two sister genetic clades of chloroplast (cpDNA) and nuclear microsatellite (nSSR), both of which show discontinuous distribution in northern and southern East Asia. In this study, we used the Mantel test and multiple matrix regression with randomization (MMRR) to determine the relative contributions of IBD, IBE, and IBI with respect to L. obtusiloba populations. Independent Mantel tests and MMRR calculations were conducted for two genetic data set (cpDNA and nSSR), and for different regions (the overall species range, and northern and southern sub-regions of the range). We found a significant IBI pattern in nSSRs divergence for all assessed regions, whereas no clear IBI pattern was detected with respect to cpDNA. In contrast, significant (or marginal) divergent IBD patterns were detected for cpDNA in all regions, whereas although a significant IBE was apparent with respect to the overall range, the effect was not detected in the two sub-regions. The differences identified in nSSR and cpDNA population divergence may be related to differences in the heredity and ploidy of the markers. Compared with the southern region, the northern region showed less significant correlation patterns, which may be related to the shorter population history and restricted population range. The findings of this study serve to illustrate that comparing between markers or regions can contribute to gaining a better understanding the population histories of different genomes or within different regions of a species’ range.

空间距离隔离（Isolation by Spatial Distance, IBD）、环境隔离（Isolation by Environment, IBE）与历史气候稳定性隔离（Isolation by Historical Climatic Stability, IBI）是系统地理学与/或景观遗传学研究中常见的三类评估过程。然而，针对空间遗传格局，这三类过程的相对贡献却鲜有比较研究。此外，这类相对贡献是否因研究区域不同，或是因使用的遗传标记不同而存在差异，相关报道也极为匮乏。已有研究显示，三桠乌药（Lindera obtusiloba）存在叶绿体基因组（chloroplast DNA, cpDNA）与核微卫星（nuclear microsatellite, nSSR）两类姊妹遗传支系，二者在东亚北部与南部均呈现间断分布格局。本研究以三桠乌药种群为研究对象，采用曼特尔检验（Mantel test）与随机化多重矩阵回归（multiple matrix regression with randomization, MMRR）方法，解析IBD、IBE与IBI三类过程对三桠乌药种群空间遗传格局的相对贡献。本研究针对两类遗传数据集（cpDNA与nSSR）以及不同研究区域（物种全分布区、分布区北部亚区与南部亚区）分别开展独立的曼特尔检验与随机化多重矩阵回归计算。研究结果显示，所有评估区域内的核微卫星分化均呈现显著的IBI格局，而叶绿体基因组未检测到明显的IBI信号。与之相反，所有区域的叶绿体基因组分化均检测到显著（或边际显著）的IBD格局；而尽管在物种全分布区内存在显著的IBE效应，但在南北两个亚区内并未观测到该效应。核微卫星与叶绿体基因组种群分化间的差异，可能与两类遗传标记的遗传特性及倍性差异相关。相较于南部区域，北部区域的相关关联格局显著性更低，这可能与其种群历史较短、分布范围受限有关。本研究结果表明，针对不同遗传标记或不同研究区域开展对比分析，有助于更深入地解析物种不同基因组的种群历史，或是其分布区内不同区域的种群演化历程。