Data from: Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test if the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of post-glacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian Computation approach but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. This strongly impoverished mtDNA diversity, without change in nuclear DNA diversity, has been interpreted as evidence of a selective sweep of mtDNA variants in other species. However we suggest that, on the contrary, it can be explained by the different effective population size of these markers, and perhaps also by sex-biased dispersal during postglacial range expansion. Although dispersal in this species is probably highly restricted at all spatial scales, colonisation abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.历史因素、当前种群规模、种群连通性以及连锁位点的选择过程，共同塑造了当代中性遗传多样性的分布模式。目前学界已普遍认可，核基因标记（nuclear markers）与线粒体标记（mitochondrial markers）对当前种群动态及过往历史的响应模式存在显著差异，因此常被建议联合使用两类标记，以同时解析历史与当代的演化过程。本研究针对13个山地蜥蜴（*Iberolacerta bonnali*）种群的12个微卫星位点（microsatellite loci）进行基因分型，旨在验证此前线粒体研究支持的历史演化场景是否同样得到核基因标记的支持，并借此评估冰期后分布区迁移对核基因多样性的影响。通过近似贝叶斯计算（Approximate Bayesian Computation）方法分析，核基因与线粒体标记均揭示了一致的近期历史信号，但二者的当代遗传多样性模式却存在根本性差异。线粒体DNA（mtDNA）多样性显著降低而核DNA（nuclear DNA）多样性未发生改变这一现象，此前在其他物种中被解读为线粒体DNA变异发生选择清扫（selective sweep）的证据。但本研究提出，与之相反，该现象可通过两类标记的有效种群规模差异加以解释，也可能与冰期后分布区扩张过程中的性别偏向扩散有关。尽管该物种在所有空间尺度上的扩散能力大概率均受到严格限制，但其历史上的定殖能力较强，这表明除完全隔离的生境外，该物种具备重建局部灭绝种群的能力。