Data from: Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia

Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.

将集合种群（metapopulation）的遗传结构解读为不同时间尺度下基因流作用的产物，对于正确理解景观变化如何影响生物连通性至关重要。本研究对比了巴塔哥尼亚北部与最南部两处扁身南乳鱼（Galaxias platei）集合种群的历史与当代连通性：两处区域分别在全新世与更新世时期存在古湖。北部区域的当代基因流整体呈现高连通性且不对称特征，而最南部区域的当代基因流则极度受限。历史基因交流模式方面，北部区域为高连通性且对称，最南部区域则为高连通性且整体不对称。两处区域的种群遗传结构均处于中等分化水平，且呈现清晰的距离隔离（isolation by distance, IBD）模式。当代基因流较低的种群，其有效种群规模（effective population size）更小。近似贝叶斯计算（approximate Bayesian computation, ABC）方法显示，北部区域的湖泊种群是在全新世晚期完成定殖的，当前种群均源自安第斯山脉东西两侧的避难所种群，并发生了近期分化。针对南部区域，ABC方法揭示部分现存扁身南乳鱼种群极有可能源自栖息于大型更新世古湖的祖先种群，其余种群则来自高海拔湖泊。本研究结果表明，仅靠历史过程或当代过程中的任意一种，均无法完全解释观测到的种群结构与基因流模式，二者缺一不可，才能充分理解影响生物多样性及其分布的相关因素。本研究强调，采用时间维度视角分析连通性，对于解析空间结构复杂的集合种群多样性具有重要意义。