Data from: Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis

BACKGROUND: Multiple loci and population genetic methods were employed to study the phylogeographic history of the Patagonian freshwater crab Aegla neuquensis (Aeglidae: Decopoda). This taxon occurs in two large river systems in the Patagonian Steppe, from the foothills of the Andes Mountains east to the Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS: A nuclear phylogeny and multilocus nested clade phylogeographic analysis detected a fragmentation event between the Negro and Chico-Chubut river systems. This event occurred approximately 137 thousand years ago. An isolation-with-migration analysis and maximum-likelihood estimates of gene flow showed asymmetrical exchange of genetic material between these two river systems exclusively in their headwaters. We used information theory to determine the best-fit demographic history between these two river systems under an isolation-with-migration model. The best-fit model suggests that the Negro and the ancestral populations have the same effective population sizes; whereas the Chico-Chubut population is smaller and shows that gene flow from the Chico-Chubut into the Negro is four times higher than in the reverse direction. Much of the Chico-Chubut system appears to have only been recently colonized while the Negro populations appear to have been in place for most of the evolutionary history of this taxon. CONCLUSIONS/SIGNIFICANCE: Due to mitochondrial introgression, three nuclear loci provided different phylogeographic resolution than the three mitochondrial genes for an ancient fragmentation event observed in the nuclear phylogeny. However, the mitochondrial locus provided greater resolution on more recent evolutionary events. Our study, therefore, demonstrates the need to include both nuclear and mitochondrial loci for a more complete understanding of evolutionary histories and associated phylogeographic events. Our results suggest that gene flow between these systems, before and after fragmentation was through periodic paleolakes that formed in the headwaters region. Fragmentation between the Negro and Chico-Chubut systems was driven by the disappearance of these paleolakes during the Patagonian Glaciation.

背景：本研究采用多位点与群体遗传学方法，对巴塔哥尼亚淡水蟹新奎氏真螯虾（Aegla neuquensis，Aeglidae: Decopoda）的系统生物地理学历史展开研究。该分类群分布于巴塔哥尼亚草原的两大河流水系中，分布范围从安第斯山脉山麓向东延伸至大西洋沿岸。
材料与方法/主要发现：核基因系统发育分析与多位点嵌套进化枝系统生物地理学分析结果显示，内格罗河与奇科-丘布特河两大水系间存在一次片段化事件，该事件发生于约13.7万年前。隔离-迁移分析与基因流最大似然估计结果表明，两大水系间仅在河源区域存在不对称的遗传物质交流。本研究借助信息论，在隔离-迁移模型框架下确定了两大水系间最优拟合的种群演化历史。最优拟合模型显示，内格罗河种群与祖先种群的有效种群大小一致，而奇科-丘布特河种群的有效种群规模更小；同时该模型还表明，从奇科-丘布特河向内格罗河的基因流强度是反向流动的4倍。奇科-丘布特河水系的大部分区域似乎仅在近期才被该物种定殖，而内格罗河种群则在该物种的大部分演化历史中都持续存在于当地。
结论与意义：受线粒体基因渐渗影响，针对核基因系统发育中观察到的古老片段化事件，3个核基因座所提供的系统生物地理学分辨能力与3个线粒体基因存在差异。但线粒体基因座对较晚近的演化事件具有更高的分辨能力。因此，本研究表明，若要全面理解物种演化历史及其相关的系统生物地理学事件，需同时纳入核基因与线粒体基因座进行分析。本研究结果显示，两大水系在片段化发生前后的基因交流，均通过河源区域周期性形成的古湖完成。内格罗河与奇科-丘布特河水系间的片段化事件，正是由巴塔哥尼亚冰期期间这些古湖的消失所驱动的。