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.研究背景：本研究采用多位点（multiple loci）与群体遗传学方法，探究巴塔哥尼亚淡水蟹新奎内斯螯蟹（Aegla neuquensis，螯蟹科（Aeglidae）：十足目（Decopoda））的系统发生生物地理学（phylogeography）历史。该分类群（taxon）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海域。 材料与方法/主要结果：本研究通过核基因系统发育分析与多位点嵌套式分支系统发生生物地理学分析（multilocus nested clade phylogeographic analysis），检测到内格罗河（Negro）与奇科-丘布特河（Chico-Chubut）两大水系间存在一次分化事件，该事件发生于约13.7万年前。基于隔离与迁移模型（isolation-with-migration model）的分析以及基因流的最大似然（maximum-likelihood）估计结果显示，两大水系间仅在其源头区域存在不对称的遗传物质交流。本研究利用信息论（information theory）方法，在隔离与迁移模型框架下筛选出最适配两大水系的种群演化历史模型。最优模型表明，内格罗河种群与祖先种群的有效种群大小（effective population size）一致，而奇科-丘布特河种群的有效种群规模更小，且奇科-丘布特河种群向内格罗河种群的基因流强度是反向交流的4倍。奇科-丘布特河水系的多数区域似乎仅在近期才被该类群定植，而内格罗河种群则在该物种的大部分演化历史中都已稳定存在。 结论与意义：受线粒体基因渐渗（introgression）现象影响，针对核基因系统发育中观测到的古老分化事件，3个核基因座（locus，复数loci）提供的系统发生生物地理学分辨率与3个线粒体基因存在差异。但线粒体基因座对较近期的演化事件具备更高的分辨率。因此，本研究证实，若要全面理解物种演化历史及其相关的系统发生生物地理学事件，需同时纳入核基因与线粒体基因座进行分析。本研究结果表明，在分化事件发生前后，两大水系间的基因交流均通过源头区域形成的周期性古湖完成。内格罗河与奇科-丘布特河水系间的分化，是由巴塔哥尼亚冰期期间上述古湖的消失所驱动的。