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：本研究采用多基因座（loci，locus的复数形式）与群体遗传学方法，探究巴塔哥尼亚淡水蟹内乌肯阿格拉蟹（Aegla neuquensis，隶属于阿格拉蟹科（Aeglidae）十足目（Decopoda））的系统发生生物地理学（phylogeography）历史。该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。 方法/主要发现：核基因系统发育树与多基因座嵌套式分支系统发生生物地理学分析检测到内格罗河与奇科-丘布特河两大水系之间存在分化事件，该事件发生于约13.7万年前。隔离-迁移分析（isolation-with-migration analysis）与基因流最大似然估计（maximum-likelihood estimates）结果显示，两大水系仅在其源头区域存在不对称的遗传物质交流。本研究借助信息论方法，在隔离-迁移模型（isolation-with-migration model）框架下确定了适配两大水系的最优种群历史模型。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-丘布特河种群规模更小，且从奇科-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是近期才被该蟹类定植，而内格罗河种群则在该类群的大部分进化历史中都已稳定存续。 结论与意义：受线粒体基因渐渗（introgression）现象影响，三个核基因座对核基因系统发育树中观测到的古老分化事件的解析结果，与三个线粒体基因的解析结果存在差异；但线粒体基因座对近期进化事件的分辨率更高。因此，本研究证明，若要全面理解类群的进化历史及其伴随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开展分析。本研究结果表明，两大水系在分化前后的基因交流均通过形成于源头区域的周期性古湖泊实现。内格罗河与奇科-丘布特河水系的分化，是由巴塔哥尼亚冰期期间这些古湖泊的消失所驱动的。