Data from: Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

Young species complexes that are widespread across ecologically disparate
regions offer important insights into the process of speciation because of
their relevance to how local adaptation and gene flow influence
diversification. We used mitochondrial DNA and up to 28,152 genome-wide
SNPs from polytypic barking frogs (Craugastor augusti complex) to infer
phylogenetic relationships and test for the signature of introgressive
hybridization among diverging lineages. Our phylogenetic reconstructions
suggest (1) a rapid Pliocene-Pleistocene radiation that produced at least
nine distinct lineages and (2) that geographic features of the arid
Central Mexican Plateau contributed to two independent northward
expansions. Despite clear lineage differentiation (many private alleles
and high between-lineage Fst scores), D-statistic tests, which
differentiate introgression from ancestral polymorphism, allowed us to
identify two putative instances of reticulate gene flow. Partitioned
D-statistics provided evidence that these events occurred in the same
direction between clades but at different points in time. After correcting
for geographic distance, we found that lineages involved in hybrid gene
flow interactions had higher levels of genetic variation than
independently evolving lineages. These findings suggest that the nature of
hybrid compatibility can be conserved over long periods of evolutionary
time and that hybridization between diverging lineages may contribute to
standing levels of genetic variation.

广泛分布于生态迥异区域的年轻物种复合体，因其与局部适应和基因流（gene flow）如何影响物种分化密切相关，可为物种形成过程提供重要研究视角。本研究以多型犬吠蛙（Craugastor augusti复合体）为研究对象，利用其线粒体DNA（mitochondrial DNA）及多达28152个全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）位点，推断其系统发育关系，并检验分化支系间的渐渗杂交（introgressive hybridization）信号。系统发育重建结果显示：其一，上新世-更新世时期发生了一次快速辐射演化，产生至少9个独立支系；其二，干旱的墨西哥中央高原的地理特征推动了两次独立的北扩事件。尽管支系间已形成清晰分化（存在大量私有等位基因，且支系间遗传分化系数（Fixation Index, Fst）得分较高），但通过区分渐渗与祖先多态性的D统计量（D-statistic）检验，我们成功识别出两例疑似网状基因流（reticulate gene flow）事件。分区D统计量（Partitioned D-statistics）分析结果证实，这两次事件均发生于不同演化时间点，但支系间的基因交流方向一致。在校正地理距离效应后，我们发现参与杂交基因流的支系，其遗传变异水平显著高于独立演化的支系。本研究结果表明，杂交兼容性的特征可在漫长的演化时间中保持保守，而分化支系间的杂交或有助于维持种群的遗传变异水平。