Data from: A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico

Hybrid speciation may contribute significantly to generating biodiversity, but only a few well-documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hall-marks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (X. helleri and X. maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae – the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, since they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation-by-distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleri and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.杂交物种形成（Hybrid speciation）或许对生物多样性的产生具有重要贡献，但截至目前，鲜有被充分证实且不涉及多倍化（polyploidization）机制的相关案例。 剑尾鱼（swordtail fish）克氏剑尾鱼（Xiphophorus clemenciae）表现出杂交起源的典型特征，且当前地理分布与推测的亲本物种（剑尾鱼X. helleri与斑剑尾鱼X. maculatus）存在重叠。克氏剑尾鱼为探究杂交物种与其亲本物种间持续存在的潜在遗传互作提供了理想研究体系。 本研究利用微卫星（microsatellite）与线粒体标记（mitochondrial markers），对这些剑尾鱼物种的种群结构展开分析，并搜寻近期杂交的相关信号。研究样本采集自克氏剑尾鱼已知分布范围——墨西哥特万特佩克地峡（Isthmus of Tehuantepec, IT）内的21个采样点，同时记录了若干可能构成扩散障碍的环境参数。 导致克氏剑尾鱼形成的杂交事件似乎相当古老，且大概率仅起源一次。 研究发现，当前亲本物种间存在持续杂交与基因渐渗（introgression）的证据微乎其微，这是因为二者如今占据了截然不同的生态位，且绝大多数克氏剑尾鱼种群共享一套共同的单倍型。 这些物种的种群结构呈现距离隔离（isolation-by-distance, IBD）模式，多数种群间的遗传分化程度显著且较高。 我们推断，特万特佩克地峡的构造演化（tectonic evolution）极大限制了克氏剑尾鱼与剑尾鱼X. helleri的南部与中部种群间的基因流（gene flow），同时为这一地理分布受限的杂交物种——克氏剑尾鱼的保护管理提供了初步参考依据。