Data from: Semi-permeable species boundaries in Iberian barbels (Barbus and Luciobarbus, Cyprinidae)

Background The evolution of species boundaries and the relative impact of selection and gene flow on genomic divergence are best studied in populations and species pairs exhibiting various levels of divergence along the speciation continuum. We studied species boundaries in Iberian barbels, Barbus and Luciobarbus, a system of populations and species spanning a wide degree of genetic relatedness, as well as geographic distribution and range overlap. We jointly analyze multiple types of molecular markers and morphological traits to gain a comprehensive perspective on the nature of species boundaries in these cyprinid fishes. Results Intraspecific molecular and morphological differentiation is visible among many populations. Boundaries of all sympatric species studied are porous to gene flow, even if they are not sister species. Compared to their allopatric counterparts, sympatric representatives of different species share alleles and show an increase in all measures of nucleotide polymorphism (S, Hd, K, pi and theta). High molecular diversity is particularly striking in L. steindachneri from the Tejo and Guadiana rivers, which co-varies with L. comizo and with all other sympatric species. Interestingly, different nuclear markers introgress across species boundaries at various levels, with distinct impacts on population trees. As such, some loci exhibit limited introgression and population trees resemble the presumed species tree, while alleles at other loci introgress more freely and population trees reflect geographic affinities and interspecific gene flow. Additionally, extent of introgression decreases with increasing genetic divergence in hybridizing species pairs. Conclusions We show that reproductive isolation in Iberian Barbus and Luciobarbus is not complete and species boundaries are semi-permeable to (some) gene flow, as different species (including non-sister) are exchanging genes in areas of sympatry. Our results support a speciation-with-gene-flow scenario with heterogeneous barriers to gene flow across the genome, strengthening with genetic divergence. This is consistent with observations coming from other systems and supports the notion that speciation is not instantaneous but a gradual process, during which different species are still able to exchange some genes, while selection prevents gene flow at other loci. We also provide evidence for a hybrid origin of a barbel ecotype, L. steindachneri, suggesting that ecology plays a key role in species coexistence and hybridization in Iberian barbels. This ecotype with intermediate, yet variable, molecular, morphological, trophic and ecological characteristics is the local product of introgressive hybridization of L. comizo with up to three different species (specific species combinations depend on river drainage). In spite of the homogenizing effects of ongoing gene flow, species can still be discriminated using a combination of morphological and molecular markers. Iberian barbels are thus an ideal system for the study of species boundaries, since they span a wide range of genetic divergences, with diverse ecologies and degrees of sympatry.

**背景**：物种边界的演化，以及选择与基因流对基因组分化的相对影响，最佳研究对象是沿物种形成连续体呈现不同分化程度的种群与物种类群对。我们以伊比利亚须鲃（Iberian barbels）的鲃属（Barbus）与亮鲃属（Luciobarbus）类群为研究对象，该类群包含的种群与物种类群覆盖了广泛的遗传亲缘关系梯度，同时具有多样的地理分布与重叠分布范围。我们联合分析多种分子标记与形态性状，以全面解析这类鲤科鱼类的物种边界本质。

**结果**：诸多种群间均可见种内分子与形态分化。本研究涉及的所有同域物种种群边界均存在基因流渗透现象，即便这些类群并非姊妹种。相较于异域分布的类群，不同物种的同域代表类群共享等位基因，且在核苷酸多态性的各项指标（S、Hd、K、π与θ）上均呈现升高趋势。来自特茹河（Tejo）与瓜迪亚纳河（Guadiana）的卢氏亮鲃（L. steindachneri）具有极高的分子多样性，该特征与其同域分布的科米佐亮鲃（L. comizo）及其他所有同域物种类群均呈协同变化趋势。有趣的是，不同的核标记在物种边界间的渐渗水平存在差异，且对种群树构建产生截然不同的影响。据此，部分基因座的渐渗程度有限，种群树与推定的物种树较为相似；而其他基因座的等位基因则更易发生渐渗，种群树反映出地理亲缘关系与种间基因流特征。此外，在杂交物种类群对中，渐渗程度随遗传分化水平升高而降低。

**结论**：我们的研究表明，伊比利亚鲃属（Barbus）与亮鲃属（Luciobarbus）类群的生殖隔离并不完全，物种边界对（部分）基因流呈现半透性——不同物种（包括非姊妹种）在同域分布区域内存在基因交流。本研究结果支持“物种形成伴随基因流”的演化场景：基因组上的基因流屏障存在异质性，且随遗传分化水平增强。该结论与其他研究系统的观测结果一致，同时支持“物种形成并非瞬时过程，而是渐进演化过程”的观点——在此过程中，不同物种仍可交换部分基因，而选择作用会阻断部分基因座间的基因流。我们还为须鲃生态型卢氏亮鲃（L. steindachneri）的杂交起源提供了证据，表明生态因素在伊比利亚须鲃的物种共存与杂交过程中发挥关键作用。该生态型具有介于不同物种之间但存在变异的分子、形态、营养与生态特征，是科米佐亮鲃（L. comizo）与至多3个不同物种（具体组合依河流流域而定）发生渐渗杂交的本地产物。尽管持续的基因流存在同质化效应，但通过联合使用形态与分子标记，仍可区分不同物种。因此，伊比利亚须鲃是研究物种边界的理想模型系统——其类群覆盖了广泛的遗传分化范围，且具有多样的生态特征与同域分布程度。