Data from: Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)

Background: Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson's D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to
explore potential effects of concatenation.
Results: We employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus.
Conclusions: Complex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition.

背景：物种分界的渗透性往往会引发相互矛盾的假说，尤其是当结合可变的数据或不同的研究方法时。当研究具有复杂网状进化历史的非模式生物时，这种影响往往会被放大。吸口鲤属（Catostomus，硬骨鱼纲，吸口鲤科）便是其中一例：该淡水鱼类支系的形态学系统发育树与线粒体系统发育树存在显著冲突。前者被推测反映了形态分化支系内存在混合基因型，而后者则被解读为通过趋同演化多次独立产生了不同的形态表型。本研究采用多种方法对上述假说进行了验证，其中包括多物种溯祖法（multispecies coalescent）与串联分析法。我们运用帕特森D统计量（Patterson's D-statistic）以解决潜在的系统发育冲突、检测基因渐渗现象，并验证两个推定杂交物种的起源。此外，我们还采用了朴素分箱法（naïve binning）以探究串联分析的潜在影响。
结果：我们对184个个体进行ddRAD测序，共获得14007个基因座，据此构建了首份高支持度的吸口鲤属核基因系统发育树。我们的系统发育组学分析结果与形态学解释基本一致，仅德克萨斯异口鱼（Xyrauchen texanus）的系统发育位置例外，其与形态学及线粒体系统发育树的推断均存在差异。此外，我们对推定杂交物种哥伦比亚吸口鲤（C. columbianus）的评估显示其未检测到基因渐渗，其系统发育位置反而与线粒体系统发育树一致。帕特森D统计量检验澄清了仅基于线粒体数据得出的所有不一致性，串联分析法与多物种溯祖法得到的拓扑结构均达成一致。研究在六对物种类群中检测到了广泛的历史基因渐渗现象。弗吉尼河与小科罗拉多河流域还存在潜在的特有类群；原潘斯托亚斯属（Pantosteus）除哥伦比亚吸口鲤（C. columbianus）外，均被重建为单系群。
结论：本研究检测到的复杂网状进化历史，支持了基因渐渗是导致线粒体系统发育树内部出现冲突的原因这一假说，并解释了其与以往形态学系统发育树之间的不一致性。此外，哥伦比亚吸口鲤（C. columbianus）的杂交起源假说被推翻，但仍需注意的是，后续还需要开展更精细的采样工作。我们采用的多样系统发育组学分析方法得到了基本一致的结果，其中朴素分箱法可有效用于探究这一唯一的系统发育冲突。在北美西南部的吸口鲤属（Catostomus）类群中检测到了丰富的物种多样性，其中两处水系——犹他州弗吉尼河与亚利桑那州小科罗拉多河，具有独特的类群组成。