Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world’s most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, Lepomis megalotis and Lepomis peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between nonsister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.[ddRAD; genealogical divergence index; hybridization; integrative species delimitation; phylogeny; secondary contact; systematics; taxonomy.]

中文翻译：

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长耳翻车鱼 Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae) 的基因渗入和物种界定

基因渗入和杂交是基于基因组的物种划分的主要障碍，因为多物种聚结框架的许多实施都假设物种之间没有基因流动。翻车鱼属 Lepomis 是世界上最受欢迎的淡水运动鱼群之一，具有复杂的分类历史。ddRAD 系统基因组分析的结果不支持当前的分类学，即在 L. megalotis 复合体中识别两个物种，Lepomis megalotis 和 Lepomis peltastes。相反，来自系统基因组学和表型的证据证明了该复合体中六个相对古老的进化谱系。L. megalotis 复合体中的渗入和杂交种群是本地化的，似乎是非姐妹物种之间的二次接触或罕见杂交事件的结果。从我们的多物种聚结分析中分离出混合种群，确定了六种具有中度至高度谱系分歧的物种，而包括混合种群则使除一个谱系之外的所有谱系都低于谱系分歧的物种阈值。混合个体的分离也有助于揭示过去两个世纪鱼类学家用来发现和划定物种的形态特征中六种​​物种之间的表型独特性。我们的协议允许在物种划界中识别和适应杂交和基因渗入。通过多条证据验证的基于基因组的物种划界为发现新的生物多样性和解决长期存在的分类问题提供了一条途径。[ddRAD; 家谱分歧指数；杂交；综合物种划界；系统发育; 二次接触；系统学；分类。]