Species are indisputable units for biodiversity conservation, yet their delimitation is fraught with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern North America. Nominal species designations were originally defined according to weakly diagnostic morphological differences, but these conflicted with subsequent genetic analyses. Given this ambiguity, the complex was re-defined as a single polytypic unit, with the proposed “threatened” status under the U.S. Endangered Species Act of two elements being withdrawn. Here we re-evaluated the status of the complex by utilizing dense spatial and genomic sampling (n = 387 and >22 k loci), coupled with SNP-based coalescent and polymorphism-aware phylogenetic models. In doing so, we found that all three species were indeed supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To juxtapose this discrepancy with previous studies, we first categorized those evolutionary mechanisms driving discordance, then tested (and subsequently rejected) prior hypotheses which argued phylogenetic discord in the complex was driven by the hybrid origin of Gila nigra. The inconsistent patterns of diversity we found within G. robusta were instead associated with rapid Plio-Pleistocene drainage evolution, with subsequent divergence within the “anomaly zone” of tree space producing ambiguities that served to confound prior studies. Our results not only support the resurrection of the three species as distinct entities but also offer an empirical example of how phylogenetic discordance can be categorized within other recalcitrant taxa, particularly when variation is primarily partitioned at the species level.

中文翻译：

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分类学不确定性和异常区：系统基因学解开快速辐射以解决科罗拉多河中有争议的物种（吉拉罗布斯塔复合体）


物种是生物多样性保护无可争议的单位，但它们的界定充满了概念和方法上的困难。一个典型的例子是围绕北美西南部科罗拉多河下游吉拉罗布斯塔复合体的分类学争议。名义物种名称最初是根据弱诊断形态差异来定义的，但这些与随后的遗传分析相冲突。鉴于这种模糊性，该综合体被重新定义为一个单一的多型单元，并根据美国濒危物种法案提议的两个要素的“受威胁”地位被撤销。在这里，我们利用密集的空间和基因组采样（n = 387 和 >22 k 位点），结合基于 SNP 的合并和多态性感知系统发育模型，重新评估了复合体的状态。在此过程中，我们发现所有三个物种确实被支持为进化上独立的谱系，尽管存在广泛的系统发育不一致。为了将这种差异与以前的研究并列，我们首先对那些导致不一致的进化机制进行了分类，然后测试（并随后拒绝）先前的假设，这些假设认为复合体中的系统发育不一致是由吉拉黑蜥的杂交起源驱动的。我们在鲁布斯塔中发现的不一致的多样性模式反而与上更新世排水系统的快速演化有关，随后树空间“异常区域”内的分歧产生了模糊性，从而混淆了先前的研究。 我们的结果不仅支持这三个物种作为不同实体的复活，而且还提供了一个经验例子，说明如何将系统发育的不一致分类到其他顽固的类群中，特别是当变异主要在物种水平上划分时。