FrogCap for the Taxonomic Gap: Harnessing Hybrid Enrichment for Next-Generation Taxonomy

在分类上未被描述的大约800万个物种中，有不可估量但无疑很大一部分无法进行分类分析，因为它们属于物种复群或隐种，或者是因为历史名称的分配存在不确定性，历史名称优先于新名称。这种对解决分类学差距的障碍是推迟完成全球生物多样性清查的一个主要因素。为了解决这一障碍，并为更全面地理解生命的多样性奠定基础，我们需要严格的方法来识别和描述物种，同时避免因任意命名所有略微不同的物种而膨胀。在这个项目中，我将使用FrogCap（一种最近开发的用于杂交富集序列捕获的诱饵），对可能储存在福尔马林中的museomic型材料以及马达加斯加特有的Cophylinae亚科窄口蛙的高质量组织样本进行大约13,000个核标记的测序。这些青蛙是一个高度多样化的群体，有许多神秘的物种和经常模棱两可的类型材料，使它们非常适合作为一个分支来测试新方法，以提高分类学进展的速度和可靠性，面对典型的分类学挑战。我将整合基因组FrogCap数据集与现有的微ct和形态测量数据集在一个新的，类型标本明确的物种划分协议，并使用谱系分化指数来识别在异源或旁源中划分模糊的姐妹物种。然后，将沿着其核心范围之间的样带进行实地取样，并进行基因组突变分析，以确定它们之间基因流动的程度，从而对这些划分模糊的单位进行选择。由此产生的严格的物种划分将用于对单个属进行同行评议的分类专著的汇编，这些属描述了这些青蛙迄今为止难以描述的多样性的重要部分。这个项目中使用的总体方法将产生一个健壮的分类框架，产生同义词和错误应用名称的风险较低，并且对其他分类群具有广泛的适用性和可伸缩性。

Of the estimated eight million species that are taxonomically undescribed, an inestimable but undoubtedly large portion are blocked from taxonomic resolution because they belong to species complexes or cryptic species, or because there is uncertainty surrounding the assignment of historical names, which take precedence over new names. This impediment to the resolution of the taxonomic gap is a major factor delaying the completion of the global biodiversity inventory. To tackle this impediment and set the stage for understanding the diversity of life more completely, we need rigorous methods to identify and describe species that also avoid inflation by arbitrarily naming everything that is marginally distinct. In this project, I will use FrogCap, a recently developed bait set for hybrid enrichment sequence capture, to sequence around 13,000 nuclear markers from museomic type material potentially stored in formalin, as well as high-quality tissue samples, of narrow-mouthed frogs of the Madagascar-endemic subfamily Cophylinae. These frogs exemplify the case of a highly diverse group with many cryptic species and often ambiguous type material, making them ideally suited as a clade in which to test new methods to increase the rate and reliability of taxonomic progress in the face of typical taxonomic challenges. I will integrate the genomic FrogCap dataset with an existing micro-CT and morphometric dataset in a novel, type-specimen explicit species delimitation protocol, and use the genealogical divergence index to identify ambiguously delimited sister species in allopatry or parapatry. A selection of such ambiguously delimited units will then be proofed by field sampling along a transect between their core ranges, and subjected to genomic cline analyses to identify the extent of gene flow between them. The resulting rigorous species delimitation will be used in the assembly of peer-reviewed taxonomic monographs on the individual genera, describing a significant portion of the hitherto indescribable diversity of these frogs. The overall approach used in this project will yield a robust taxonomic framework with lower risk of producing synonyms and incorrectly applying names, and will have broad applicability and scalability to other taxa.