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

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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.