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FrogCap: a modular sequence capture probe set for phylogenomics and population genetics for Anurans, assessed across multiple phylogenetic scales

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posted on 2018-07-13, 22:19 authored by Carl HutterCarl Hutter, Kerry A. Cobb, Daniel Portik, Scott Travers, Rafe Brown
The widespread use of high-throughput sequencing technologies has led to new challenges for biodiversity researchers in designing projects and deciding which method to use to sequence reduced portions of the genome. Targeted sequence capture is one method shown to work well across divergent taxa; however, this requires a specifically designed probe set for the focal taxon, which is largely unavailable for frogs. Herein, we introduce and demonstrate the utility of a new and publicly available sequence capture probe set and data analysis pipeline for all frogs. We provide a modular, large, and flexible set of probes for up to ~15,000 loci that unifies all previous sequencing work on frogs by including legacy loci previously used in phylogenetic studies in frogs (e.g. Sanger Loci, UCEs, functional loci). The probe set is designed to be modular, such that subset of the loci can be selected and used based on the type of research question and taxonomic scale being addressed. Finally, we evaluate our sequence capture results using six different phylogenetic scales from the Order level down to within a species. We evaluate the number of loci captured per taxa and compare differences in topology across the six phylogenetic scales. Furthermore, we demonstrate the utility of exons, introns, and UCEs and compare these types of data across these phylogenetic scales as well as within each scale. We find that introns give different topologies when compared to exons and UCEs, and exons are most similar to UCEs in topology.

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    AnuraAmphibiaFrogCapSequence CaptureGenomicsBig DataPhylogeneticsSystematicsGenomics

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