Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting genomic signal. Selection of different types of molecular markers from different genomic regions is becoming important to alleviate these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large and flexible collection of ~15,000 markers that unifies previous frog sequencing. FrogCap is designed to be modular, such that subsets of markers can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include new exons and introns, ultra-conserved elements, and Sanger-sequencing markers, which span a range of alignment lengths. We tested three FrogCap probe sets using 105 samples across five phylogenetic scales, comparing probes designed using a consensus- or genome-based approach. We found that sensitivity, specificity, and missing data are not related to genetic distance in the consensus-based probe design, suggesting that this approach has greater success and overcomes a major hurdle in probe design. We also tested the impact of different bait kit sizes on depth of coverage and missing data, finding that larger kits were not disadvantageous. We observed sequence capture success (missing data, sequence data quantity, recovered marker length, and informative sites) and compared them across phylogenetic scales. The incorporation of different marker types allowed for the variation required for resolving phylogenetic relationships and for performing population genetic studies. Altogether, FrogCap is a valuable and adaptable resource for high-throughput sequencing projects across variable timescales.
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