FrogCap

FrogCap provides a modular sequence-capture probe set for phylogenomics and population genetics in frogs by integrating diverse molecular markers to resolve relationships across multiple evolutionary scales.

Key Features:

• Modular Design: A modular probe set permits selection of marker subsets tailored to specific phylogenetic study scales.
• Diverse Marker Types: Contains approximately 15,000 markers including protein-coding exons, non-coding introns, ultra-conserved elements (UCEs), and Sanger-sequencing markers with alignment lengths from 100 to 12,000 base pairs.
• Consensus-Based Probe Design: Employs a consensus-based probe-design approach to maintain sensitivity, specificity, and low missing data across varying genetic distances.

Scientific Applications:

• Phylogenetic resolution: Resolves complex phylogenetic relationships among frog taxa across shallow to deep evolutionary timescales.
• Phylogenomics: Supports high-throughput sequencing projects for genome-scale phylogenomic analyses in frogs.
• Population genetics: Enables population-genetic inference by capturing markers suitable for within-species and between-population analyses.
• Multi-marker integration: Integrates multiple molecular marker types to improve data recovery and robustness of evolutionary analyses.

Methodology:

Tested on 105 samples across five phylogenetic scales, compared the performance of three probe sets designed with consensus- and genome-based approaches, and evaluated the effects of varying bait kit sizes on sequencing depth and data completeness.