ddRadseq data of Rallus crepitans
We collected ddRADseq data using the Peterson et al. 2012 protocol modified to use separate indexing reads. We digested genomic DNA with EcoR1 and Mse1 (New England Biolabs) in a single reaction and used Solid Phase Reversible Immobilization (SPRI) beads (Beckman Coulter) to purify the digestions prior to ligating uniquely bar-coded adapters with T4 ligase (New England Biolabs). Libraries were size-selected between 250 and 400 base pairs (bp) using a Pippin Prep size fractionator (Sage Science). The final library amplification used proofreading Taq and Illumina's indexed primers. The fragment size distribution and concentration of each pool was determined on an Agilent Bioanalyzer and qPCR was performed to determine library concentrations. Sequencing was conducted on one lane of an Illumina NovaSeq X+ platforms at MedGenome, Inc and PE 150 reads. (Foster City, CA). Samples from different sampling locations and regions were mixed across libraries and sequencing lanes to avoid confounding batch effects.