ddRADseq phylogeny study of phrynosomatid lizards

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We collected double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae to investigate the accuracy of RAD loci for phylogenetic inference.