Raw sequence filtering and processing
Raw sequence quality was first assessed using FastQC v.0.11.9 and MultiQC v.1.7 (Andrews, 2010; Ewels, Magnusson, Lundin, & Käller, 2016), and then reads were filtered and processed using Stacks v.2.3 (Rochette, Rivera‐Colón, & Catchen, 2019). Reads with a phred score below 25 were removed as well as individuals with a >75.0% missing data. Next, reads were aligned to the C. sonorensisgenome (Morales-Hojas et al., 2018) (Accession: PRJEB19938) using the Burrows-Wheeler Aligner (BWA-mem) (Li & Durbin, 2009). Finally, aligned reads were run through the reference-based pipeline of Stacks, with filtering parameters set to keep SNPs occurring in at least half of the sampling locations and at least 50% of individuals within those sites (Pante, Abdelkrim, et al., 2015). The minimum allele frequency was set to 0.05 to protect against potential sequencing errors (Benestan et al., 2016), and only the first SNP per locus was kept to minimize linkage disequilibrium between SNPs from influencing population structure and phylogenetic analyses. All subsequent file reformatting was done with PGDSpider v.2.1.1.5 (Lischer & Excoffier, 2012).