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).