Spatial and host related genomic variation in partially sympatric cactophagous moth species

Raw reads were demultiplexed, filtered and assembled using iPYRAD v0.9.59 (Eaton and Overcast, 2020). Demultiplexing was done using the unique barcode and adapter sequences. Then, samples’ reads were filtered using the stricter filter for Illumina adapters, and filtered to clean up the edges of poor quality reads. A Reference based assembly method was implemented using the reference draft genome CactoFuEDEI.fa. We set 2 as the maximum number of unique alleles allowed in consensus reads, and ran ipyrad to obtain four datasets, each one controlling 25%, 50%, 80% and 90% of the minimum number of samples per locus (msl), respectively.