Phylogeography of the Mojave Giant Tiger Beetle, Amblycheila schwarzi (Coleoptera: Cicindelidae), supports the Colorado River as a leaky barrier

Amblycheila schwarzi is a flightless, nocturnal tiger beetle endemic to the Mojave Desert. This study explored the potential influence of the Colorado River on gene flow and dispersal for A. schwarzi populations. Sampling includes 26 fresh and 4 museum specimens from nine different localities in the Mojave Desert. Outgroups include closely related A.baroni (3) and A.picolominii (1) specimens. Supplementary information regarding sampling and sequence statistics can be found in "Supplementary_1_Table1_final.pdf". The data includes two types of high-throughput Illumina read data from targeted capture and low-coverage genome skimming. Two datasets were created: comprehensive (ALL) and museum-omitted (MSX), using two different completeness matrices (60% and 80%). The Phyluce pipeline (Faircloth 2016) was used to extract ultraconserved elements for the maximum likelihood, wASTRAL, and SVD Quartets analyses. All raw reads are submitted to NCIB (SRA data #PRJNA1379884). Included here are the FASTA alignments for each dataset and the completeness matrices (60perc_all_aligned.zip, 80perc_all_aligned.zip, 60perc_msx_aligned.zip, 80perc_msx_aligned.zip). Supplementary files using the aforementioned data include results for Maximum Likelihood with Sliding Windows Site Characteristic partitioning scheme, wASTRAL partitioned by cogenic loci, and SVD Quartets (Supplementary 2-13). For population-level analyses, single-nucleotide polymorphisms were used in Principal Component Analysis (PCA), Splitstree, and ADMIXTURE. We include the VCF files used in these analyses (schwarzi_all_94_nosingle.thinned.vcf.gz and schwarzi_nomuse_94_nosingle.thinned.vcf.gz). Supplementary materials of phylogeographic analyses include CV error plots, ADMIXTURE, PCA, and Splitstree results for the ALL and MSX datasets (Supplementary 14-21).