Genetic variability within Triatoma sanguisuga complex in North America and the re- description of Triatoma ambigua Neiva, 1911, with specimens from Florida, USA

R script accompanying the article: Beatty NL, Pita S, et al. "Genetic variability within Triatoma sanguisuga complex in North America and the re-description of Triatoma ambigua Neiva, 1911, with specimens from Florida, USA." Scientific Reports (in revision). The script tests for isolation by distance (IBD) between genetic and geographic distances among individuals of the Triatoma sanguisuga complex. Genetic distances are Kimura 2-parameter (K2-p, %) distances between cytochrome b haplotypes, and geographic distances are great-circle (haversine) distances in km between collection sites. It performs: - a Mantel test of genetic vs. geographic distance;- partial Mantel tests of genetic distance vs. Group 1 (Florida, T. ambigua) membership or GMYC group membership, each controlling for geographic distance, and the reverse;- a correlation check between the geographic and group-membership matrices;- an individual-level permutation test comparing the residuals of the IBD regression for pairs involving Group 1 with all other pairs. All tests use 9,999 permutations (random seed 42). The script reproduces the isolation-by-distance results and Supplementary Table 8 of the article. It requires R with the packages ape and vegan. See README.txt for input file formats, usage and outputs.