Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity.

Script to call function that calculates f4 statistic in sliding windows across genomePython script used to call the function that calculates f4 statistic in sliding windows across genome that is described in genomics_f4_ejredit.py. Modified from Simon H. Martin's script for calculating D and fd statistics in sliding windows (https://github.com/simonhmartin/genomics_general/ABBABABBA.py).ABBABABAwindows_f4_ejredit.pyScript to calculate f4 statistic in sliding window across genomeScript to calculate f4 statistic in sliding window across genome. Modified from Simon H. Martin's script to calculate D and fd statistics in sliding windows across genome (https://github.com/simonhmartin/genomics_general/genomics.py). See this website for details and options for running the function.genomics_f4_ejredit.pySAGUARO input fileThe feature file required for SAGUARO analysis consisting of information on SNPs from 43 pupfishes. This file was converted into this format from a vcf file.filtered_snps_all.feature.tar.gzSliding window f4 statistic fileInput file of SNP genotypes across 43 pupfishes used for calculating f4 statistic in sliding windows across genome. This file was converted into this format from a vcf file.filtered_snps_all_diplo.geno.tar.gzTreemix input files for candidate adaptive introgression regionsThe SNP matrix files used in the Treemix analysis of each candidate region. Files are labeled by scaffold and starting position of the region.treemix_files.tar.gz