final size-corrected morphology color and lightness of pairs

Size-correct morphological traits, PC1-3 of color measurements, and PC1-2 for lightness of mated pairs. This dataset used for canonical correlation analysis between males and females

raw diet morphology color and lightness of pairs

raw diet morphology color and lightness of pair

Sliding window f4 statistic file

Input 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

Treemix input files for candidate adaptive introgression regions

The SNP matrix files used in the Treemix analysis of each candidate region. Files are labeled by scaffold and starting position of the region

Script to call function that calculates f4 statistic in sliding windows across genome

Python 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)

SAGUARO input file

The 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

Adaptive introgression candidates in San Salvador Island specialists.

<p>These 11 candidate regions feature significant <i>f</i>_<i>4</i> values and signatures of selective sweeps in specialists, SNPs fixed between specialists, and low genetic divergence (<i>D</i>_xy) between <i>C</i>. <i>laciniatus</i> and one of the specialists. The number of fixed SNPs that were in coding positions of a gene are provided in parentheses after the total number in the region. The specialist(s) with a selective sweep detected in the 98^th percentile of the SweeD composite likelihood ratio test and the lowest levels of genetic diversity (π) and Tajima’s D estimates within the 2% lower tail of the simulated Tajima’s D distribution are listed for each region.</p

Genetic diversity surrounding the fixed variant in <i>ski</i> region assigned to the combined scale-eater topology.

<p>(A) The 3’ untranslated region variant fixed between the two specialists. The number of individuals with the haplotype(s) are located in parentheses next to species names. The other two fixed SNPs follow the same pattern across species as the SNP shown.(B) A comparison of the San Salvador Island genotypes (green = molluscivore; red = generalists; blue = scale-eater) with the <i>C</i>. <i>laciniatus</i> genotype (black) across an 8-kb window surrounding the fixed variant (orange arrow). The alleles that do not match the alleles of <i>C</i>. <i>laciniatus</i> are highlighted with black bars. The arrow points to the conflicting genotypes in the surrounding 8-kb region of the SNPs.</p

Variable introgression from distant Caribbean islands across the genomes of the San Salvador Island trophic specialists.

<p>Manhattan plot of the <i>f</i>_<i>4</i> values between the <i>C</i>. <i>laciniatus</i> from New Providence Island, Bahamas, <i>C</i>. <i>bondi</i> from Etang Saumatre, Dominican Republic and (A) molluscivores and scale-eaters on San Salvador Island, (B) molluscivores and generalists from San Salvador Island, (C) scale-eaters and generalists on San Salvador Island. Alternating gray/black colors indicate different scaffolds from the largest 170 scaffolds of the genome. Dotted red lines mark the permutation based significance threshold. Full Manhattan plots for each comparison are presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006919#pgen.1006919.s003" target="_blank">S3</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006919#pgen.1006919.s005" target="_blank">S5</a> Figs.</p

The most common topology estimated in SAGUARO showing a monophyletic San Salvador Island clade covered 64% of the genome.

<p>San Salvador Island generalists (red), molluscivores (green), large-jawed scale-eaters (dark blue), small-jawed scale-eaters (light blue), and outgroup species (black) in the Caribbean, California, and Mexico. Other topologies featuring a monophyletic San Salvador Island clade are presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006919#pgen.1006919.s001" target="_blank">S1 Fig</a>.</p