(A) Map: average genetic distance between Galápagos PIM collections and each of the 132 mainland accessions. Plot: multi-locus principal components analysis (PCA). Squares, diamonds, and circles indicate Peruvian, Ecuadorian, and Galápagos collections, respectively. Inset: Predicted continental origins for Galápagos PIM collections. Colors are same as shown in the multi-locus PCA (†Exact locations vary substantially between runs. Results from a single run are shown). (B) Maximum likelihood relationships among focal populations calculated with Treemix (allowing no migration). Left: inferred trees of 1000 resampled datasets (500 SNPs, with replacement). Right: consensus topology. All trees were rate-smoothed (λ = 1). (C) Diversity and divergence metrics. Left: nucleotide diversity (π) calculated for Galápagos PIM, Ecuador-PIM, and Peru PIM in overlapping 100 kb windows. Invariant windows (π = 0) are truncated and are instead shown in the inset bar plot. Right: average pairwise sequence divergence for three PIM comparisons: Gal×Gal, Gal×Ecu, and Gal×Peru. Each point represents a comparison between individuals, averaged over all loci.