Fig. 1. Map of collections sites, phylogenetic tree, and population structure.

a Representative photos of a surface environment containing the surface A. mexicanus ecotype (left) and a cave environment containing the cave A. mexicanus ecotype (right). b Sampling locations for the present study. Locations of 29 caves within the Sierra de El Abra region of Mexico with known Astyanax mexicanus cavefish populations are labeled in black. Cavefish populations sampled for the current study (18 caves) are marked with an asterisk. The Guatemala caves are shown within a purple box. The El Abra and Micos caves are shown within orange boxes (these cave regions contain cavefish from a lineage of surface stock independent from the surface lineage that invaded the Guatemala caves). Surface fish populations sampled for the current study (8 surface locations) are labeled in blue. One surface population, Jalpan, is not shown (collected approximately 100 km south of the Subterráneo cave). Map modified with permission from Gross⁵⁰. c Multi-species-coalescent tree inferred using 1,121,282 SNPs in SVDQuartets. SVDquartets was run with a sampling of 500,000 random quartets and 500 standard bootstrap replicates specified to obtain bootstrap node support values shown. See Supplementary Fig. 2 for the tree with each sample labeled. d ADMIXTURE bar plot for K (number of unique genetic clusters) of 11. Surface populations are labeled in blue text and cave populations are labeled in black text. Source data are provided as a Source Data file.