Maximum likelihood tree of the D-loop haplotypes found in cave and surface specimens. Most similar sequences obtained in GenBank through BLAST analyses are included in the tree. In agreement with the 16S rRNA data, two distinct lineages were identified; one that includes C. bairdii specimens and one that includes C. cognatus. Cave haplotypes within the C. bairdii clade are identified by numerals (1–8) and Cave and Antes Creek haplotypes within the C. cognatus clade are identified by letters (A–L). Notice that cave individuals are found within both lineages.