Genome-Wide Analysis of an Endangered Axolotl Endemic to Mexico Reveals Genomic Variation Associated with Body Condition, Environment, and Infection by a Pathogenic Fungus

Axolotls are species from the genus Ambystoma endemic to Mexico, which are a highly vulnerable group of salamanders due to their restricted distributions, habitat loss, invasive species, and pollution. In this study, we used a genome-wide approach to determine the genetic status of Ambystoma altamirani populations, a highly threatened species living in streams in oak and pine forests surrounding Mexico City and other large urban areas in Central Mexico. Our study found that A. altamirani genetics is highly influenced by habitat environmental conditions like temperature, but we also found genetic signatures associated with infection by the lethal pathogen Batrachochytrium dendrobatidis and with body condition. In light of the threats that this species and other species of Ambystoma currently face, our study contributes to fundamental knowledge needed to implement genomic-based management and conservation strategies of axolotl populations and establish the first basis for genome-wide single-nucleotide polymorphism analyses for Ambystoma species.