Genome-wide analysis of an endangered axolotl endemic to Mexico reveals genomic variation associated with body condition, environment and infection by a pathogenic fungus

Amphibians are the most threatened group of vertebrates on the planet due to habitat loss, climate change and the emerging disease chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Axolotls, species from the genus Ambystoma endemic to Mexico, are a highly vulnerable group of salamanders with restricted distributions and are severely affected by habitat fragmentation, invasive species, and pollution. In this context, population genomic studies are urgently needed to implement adequate conservation and management decisions. In this study, we identified abiotic and biotic factors associated with the genomic diversity and structure of Ambystoma altamirani through genome-wide single-nucleotide polymorphism (SNP) analyses. Based on 110,761 neutral SNPs from 99 individuals across five populations of A. altamirani, we found that genomic diversity of individuals was positively correlated with their body condition. Moreover, patterns of genetic structure identified three main genetic clusters which were correlated with habitat environmental differences. Specifically, elevation and temperature-associated variables significantly contributed to the genomic structuring of A. altamirani populations. Linear factor mixed models (LFMM) identified 1,670 SNPs associated with environmental variables as well as 80 and 47 SNPs associated with the biotic variables Bd infection intensity and body condition, respectively. We identified SNPs significantly associated with differences in Bd infection and body condition among homozygous or heterozygous genotypes. Overall, our study teases apart some of the factors likely influencing axolotl genetic diversity and population structuring, which should be considered for conservation strategies for this and other endangered amphibian species.