Genetic diversity and detection of candidate loci associated with alternative morphotypes in a tailed amphibian

Abstract

Abstract Phenotypic changes in response to environmental cues allow organisms to adapt and enhance their fitness in a given habitat. Despite the significance of phenotypic plasticity in the evolution and ecology of natural populations and the ongoing development of new genomic tools, the underlying genetic basis is still largely unknown. Herein, we examined the underlying mechanisms of genetic and phenotypic divergence among alternative morphs of a natural population of the Greek smooth newt (Lissotriton graecus). The studied population consists of fully aquatic individuals exhibiting facultative paedomorphosis, the retention of larval traits such as gills, and individuals that have passed metamorphosis (paedomorphic vs. metamorphic newts). Based on the single nucleotide polymorphisms (SNPs) obtained, we observed low genetic divergence between the two alternative morphs and similar levels of gene diversity on neutral markers. Despite the observed high gene flow between the morphs, an Fst approach for outliers detected candidate loci putatively associated with the alternative morphs that mapped to four genes. These identified genes have functional roles in metabolic processes that may mediate the persistence of alternative ontogenetic trajectories.