A new look at genome size, evolutionary duration and genetic variation in salamanders

Salamanders have some of the largest genomes among vertebrates, and also some of the lowest reported levels of genetic diversity. Paedomorphs, in particular, have the largest genomes on average among urodela, and display exceptionally low levels of nucleotide and protein variation. Here, we address the question of genetic variation in relation to genome size in eight different salamander families. Using the rag1 gene as a probe for evolutionary rates, we found that rates of substitution are exceptionally low in obligate paedomorphs (neotenes) and other salamander species. Substitution rates in some cases are as low as those reported for cartilaginous fish, which have the slowest mutation rates recorded so far in vertebrates. Confirming and extending an earlier study, we also found that genome size is correlated with phylogenetic age in Plethodontidae, indicating a more general trend in genome size evolution in urodela. The Plethodontidae, furthermore, display much higher levels of genetic variance than the obligate neotene families, consistent with greater habitat heterogeneity in terrestrial salamanders. Finally, we present the first direct evidence of a gene, rag1, whose substitution rate is negatively associated with genome size. Based on these and other observations, we propose a hypothesis according to which mutation rates in nuclear genes tend to increase as genome size decreases during the course of vertebrate evolution.