Determinants of genetic diversity in Neotropical salamanders (Plethodontidae: Bolitoglossini).

Genetic diversity is the raw material of evolution, yet the reasons why it varies among species remain poorly understood. While studies at deeper phylogenetic scales point to the influence of life history traits on genetic diversity, it appears to be more affected by population size but less predictable at shallower scales. We used proxies for population size, mutation rate, direct selection, and linked selection to test factors affecting genetic diversity within a diverse assemblage of Neotropical salamanders, which vary widely for these traits. We estimated genetic diversity of noncoding loci using ddRADseq and coding loci using RNAseq for an assemblage of Neotropical salamanders distributed from northern Mexico to Costa Rica. Using ddRADseq loci, we found no significant association with genetic diversity, while for RNAseq data we found that environmental heterogeneity and proxies of population size predict a substantial portion of the variance in genetic diversity across species. Our results indicate that diversity of coding loci may be more predictable than that of noncoding loci, which appears to be mostly unpredictable at shallower phylogenetic scales. Our results suggest that coding loci may be more appropriate for genetic diversity estimates used in conservation planning because of the lack of any association between the variables we used and genetic diversity of noncoding loci.

Miniaturization, Genome Size, and Biological Size in a Diverse Clade of Salamanders.

AbstractGenome size (C-value) can affect organismal traits across levels of biological organization from tissue complexity to metabolism. Neotropical salamanders show wide variation in genome and body sizes, including several clades with miniature species. Because miniaturization imposes strong constraints on morphology and development and because genome size is strongly correlated with cell size, we hypothesize that body size has played an important role in the evolution of genome size in bolitoglossine salamanders. If this hypothesis is correct, then genome size and body size should be correlated in this group. Using Feulgen image analysis densitometry, we estimated genome sizes for 60 species of Neotropical salamanders. We also estimated the "biological size" of species by comparing genome size and physical body sizes in a phylogenetic context. We found a significant correlation between C-value and physical body size using optimal regression with an Ornstein-Uhlenbeck model and report the smallest salamander genome found to date. Our index of biological size showed that some salamanders with large physical body size have smaller biological body size than some miniature species and that several clades demonstrate patterns of increased or decreased biological size compared with their physical size. Our results suggest a causal relationship between physical body size and genome size and show the importance of considering the impact of both on the biological size of organisms. Indeed, biological size may be a more appropriate measure than physical size when considering phenotypic consequences of genome size evolution in many groups.