Predicting genetic biodiversity in salamanders using geographic, climatic, and life history traits

roughly 25% of our species data. We encountered 5 species in which the results of previous delimitation work were either unclear or considered highly contested (e.g., Ichthyosaura alpes- tris, Batrachuperus karlschmidti, Batrachuperus taibaiensis, and Salamandrella schrenckii). Taxonomy is dynamic field [33] and given our search, it can be difficult to use current open- source data relying solely on species names. However, the current literature largely supports the delimitation results found here and suggests a number of species in further need of investi- gation (see citations in S7 Data, formal name changes, and an ability to update current open- source databases to reflect these changes). Additionally, even though there are limitations to using current open-source data that might not keep up to date with current taxonomy, we can still determine what factors might predict the presence of species likely to possess undescribed genetic diversity. Significant predictors of diversity Significance testing of the most important predictors from our best model (majority rules con- sensus with a correlation coefficient cutoff of 0.90) indicates that the species which our analysis identified as containing hidden genetic lineages often have ranges characterized by a larger variance in annual and seasonal precipitation, isothermality, and net primary productivity when compared to species that were not identified as containing hidden genetic lineages by our analysis (Fig 5B). And while the order of the most important traits is unstable across differ-

ent models, across all models most of the traits found to be important were measurements of standard deviation (vs. measurements of mean values or life history traits) (S5 Data). This sug- gests that the presence of variation in climate, rather than any species-specific trait or charac- teristic is the most identifiable driving force of within species genetic diversity for salamanders at this scale. Our findings align with similar studies of amphibians using a different measure of genetic variation within species (nucleotide diversity), which concluded that species traits were not a predictor of intraspecific genetic diversity [30,37]. Using similar methods, our results in salamanders differ from that found in mammals, where body size and range size were the most important predictors [35]. These findings are somewhat consistent with other studies of salamander diversification. Reproductive mode (larval stages, direct development) and habitat (combinations of terres- trial, aquatic, arboreal) vary across species and have evolved multiple times but have not been found to directly correlate with speciation, though being a direct developer might increase diversification rates [82]. In vertebrate clades, terrestrial organisms tend to have higher diversi- fication rates than aquatic organisms [83], but we did not have a large number of fully terres- trial species in our dataset, which might have limited our ability to detect this as an important predictor. Alternatively, in one species which has intraspecific variation in habit, Salamandra

salamandra, terrestrial-breeding individuals exhibited greater geographic genetic differentia- tion compared to aquatic-breeding individuals [84]. Not surprisingly, this species showed con- flicting results in our delimitation analyses. Because various species delimitation methods are not similarly sensitive to differing levels of population structure, we would expect these meth- ods to perform more inconsistently within species with highly variable genetic and geographic distance across different life histories [80,85]. Given that salamanders are relatively constrained in body form and ecological niches, varia- tion in climatic variables seems like a reasonable explanation for species containing cryptic diversity. This follows the suggestion that change in climatic niche variables increases diversifi- cation rates in plethodontid salamanders [86]). Diversification rates in frogs and salamanders have been shown to be higher near the tropics [83], so one might expect latitude to be an PLOS ONE Predicting hidden lineages in salamanders PLOS ONE | https://doi.org/10.1371/journal.pone.0310932 October 18, 2024 13 / 20