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

Discussion When identifying genetic lineages or delimiting species, it is important to recognize that spe- cies concepts are complex and often differ based on various factors, such as geographic loca- tion, reproductive isolating mechanisms, genetic markers, and taxonomic practices. Therefore, it is essential to approach species delimitations with caution and to recognize that they repre- sent a hypothesis or starting point rather than a definitive answer [76]. In addition, while mito- chondrial data can be suitable for preliminary assessments of species diversity [77], these assessments should be considered in tandem with other species information and relevant data when describing species boundaries. However, with recent advances in technology rapidly increasing the quantity of publicly accessible genetic and geographic datasets, these data offer a cost effective and efficient way to explore large-scale patterns and predictors of intraspecific genetic variation (e.g., [24,29,78]). Our results suggest that there are undescribed genetic lineages that may warrant further investigation distributed within Caudata. Adequately documenting biodiversity, both at the species and population level, is a first step in understanding the eco-evolutionary processes generating this diversity. However, in most clades, the Linnean shortfall is likely to influence broad scale patterns detected using macrogenetic approaches [13], making it essential to con- sider how the taxonomic designations used to inform these approaches influence the patterns

detected. This is particularly important when dealing with clades suspected of harboring high levels of cryptic diversity. For example, Miraldo et al. [24] generated the first global map of genetic diversity within species of mammals and amphibians. One of their main conclusions was that amphibians displayed lower levels of genetic variation in areas with higher human impact. Similarly, in amphibians, several recent studies have found within species genetic diversity to be lower in temperate regions in species with smaller ranges and at higher eleva- tions [30,37]. The methods used to detect these patterns are based on current taxonomic knowledge, and as such, rely on the assumption that the species designations used are accurate. However, if species descriptions inaccurately reflect biological diversity, nominal species that contain cryptic species will display higher levels of genetic diversity, while not reflecting true within species variation, potentially skewing our interpretation of any patterns that result. Evaluating support for identified genetic lineages While our delimitation of genetic lineages are a starting point, or hypothesis generation step, for evaluating a species in nature where complex processes, such as hybrid zones, and adequate sampling must be considered [e.g., 75–77], we believe these computational approaches are use- ful for targeting species in further need of examination. We conducted a literature search to explore whether the nominal species in our dataset have been previously explored from a spe-

cies delimitation approach. We used the online American Museum of Natural History taxo- nomic and nomenclatural database, Amphibian Species of the World [79]), to evaluate current taxonomic research in each nominal species of salamander predicted to contain hidden diver- sity in our consensus model. Species in which we were able to identify research-based support for the potential of undescribed diversity were recorded, along with the related articles in which the diversity was described as well as the type of data used (see S7 Data). Nearly 70% of species the majority rules consensus suggests harbor hidden lineages, contain results that also support the potential splitting of species into separate lineages. Out of these about 38% were explored using mt DNA only, 10% with nuclear DNA only, 35% using a combination of both nuclear and mt DNA and 17% using mt DNA, nuclear DNA and morphology. Just under 10% of the species display a complex history of hybridization, making delimitations difficult, a situ- ation not uncommon in salamanders [e.g., 44,80,81]. We were unable to find results for PLOS ONE Predicting hidden lineages in salamanders PLOS ONE | https://doi.org/10.1371/journal.pone.0310932 October 18, 2024 12 / 20