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

Cytochrome b gene (cytb). These sequences were derived from 83 nominal species of salaman- ders, which were distributed among 26 distinct genera occurring across the globe. The dataset contained 13 species with sequences from the gene cytb. Comparatively, COI exhibited notably broader taxonomic coverage, with 77 nominal species represented. Out of the 83 species ana- lyzed, only seven were shared between COI and cytb. Of the remaining 76 species, 70 were unique to COI and six were unique to cytb. To supplement the genetic data collected, a total of 1676 georeferenced occurrence records from phylogatR were utilized to collect a combination of geographic, environmental, and life history trait values for each nominal species present in the dataset. Species delimitation and consensus assignment Species delimitation results were generated by analyzing COI and cytb sequences from each nominal species under three different delimitation methods, ABGD, ASAP, and GMYC. We classified each nominal species as either containing undescribed genetic lineages or not con- taining undescribed genetic lineages based on the number of genetic groups predicted by each delimitation analysis. While taxonomic overlap between COI and cytb was narrow, delimita- tion results for species shared by both loci were mostly congruent with respect to species classi- fication. Of the seven species with sequences from both genes, only two species produced conflicting results regarding the presence of undescribed genetic lineages within a specific

Fig 1. Consensus classification of species delimitation results. A, Flowchart describing the process of generating a consensus of delimitation results (among different methods and loci). B, C, Pipeline for classifying nominal species as either containing or not containing hidden genetic diversity in each consensus analysis (all agree and majority rules, respectively). https://doi.org/10.1371/journal.pone.0310932.g001 PLOS ONE Predicting hidden lineages in salamanders PLOS ONE | https://doi.org/10.1371/journal.pone.0310932 October 18, 2024 6 / 20