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

taxon based on loci. Delimitation results across different methods showed slightly less agree- ment. Classifications resulting from the GMYC and ASAP methods were similar across spe- cies. These methods, on average, resulted in slightly fewer predicted species per nominal species than the ABGD method (see Fig 3 for predicted species numbers). To account for this variation in our final random forest classification models, we generated two consensus classifications to evaluate concordance between delimitation results from dif- ferent methods and loci. The results of our consensus models indicate that roughly 2/3rds of the nominal salamander species used in this analysis are likely to contain genetic lineages that may be unexplored diversity. The strictest of these classifications produced a consensus model (all agree) consisting of 51 total species, 41 of which were classified as containing hidden diver- sity and 10 of which were classified as not containing hidden diversity. The remaining consen- sus model (majority rules) consisted of 83 total species, of which 51 were classified as containing undescribed genetic lineages and 32 were not (Fig 3). Predictive modeling For our majority rules and all agree consensus classifications, we developed random forest clas- sification models using all available predictor data. To assess potential correlation between var- iables in our dataset we used the R package ’corrplot’ [75] to generate a correlation matrix of

Fig 2. Geographic spread of salamander data. Map shows geographic distribution of salamander occurrences pulled from phylogatR [38] and used in these analyses. Pie charts show the total number of cytb and COI sequences used (left) and the number of species represented by those cytb and COI sequences (right). Basemap created with world map data from the public domain Natural Earth project (http://www.naturalearthdata.com). Salamander figures in black were obtained from Phylopic [74] and are licensed under public domain. https://doi.org/10.1371/journal.pone.0310932.g002 PLOS ONE Predicting hidden lineages in salamanders PLOS ONE | https://doi.org/10.1371/journal.pone.0310932 October 18, 2024 7 / 20