Supplementary material: Machine learning and phylogenetic models identify predictors of genetic variation in Neotropical amphibians

Aim: Intraspecific genetic variation is key for adaptation and survival in
changing environments and is known to be influenced by many factors,
including population size, dispersal, and life history traits. We
investigated genetic variation within Neotropical amphibian species to
provide insights into how natural history traits, phylogenetic
relatedness, climatic, and geographic characteristics can explain
intraspecific genetic diversity. Location: Neotropics. Taxon:
Amphibians. Methods: We assembled datasets using open-access databases for
natural history traits, genetic sequences, phylogenetic trees, climatic,
and geographic data. For each species, we calculated overall nucleotide
diversity (π) and tested for isolation by distance (IBD) and isolation by
environment (IBE). We then identified predictors of π, IBD, and IBE using
Random Forest (RF) regression or RF classification. We also fitted
phylogenetic generalized linear mixed models (PGLMMs) to predict π, IBD,
and IBE. Results: We compiled 4,052 mitochondrial DNA sequences from 256
amphibian species (230 frogs and 26 salamanders), georeferencing 2,477
sequences from 176 species that were not linked to occurrence data. RF
regressions and PGLMMs were congruent in identifying range size and
precipitation (σ) as the most important predictors of π, influencing it
positively. RF classification and PGLMMs identified minimum elevation as
an important predictor of IBD; most species without IBD tended to occur at
higher elevations. Maximum latitude and precipitation (σ) were the best
predictors of IBE, and most species without IBE occur at lower latitudes
and in areas with more variable precipitation. Main conclusions: This
study identified predictors of genetic variation in Neotropical amphibians
using both machine learning and phylogenetic methods. This approach was
valuable to determine which predictors were congruent between methods. We
found that species with small ranges or living in zones with less variable
precipitation tended to have low genetic diversity. We also showed that
Western Mesoamerica, Andes, and Atlantic Forest biogeographic units harbor
high diversity across many species that should be prioritized for
protection. These results could play a key role in the development of
conservation strategies for Neotropical amphibians.