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 ..., , , # Machine learning and phylogenetic models identify predictors of genetic variation in Neotropical amphibians - Supplementary Material

This dataset contains all data files, including genetic sequences, input text files, supplementary tables, and R scripts used in the analyses to address the determinants of intraspecific amphibian genetic diversity in the Neotropic. We repurposed this data from 256 Neotropical amphibians (frogs and salamanders) directly from open-access databases, for example, DNA sequences and occurrences from phylogatR, and natural history traits from AmphiBIO. We generated several tables and figures derived from the analyses that did not have room in the main manuscript and that we are including here as supplementary material.

## Description of the data

### MS\_Fastas\_Neotropic\_species.tar.xz

This folder contains the CytB sequence alignments of 256 species in FASTA format.

### MS\_Occurrences\_Neotropic\_species.zip

This folder contains the geographic coordina...