Biology subjects

Arroyo-Torres, I.

Publications and source records attributed to Arroyo-Torres, I..

2 recordsLinked to original sources

bioRxiv2025

Caudata macrogenetics: Species range size predicts intraspecific genetic variation in global salamanders

AimGenetic diversity contains valuable information about ecological and evolutionary aspects of species. Intraspecific genetic variation is shaped by species natural history traits and by characteristics of geography and climate within their ranges. Amphibians are of ecological and conservation interest because of their global distribution, deep history, trait diversity, and roles within ecological communities. Here, we studied genetic variation within salamanders to investigate predictors of nucleotide diversity and spatial patterns of genetic differentiation. LocationGlobal. Time PeriodPresent. Major Taxa StudiedSalamanders. MethodsWe repurposed mitochondrial DNA sequences and ecological data from open-access databases for 220 salamander species. We calculated nucleotide diversity ({pi}) and tested for isolation by distance (IBD) and isolation by environment (IBE). We analyzed these three variables with random forest and phylogenetic comparative methods using 28 predictors expected to be associated with genetic variation. ResultsWe recovered 8,108 Cytb sequences with their associated geographic coordinates, of which 7,007 sequences were manually curated by us. Range size, lineage age, and sample size were important predictors of genetic variation. We found higher diversity in regions including the Neotropics and central-eastern Europe. The absence of phylogenetic signal in {pi}, IBD, and IBE suggests that genetic variation is shaped by local ecological and geographical factors rather than by shared ancestry. Main ConclusionsOur finding of range size as an important predictor aligns with theoretical expectations that species with larger ranges tend to harbor more genetic diversity. Furthermore, lineage age being an important predictor is in line with the clade-age hypothesis, in which species with longer divergence times have higher genetic diversity because they have had more time to accumulate genetic variation. Our results underscore the importance of integrating spatial data into macrogenetic studies, providing valuable information for future studies and conservation strategies targeting regions with high or low genetic diversity.

evolutionary biology↗

bioRxiv2023

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

AimIntraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, migration, and life history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogeny, climatic, and geographic characteristics influence intraspecific diversity. LocationNeotropics. TaxonAmphibians. MethodsWe 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 ({pi}) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors of {pi}, IBD, and IBE using Random Forest (RF) regression or RF classification. To incorporate phylogenetic relationships, we fitted phylogenetic generalized linear mixed models (PGLMMs) to predict {pi}, IBD, and IBE. ResultsWe 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 ({sigma}) as the most important predictors of {pi}. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD, and maximum latitude and precipitation ({sigma}) as the best predictors of IBE. Main conclusionsThis study unified machine learning and phylogenetic methods and identified predictors of genetic variation in Neotropical amphibians. 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.

evolutionary biology↗