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Biology subjects

Pelletier, T. A.

Publications and source records attributed to Pelletier, T. A..

4 recordsLinked to original sources

Environmental and geographic drivers of global bat phylogenetic diversity

AimUnderstanding the patterns and factors that shape biodiversity is vital to conserving species. We combined open-source genetic, environmental, and geographic information to analyze bat phylogenetic diversity (PD) patterns in continuous ecoregions across the globe. This information is important for developing bat conservation strategies, and our methodology can work for any taxa with sufficient georeferenced genetic data available. LocationGlobal. MethodsAfter curating a global dataset containing 14,037 COI DNA sequences from 343 described species of bats, we calculated PD for continuous ecoregions at different spatial scales. To avoid the difficulties of using current species names, we used genetic OTUs identified by a single-locus species delimitation method to reconstruct and date a phylogeny. We then calculated PD, estimated a lineage through time plot, and used random forest predictive modeling to identify environmental and geographic predictors of PD. ResultsIn addition to current temperature, temperature during the last glacial maximum and temperature changes between the last glacial maximum and last interglacial were most closely associated with PD. However, at different spatial scales, the top variables differed slightly. When using smaller ecoregions, latitude and population density were also identified as important, though not significant. Southeast Asia and South America had the highest levels of PD, along with parts of Africa and the Himalayas. We demonstrate that, regardless of spatial scale and uneven sampling across the globe, single-locus genetic data can reflect species diversity gradients and identify predictors of PD. Main conclusionsWe show that publicly-available, single-locus data can be used to analyze large-scale evolutionary patterns and inform conservation efforts. Additionally, choice of biodiversity measure and spatial scale matter when assessing species patterns. When looking at bats, temperature variables with a historical component are most important for predicting PD broadly, but latitude and population density could also be important on smaller scales.

evolutionary biology↗

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↗

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

The geographic distribution of genetic variation within a species reveals information about its evolutionary history, including responses to historical climate change and dispersal ability across various habitat types. We combine genetic data from salamander species with geographic, climatic, and life history data collected from open-source online repositories to develop a machine learning model designed to identify the traits that are most predictive of unrecognized genetic lineages. We find evidence of hidden diversity distributed throughout the clade Caudata that is largely the result of variation in climatic variables. We highlight some of the difficulties in using machine-learning models on open-source data that are often messy and potentially taxonomically and geographically biased.

evolutionary biology↗

phylogatR: Phylogeographic data aggregation and repurposing

Patterns of genetic diversity within species contain information about the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyze sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR, large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology and student- or citizen-science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalyzed and increase accessibility to big data for research labs and classroom instructors with limited computational expertise and resources.

bioinformatics↗