Determinants of genetic diversity and species richness of North American amphibians

Schmidt, Chloé; Munshi‐South, Jason; Dray, Stéphane; Garroway, Colin J.

doi:10.1111/jbi.14480

Cited by 7 publications

(12 citation statements)

References 89 publications

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“…From a geographic perspective, protecting areas that contain high intraspecific genetic diversity, not just high species richness (e.g., ref. 117 ), must become an important component in evaluating biodiversity hotspots ( 118 , 119 ). Genomic taxonomy now provides the means to acknowledge more biodiversity without more species, so researchers and conservationists are better armed to unveil those species’ secrets and plan their survival.…”

Section: General Recommendationsmentioning

confidence: 99%

Acknowledging more biodiversity without more species

Dufresnes,

Poyarkov,

Jablonski

2023

Proc. Natl. Acad. Sci. U.S.A.

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Delimiting and naming biodiversity is a vital step toward wildlife conservation and research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can be spent effectively and objectively. To date, newly discovered lineages typically are either left undescribed and thus remain unprotected or are being erroneously proposed as new species despite mixed evidence for completed speciation, in turn contributing to the emerging problem of taxonomic inflation. Inspired by recent conceptual and methodological progress, we propose a standardized workflow for species delimitation that combines phylogenetic and hybrid zone analyses of genomic datasets (“genomic taxonomy”), in which phylogeographic lineages that do not freely admix are ranked as species, while those that have remained fully genetically compatible are ranked as subspecies. In both cases, we encourage their formal taxonomic naming, diagnosis, and description to promote social awareness toward biodiversity. The use of loci throughout the genome overcomes the unreliability of widely used barcoding genes when phylogeographic patterns are complex, while the evaluation of divergence and reproductive isolation unifies the long-opposed concepts of lineage species and biological species. We suggest that a shift in conservation assessments from a single level (species) toward a two-level hierarchy (species and subspecies) will lead to a more balanced perception of biodiversity in which both intraspecific and interspecific diversity are valued and more adequately protected.

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Section: General Recommendationsmentioning

confidence: 99%

Acknowledging more biodiversity without more species

Dufresnes,

Poyarkov,

Jablonski

2023

Proc. Natl. Acad. Sci. U.S.A.

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“…In the same region, Schmidt et al. (2022) analysed microsatellite data from 19 amphibian species; they found that genetic diversity was not predicted by the environmental variables they used and that areas with high species richness also had high genetic structure, but low genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

“…In a study of Nearctic amphibian species, the most important predictors of genetic diversity were taxonomic family, number of sequences, and for salamander species (N = 98), those at more northern latitudes had lower genetic diversity (Barrow et al, 2021). In the same region, Schmidt et al (2022) analysed microsatellite data from 19 amphibian species; they found that genetic diversity was not predicted by the environmental variables they used and that areas with high species richness also had high genetic structure, but low genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

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

Amador,

Arroyo‐Torres,

Barrow

2024

Journal of Biogeography

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AimIntraspecific 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.LocationNeotropics.TaxonAmphibians.MethodsWe assembled data sets 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.ResultsWe compiled 4052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2477 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 ConclusionsThis 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 harbour 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.

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“…In a study of Nearctic amphibian species, the most important predictors of genetic diversity were taxonomic family, number of sequences, and for salamander species (N = 98), those at more northern latitudes had lower genetic diversity (Barrow et al, 2021). In the same region, Schmidt et al (2022) analyzed microsatellite data from 19 amphibian species; they found that genetic diversity was not predicted by the environmental variables they used and that areas with high species richness also had high genetic structure, but low genetic diversity.…”

Section: Introductionmentioning

confidence: 99%

“…In a study of Nearctic amphibian species, the most important predictors of GD were taxonomic family, number of sequences, and for salamander species (N = 98), those at more northern latitudes had lower GD (Barrow et al, 2021). In the same region, Schmidt et al (2022) analyzed microsatellite data from 19 amphibian species; they found that GD was not predicted by the environmental variables they used and that areas with high species richness also had high GS, but low GD. Amphibians are the most threatened group of vertebrates on the planet (Harfoot et al, 2021), and are also particularly vulnerable to habitat loss, pollution, climate change, and disease.…”

Section: Introductionmentioning

confidence: 99%

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

Amador,

Arroyo-Torres,

Barrow

2023

Preprint

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Many factors influence genetic variation within species, which is key for adaptation and survival in changing environments. Using amphibians as a study system, we investigated genetic diversity and structure within Neotropical species to provide insights into how natural history traits, phylogeny, and geographic characteristics influence intraspecific genetic variation. We assembled datasets for Neotropical amphibians using open-access databases for natural history traits, genetic sequences, phylogenetic trees, and geographic data. For each species, we calculated overall nucleotide diversity (π) and tested for isolation by distance (IBD). We then identified predictors of genetic diversity and genetic structure (IBD) using Random Forest (RF) regression or RF classification, respectively. To more explicitly incorporate phylogenetic relationships, we also used phylogenetic generalized linear mixed models (PGLMMs), and phylogenetic linear regression or phylogenetic logistic regression models to predict π and IBD, respectively. We compiled > 4,000 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2,468 sequences from 176 species that were not already linked to occurrence data. RF regressions, phylogenetic linear regression, and PGLMMs were congruent in identifying range size and elevation as the most important predictors of π. Species with larger ranges and at lower elevations tended to have higher overall genetic diversity. RF classification and phylogenetic comparative methods identified minimum elevation as the most important predictor of IBD, with species at lower elevations being more likely to exhibit genetic structure. These results could play a key role in the development of conservation strategies for amphibians. For example, species living at high elevations or with small ranges need substantial protection due to their low genetic diversity. We also show that the Choco, Andes, and Atlantic Forests biogeographic units harbor high diversity across many species that should be prioritized for protection.

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Determinants of genetic diversity and species richness of North American amphibians

Cited by 7 publications

References 89 publications

Acknowledging more biodiversity without more species

Acknowledging more biodiversity without more species

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

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

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