Species IUCN threat status level increases with elevation: a phylogenetic approach for Neotropical tree frog conservation

Caviedes-Solís, Itzue W.; Kim, Nicholas; Leaché, Adam D.

doi:10.1007/s10531-020-01986-8

Cited by 7 publications

(3 citation statements)

References 53 publications

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“…In amphibians, Caviedes‐Solis et al. (2020) found that Neotropical treefrogs living in high elevations were more likely to be classified with threatened status. Our analysis of Neotropical amphibians from several taxonomic families confirmed expected differences between geographic range sizes based on IUCN conservation status, with Least Concern amphibian species occurring in larger ranges and Data Deficient, Endangered and Critically Endangered species occurring in smaller ranges.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…Geographically restricted species are expected to have less genetic variation, which may also indicate an increased risk of extinction (Levy et al, 2016). In amphibians, Caviedes-Solis et al (2020) found that Neotropical treefrogs living in high elevations were more likely to be classified with threatened status. Our analysis of Neotropical amphibians from several taxonomic families confirmed expected differences between geographic range sizes based on IUCN conservation status, with Least Concern (LC) amphibian species occurring in larger ranges and Data Deficient (DD), Endangered (EN) and Critically Endangered (CR) species occurring in smaller ranges (Figure S12).…”

Section: Discussionmentioning

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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“…Additionally, 55% of the species classified as critically endangered (CR) or endangered (EN) were endemic species with low phylogenetic diversity values and shorter branch lengths. According to the IUCN, high threat levels do not always correlate with high evolutionary distinctiveness ( Caviedes-Solis, Kim & Leaché, 2020 ). Therefore, considering that the threat of extinction is vital for conservation, it is essential to consider other factors, such as evolutionary distinctiveness and phylogenetic diversity, to ensure comprehensive and effective conservation planning.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic diversity and North Andean block conservation

Leon-Alvarado,

Miranda-Esquivel

2023

PeerJ

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Background The Northern Andean Block (NAB) harbors high biodiversity; therefore, it is one of the most important areas in the Neotropics. Nevertheless, the settlement of several human populations has triggered the rapid transformation of ecosystems, leading to the extinction or endangerment of many species. Methods Because phylogenetic diversity indices quantify the historical distinctness between species, they are adequate tools for evaluating priority conservation areas. We reconstructed 93 phylogenies encompassing 1,252 species and, utilizing their occurrence data sourced from the Global Biodiversity Information Facility, computed the Average Taxonomic Distinctness Index (AvTD) for each grid cell with a spatial resolution of 0.25° within the NAB. The index values for each grid cell were categorized into quantiles, and grid cells displaying values within the upper quantile (Q5) were identified as the most significant in terms of phylogenetic diversity. We also calculated the contribution of endemic species to overall phylogenetic diversity within the NAB, specifically focusing on areas preserved within protected areas. Results The NAB Andean region exhibited the highest AvTD, with high AvTD values observed in the middle and southern areas of Cordilleras. Endemic species made a relatively modest contribution to the overall phylogenetic diversity of the NAB, accounting for only 1.2% of the total. Despite their relatively small geographical footprints, protected areas within the NAB have emerged as crucial repositories of biodiversity, encompassing 40% of the total phylogenetic diversity in the region. Discussion Although the NAB Andean region has been identified as the most crucial area in terms of AvTD, some regions in the Amazonian Piedemonte and Pacific lowlands have high AvTD levels. Interestingly, some protected areas have been found to harbor higher AvTDs than expected, given their smaller size. Although the delimitation of new PAs and species richness have been the primary factors driving the expansion of PAs, it is also essential to consider the evolutionary information of species to conserve all aspects of biodiversity, or at least cover most of them. Therefore, using phylogenetic diversity measures and the results of this study can contribute to expanding the PA network and improving the connectivity between PAs. This approach will help conserve different aspects of biodiversity and preserve evolutionary relationships between species.

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Species IUCN threat status level increases with elevation: a phylogenetic approach for Neotropical tree frog conservation

Cited by 7 publications

References 53 publications

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

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

Phylogenetic diversity and North Andean block conservation

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