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Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders ( Desmognathus monticola )

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Why does the magnitude of genotype‐by‐environment interaction vary?
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Alternative forms for genomic clines
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Rivers, not refugia, drove diversification in arboreal, sub‐Saharan African snakes
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Candidate‐species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones
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Empirical and philosophical problems with the subspecies rank
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WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas
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Points of View on Defining and Naming Species of Plethodontid Salamanders
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Goldilocks Meets Santa Rosalia: An Ephemeral Speciation Model Explains Patterns of Diversification Across Time Scales
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Finding Evolutionary Processes Hidden in Cryptic Species
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A demonstration of unsupervised machine learning in species delimitation
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Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
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Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema species complex (Serpentes: Elapidae)
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How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake
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The self-organizing map
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The phylogenetics of Desmognathine salamander populations across the southern Appalachians
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Taxonomy anarchy hampers conservation
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Visualizing spatial population structure with estimated effective migration surfaces
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Multilevel fine-scale diversity challenges the ‘cryptic species’ concept
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All are one and one is all: sexual uniformity among widely separated populations of the North American seal salamander, Desmognathus monticola
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The One‐Migrant‐per‐Generation Rule in Conservation and Management
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Reticulation, divergence, and the phylogeography–phylogenetics continuum
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Multispecies coalescent delimits structure, not species
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Geography is more important than life history in the recent diversification of the tiger salamander complex
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Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation
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Desmognathus monticola
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Species Concepts and Species Delimitation
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Adding More Ecology into Species Delimitation: Ecological Niche Models and Phylogeography Help Define Cryptic Species in the Black Salamander (Aneides flavipunctatus)
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The Type Locality Project: collecting genomic-quality, topotypic vouchers and training the next generation of specimen-based researchers
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Geographic Range Shifts Do Not Erase the Historic Signal of Speciation in Mammals
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adegenet : a R package for the multivariate analysis of genetic markers
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Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths
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ISOLATION BY DISTANCE
inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
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UFBoot2: Improving the Ultrafast Bootstrap Approximation
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An overview of speciation and species limits in birds
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Genetic Analysis of Hybrid Zones
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Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)
inferredcites →https://doi.org/10.1093/sysbio/syab034openalex-snapshot
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs ( Occidozyga laevis )
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Evaluating Species Delimitation Methods in Radiations: The Land SnailAlbinaria cretensisComplex on Crete
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Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation
inferredcites →https://doi.org/10.1093/sysbio/syab093openalex-snapshot
Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes ( Lampropeltis triangulum Complex)
inferredcites →https://doi.org/10.1093/sysbio/syac034openalex-snapshot
Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
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Multilocus Species Delimitation in a Complex of Morphologically Conserved Trapdoor Spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)
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Species Delimitation using Genome-Wide SNP Data
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Historical Species Distribution Models Predict Species Limits in WesternPlethodonSalamanders
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Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
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Species Delimitation with Gene Flow
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THE CHALLENGE OF SPECIES DELIMITATION AT THE EXTREMES: DIVERSIFICATION WITHOUT MORPHOLOGICAL CHANGE IN PHILIPPINE SUN SKINKS
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Process‐based species delimitation leads to identification of more biologically relevant species*
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ABGD, Automatic Barcode Gap Discovery for primary species delimitation
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MULTILOCUS CLINES
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Species are hypotheses: avoid connectivity assessments based on pillars of sand
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Cryptic species as a window into the paradigm shift of the species concept
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Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex)
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Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex
inferredcites →https://doi.org/10.1111/zoj.12392openalex-snapshot
Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)
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Strong Inference
inferredcites →https://doi.org/10.1146/annurev-ento-112408-085432openalex-snapshot
Integrative Taxonomy: A Multisource Approach to Exploring Biodiversity
inferredcites →https://doi.org/10.1146/annurev.es.26.110195.003051openalex-snapshot
SPECIATION IN EASTERN NORTH AMERICAN SALAMANDERS OF THE GENUS PLETHODON
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Defining Loci in Restriction-Based Reduced Representation Genomic Data from Nonmodel Species: Sources of Bias and Diagnostics for Optimal Clustering
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Nomenclatural solutions for diagnosing ‘cryptic’ species using molecular and morphological data facilitate a taxonomic revision of the Black-bellied Salamanders (Urodela, Desmognathus ‘quadramaculatus’) from the southern Appalachian Mountains
inferredcites →https://doi.org/10.11646/zootaxa.4263.3.3openalex-snapshot
A new species of dusky salamander (Amphibia: Plethodontidae: Desmognathus) from the Eastern Gulf Coastal Plain of the United States and a redescription of D. auriculatus
inferredcites →https://doi.org/10.11646/zootaxa.4734.1.1openalex-snapshot
Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades
inferredcites →https://doi.org/10.11646/zootaxa.5133.1.3openalex-snapshot
A new, narrowly endemic species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus) from the Gulf Coastal Plain of Mississippi and Alabama
inferredcites →https://doi.org/10.1186/1471-2156-11-94openalex-snapshot
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
inferredcites →https://doi.org/10.1186/1471-2164-14-347openalex-snapshot
Unsupervised genome-wide recognition of local relationship patterns
inferredcites →https://doi.org/10.1186/1472-6785-7-7openalex-snapshot
The importance of comparative phylogeography in diagnosing introduced species: a lesson from the seal salamander, Desmognathus monticola
inferredcites →https://doi.org/10.1186/s12862-019-1427-yopenalex-snapshot
A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals
inferredcites →https://doi.org/10.1186/s12862-020-01642-3openalex-snapshot
Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs)
inferredcites →https://doi.org/10.1186/s12983-022-00453-0openalex-snapshot
Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data
inferredcites →https://doi.org/10.1371/journal.pbio.2000234openalex-snapshot
Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence
inferredcites →https://doi.org/10.1371/journal.pcbi.1008924openalex-snapshot
Incorporating the speciation process into species delimitation
inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
inferredcites →https://doi.org/10.1371/journal.pone.0068242openalex-snapshot
New Metrics for Comparison of Taxonomies Reveal Striking Discrepancies among Species Delimitation Methods in Madascincus Lizards
inferredcites →https://doi.org/10.1371/journal.pone.0154363openalex-snapshot
Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections
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Fast and Efficient Estimation of Individual Ancestry Coefficients
inferredcites →https://doi.org/10.1643/ch-17-579openalex-snapshot
Distribution and Abundance of Introduced Seal Salamanders (Desmognathus monticola) in Northwest Arkansas, USA
inferredcites →https://doi.org/10.1643/ch-18-052openalex-snapshot
A New Green Salamander in the Southern Appalachians: Evolutionary History of Aneides aeneus and Implications for Management and Conservation with the Description of a Cryptic Microendemic Species
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Self- and Super-organizing Maps in R : The kohonen Package
inferredcites →https://doi.org/10.18637/jss.v087.i07openalex-snapshot
Flexible Self-Organizing Maps in kohonen 3.0
inferredcites →https://doi.org/10.2307/1547159openalex-snapshot
Cryptic Species, Species Delimitation, and Taxonomic Practice in the Homosporous Ferns
inferredcites →https://doi.org/10.2307/1950754openalex-snapshot
Studies of the Local Distribution, Life History, and Population Dynamics of the Salamander Genus Desmognathus in Virginia
inferredcites →https://doi.org/10.2307/j.ctv1nzfgj7openalex-snapshot
Phylogeography
inferredcites →https://doi.org/10.26153/tsw/8432openalex-snapshot
Desmognathus monticola
inferredcites →https://doi.org/10.3099/mcz42.1openalex-snapshot
Phylogeography and Species Boundaries In theHydromantes shastaeComplex, With Description of Two New Species (Amphibia; Caudata; Plethodontidae)
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A Guide to Sexing Salamanders in Central Appalachia, United States
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Two new salamanders of the genus Desmognathus
inferredcites →https://doi.org/10.5281/zenodo.16004628openalex-snapshot
Genetic Evidence for Premature Taxonomic Inflation in Middle Eastern Tortoises
inferredcites →https://doi.org/10.5962/bhl.title.49905openalex-snapshot
Biochemical evolution in the slimy salamanders of the Plethodon glutinosus Complex in the Eastern United States
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Fast and flexible estimation of effective migration surfaces

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.11646/zootaxa.5270.2.5zenodo-depositor-declared
A systematic revision of the Shovel-nosed Salamander (Plethodontidae: Desmognathus marmoratus), with re-description of the related D. aureatus and D. intermedius
inferred← citeshttps://doi.org/10.11646/zootaxa.5397.4.1zenodo-depositor-declared
Unexpected diversity and co-occurrence of phytotelmic frogs (Guibemantis) around Andasibe, one of the most intensively surveyed amphibian hotspots of Madagascar, and descriptions of three new species
inferred← citeshttps://doi.org/10.1002/ece3.70263openalex-snapshot
Understanding species limits through the formation of phylogeographic lineages
inferred← citeshttps://doi.org/10.1016/j.pld.2025.05.010openalex-snapshot
Phylogenomic insights into Adenophora and its allies (Campanulaceae): Revisiting generic delimitation and hybridization dynamics
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107939openalex-snapshot
Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108061openalex-snapshot
Machine learning approaches delimit cryptic taxa in a previously intractable species complex
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108272openalex-snapshot
A time-calibrated salamander phylogeny including 765 species and 503 genes
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108368openalex-snapshot
Towards the next generation of species delimitation methods: an overview of machine learning applications
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108442openalex-snapshot
Isolation and divergence of Greater Earless Lizards (Phrynosomatidae: Cophosaurus) in western North America support multiple diversification processes and a complex demographic history
inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108554openalex-snapshot
Genomic insights unveil taxonomic incongruities and evolutionary origins of solifuges across the southern Levant
inferred← citeshttps://doi.org/10.1016/j.ympev.2026.108579openalex-snapshot
Phylogenomics of the woodland salamanders (Plethodon): Reticulate evolution and indistinct species boundaries
inferred← citeshttps://doi.org/10.1038/s41437-025-00748-yopenalex-snapshot
Deforestation-induced Hybridization in Philippine Frogs Creates a Distinct Phenotype With an Inviable Genotype
inferred← citeshttps://doi.org/10.1038/s44358-025-00125-xopenalex-snapshot
The species problem evolving in the Anthropocene
inferred← citeshttps://doi.org/10.1093/evolut/qpae009openalex-snapshot
Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group)
inferred← citeshttps://doi.org/10.1093/isd/ixaf044openalex-snapshot
Integrating phylogeography and morphology in Pachygrontha antennata (Heteroptera: Pachygronthidae): toward a new subspecies concept in the genomic era
inferred← citeshttps://doi.org/10.1093/sysbio/syad064openalex-snapshot
River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex
inferred← citeshttps://doi.org/10.1093/sysbio/syae023openalex-snapshot
Caught in the Act: Incipient Speciation at the Southern Limit of Viburnum in the Central Andes
inferred← citeshttps://doi.org/10.1093/sysbio/syae040openalex-snapshot
Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards
inferred← citeshttps://doi.org/10.1093/sysbio/syae053openalex-snapshot
The Limits of the Metapopulation: Lineage Fragmentation in a Widespread Terrestrial Salamander (Plethodon cinereus)
inferred← citeshttps://doi.org/10.1093/sysbio/syaf064openalex-snapshot
Integrating Genomics, Collections, and Community Science to Delimit Species Clarifies the Taxonomy of a Variable Monitor Lizard ( Varanus tristis )
inferred← citeshttps://doi.org/10.1093/sysbio/syag001openalex-snapshot
A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlaf141openalex-snapshot
Mountain speciation driven by high rates of lineage formation and rapid evolution of partial reproductive isolation: insights from a recent radiation of grasshoppers (Orthoptera: Gomphocerinae)
inferred← citeshttps://doi.org/10.1101/2023.10.03.560725openalex-snapshot
Integrating Genomics, Collections, and Community Science to Reveal Speciation in a Variable Monitor Lizard ( Varanus tristis )
inferred← citeshttps://doi.org/10.1111/jbi.14807openalex-snapshot
Next‐generation species delimitation and taxonomy: Implications for biogeography
inferred← citeshttps://doi.org/10.1111/mec.17219openalex-snapshot
Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype
inferred← citeshttps://doi.org/10.1111/mec.70361openalex-snapshot
Inferring Time‐to‐Speciation From Hybrid Zone Analysis Informs Assessments of Taxonomic Inflation
inferred← citeshttps://doi.org/10.11646/zootaxa.5311.4.1openalex-snapshot
Systematic revision of the Spotted and Northern Dusky Salamanders (Plethodontidae: Desmognathus conanti and D. fuscus), with six new species from the eastern United States
inferred← citeshttps://doi.org/10.1186/s12862-025-02442-3openalex-snapshot
Climatic data sources and limitations of ecological niche models impact the estimations of historical ranges and niche overlaps in distantly related Korean salamanders
inferred← citeshttps://doi.org/10.1656/058.025.0301openalex-snapshot
A Disjunct Population of the Three-Lined Salamander (Eurycea guttolineata) in Alachua County, Florida
inferred← citeshttps://doi.org/10.56179/001c.116891openalex-snapshot
The Draft Genome Sequences of 50 Salamander species (Caudata, Amphibia)
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