R. Alexander Pyron's research while affiliated with George Washington University and other places

Publications (180)

Article
A great deal of macroevolutionary research on extinction has focused on large-scale processes, particularly mass episodes. In contrast, many recent conservation studies focus on Anthropocene dynamics at the population level. We discuss three ways in which a synthesis between these perspectives might illuminate hidden assumptions of value and reveal...
Article
The “mountain” dusky is a charismatic ecomorph of Dusky Salamander (Desmognathus): smaller (~20–50mm SVL), more terrestrial and montane woodland species, typically with round tails and extremely variable, often colorful patterns. Originally considered a single species (D. ochrophaeus), populations across the Appalachians are now divided into D. abd...
Article
Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases; a h...
Article
Most swamp-dwelling dusky salamanders of the genus Desmognathus from the Coastal Plain were long treated as a single species (Desmognathus auriculatus) ranging from east Texas to southeastern Virginia. This taxon concept was based on the name Salamandra auriculata Holbrook, 1838 with type locality Riceboro, Liberty County, Georgia and a type series...
Article
To be available under the International Code of Zoological Nomenclature, nomina erected after 1930 must “be accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (Article 13.1.1). For many so-called ‘cryptic’ species, this may prove difficult when relying on external morphology. Ye...
Article
We address here a few nomenclatural problems concerning some salamander nomina of the plethodontid genus Desmognathus Baird, 1850: the identification of the scriptores (first users) of aponyms (subsequent spellings) in cases of primary homonymy; the validity of airesies (first reviser actions) in special cases; and the validity of neotype designati...
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Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thin...
Article
The translation of scientific data, analyses, and conclusions into public policy and social action almost always contains an implication of the investigator's ethics and values. Direct statements of these values are often deeply considered, but the ethical implications of structural constraints and upstream analytical choices are often hidden. This...
Article
Hemipenial characteristics have historically provided a wealth of comparative morphological characters for the systematic classification of snakes. However, the organs remain poorly known in many groups, particularly tropical and burrowing lineages. Here, we report on hemipenial morphology for 12 species from five genera from the family Uropeltidae...
Article
John Edwards Holbrook published North American Herpetology in 11 volumes from 1836–1842, authoring the first accounts of numerous amphibians and reptiles from the eastern and central United States, including 32 salamanders (Urodela). We reviewed these and located 51 extant salamander specimens from Holbrook in the Academy of Natural Sciences (Phila...
Article
We describe a new, narrowly endemic species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus pascagoula sp. nov.) from the Gulf Coastal Plain of southeastern Mississippi and southwestern Alabama based on linear morphometrics, mitochondrial DNA, and single nucleotide polymorphisms from 881 loci produced using genotype-by-sequencing....
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Species that went extinct prior to the genomic era are often considered out-of-reach for modern phylogenetic studies. This is particularly limiting for conservation studies, as genetic data from such taxa may be key to understanding extinction risks and causes of decline that can inform the management of related, extant populations. Fortunately, co...
Preprint
Species-level taxonomy is derived from methodological sources (data and techniques) that assess the existence of spatio-temporal evolutionary lineages via various species concepts. These concepts determine if observed lineages are independent given a particular methodology supposedly connected to ontology, which relates the metaphysical concept to...
Article
Full-text available
Abstract Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other group...
Article
Here, we provide updates to our recent paper reviewing the taxonomy and nomenclature of the Eastern ratsnakes (Pantherophis obsoletus complex, Colubridae, Serpentes). Specifically, we clarify that Coluber alleghaniensis Holbrook, 1836 is a subjective, rather than objective, senior synonym of Elaphis holbrookii Duméril, Bibron & Duméril, 1854. Contr...
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The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns – but whether these factors also contribute to modern extinction risk is lar...
Article
Just after the publication of our paper (Dubois et al. 2021), we discovered that, in Table 1, pages 443 and 444 are identical, and the actual page 443 is missing. We here provide this page, and we took this opportunity to correct a few other errors in this paper. We provide below corrections only in the case of misspellings or other errors that may...
Article
Continental mountain areas cover <15% of global land surface, yet these regions concentrate >80% of global terrestrial diversity. One prominent hypothesis to explain this pattern proposes that high mountain diversities could be explained by higher diversification rates in regions of high topographic complexity (HTC). While high speciation in mounta...
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Squamates (lizards, snakes, and their kin such as amphisbaenians, or worm lizards) represent the world's most diverse clade of terrestrial vertebrates with 11,000 described extant species, representing key components in many of the world's most diverse ecosystems. With an evolutionary history dating back at least to the Middle Triassic at 242 Ma, t...
Article
Although currently most taxonomists claim to adhere to the concept of ‘phylogenetic taxonomy’, in fact most of the zoological classifications currently published are only in part ‘phylogenetic’ but include also phenetic or gradist approaches, in their arbitrary choices of the nodes formally recognised as taxa and in their attribution of ranks to th...
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Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrich...
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Background: The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic and Jurassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~ 25 crocodilian and ~ 360 turtle species now threatened by e...
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Full-text available
The Late Cretaceous saw distinctly endemic dinosaur faunas evolve in the northern and southern hemispheres. The Laurasian continents of North America and Asia were dominated by hadrosaurid and ceratopsian ornithischians, with tyrannosaurs as apex predators. In Gondwanan communities, including Africa, South America, India and Madagascar, titanosauri...
Article
Jacob Green was born in 1790 to a prominent New Jersey family of scholars and theologians. He taught at the College of New Jersey (now Princeton University) from 1818 to 1822 before co-founding Jefferson Medical College (now Thomas Jefferson University) in 1825, where he taught Chemistry until his death in 1841. Between 1818 and 1831, he published...
Article
Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life, but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger datasets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate rec...
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Many animals breed exclusively in plants that accumulate rainwater (phytotelma; e.g., bromeliad, bamboo, fruit husk, and tree hole), to which they are either physiologically or behaviorally specialized for this microhabitat. Of the numerous life‐history modes observed in frogs, few are as striking or potentially consequential as the transition from...
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Frogs of the genus Ptychadena (Boulenger, 1917) have long been identified as harboring cryptic diversity and comprising numerous species-complexes (Largen 1997; Zimkus et al. 2017), and many authors have recognized the particularly high hidden richness in the Ethiopian highlands (Largen 1997; see Largen & Spawls 2010 and refs. within). This cryptic...
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A recent molecular phylogenetic revision of the snake-eyed skinks (genus Panaspis Cope, 1868) uncovered extensive cryptic diversity, including several new species from throughout sub-Saharan Africa. Here, we describe one of these from Ethiopia as Panaspis annettesabinae sp. nov. This description is based on a previous molecular phylogeny and morpho...
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Full-text available
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrich...
Article
Full-text available
Reptiles are still being described worldwide at a pace of hundreds of species a year. While many discoveries are from remote tropical areas, biodiverse arid regions still harbor many novel taxa. Here, we present an updated phylogeny of colubrid snakes from the Western Palearctic by analyzing a supermatrix of all available global snake species with...
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Abstract Allometric constraint is a product of natural selection and physical laws, particularly with respect to body size and traits constrained by properties thereof, such as metabolism, longevity, and vocal frequency. Allometric relationships are often conserved across lineages, indicating that physical constraints dictate scaling patterns in de...
Article
Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and be...
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Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards and snakes, amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a con...
Article
Amphibians are among the most highly threatened lineages, with at least 2,000 species estimated to be in danger of extinction [1, 2]. Alarmingly, another ~2,200 species (~25% of all ~7,900 known species) are data-deficient or Not Evaluated (hereinafter termed data-deficient) by the IUCN [1]. Without an estimate of their status, data-deficient speci...
Preprint
Full-text available
The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~25 crocodilian and ~360 turtle species now threatened by exploitation and habitat loss...
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Full-text available
The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belong...
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1. Species recovery after forest disturbance is a highly studied topic in the tropics, but considerable debate remains on the role of secondary forests as biodiversity repositories, especially regarding the functional and phylogenetic dimensions of biodiversity. Also, studies generally overlook how alpha and beta diversities interact to produce gam...
Article
A recent paper dealing with the systematics of Uropeltidae (Pyron et al. 2016) made several taxonomic changes affecting Sri Lankan species in the genera Platyplectrurus Günther, 1868; Pseudotyphlops Schlegel, 1839; Rhinophis Hemprich, 1820; and Uropeltis Cuvier, 1829. Space precluded a full discussion of those changes, for which there was a wealth...
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We report four new species of geckos of the genus Cnemaspis Strauch, 1887 from the northern Western Ghats, India. Cnemaspis limayei sp. nov. is diagnosable by the following combination of characters: dorsal scales heterogeneous; spine-like tubercles absent on flank; pre-anal scales larger than ventral; 26-27 scale rows across the belly, between low...
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A molecular phylogeny of the Neotropical snail-eating snakes (tribe Dipsadini) is presented including 43 (24 for the first time) of the 77 species, sampled for both nuclear and mitochondrial genes. Morphological and phylogenetic support was found for four new species of Dipsas and one of Sibon , which are described here based on their unique combin...
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Human activities continue to erode the tree of life, requiring us to prioritize research and conservation. Amphibians represent key victims and bellwethers of global change, and the need for action to conserve them is drastically outpacing knowledge. We provide a phylogeny incorporating nearly all extant amphibians (7,238 species). Current amphibia...
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Motivation We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases. Main types...
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We describe a new species, Aspidura ravanai sp. nov., representing the eighth species of the genus known from Sri Lanka. The new species is readily distinguished from all other congeners by its colour pattern, scalation, and genetic distinctiveness. Our molecular results indicated that Aspidura began diversifying in the Miocene approximately 18 Ma,...
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The phylogenetic relationships and biogeographic history of Caribbean island ameivas (Pholidoscelis) are not well-known because of incomplete sampling, conflicting datasets, and poor support for many clades. Here, we use phylogenomic and mitochondrial DNA datasets to reconstruct a well-supported phylogeny and assess historical colonization patterns...
Data
Bayesian and maximum likelihood phylogenies of Pristimantis. Support values are presented as bootstraps and posterior probabilities. (TIFF)
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Full-text available
Geographic barriers and elevational gradients have long been recognized as important in species diversification. Here, we illustrate an example where both mechanisms have shaped the genetic structure of the Neotropical rainfrog, Pristimantis ornatissimus, which has also resulted in speciation. This species was thought to be a single evolutionary li...
Data
The loadings from the three PC axes used for the MMRR analysis. (DOCX)
Data
Results of the MMRR analysis. The analysis uses species’ genetic distances and tests whether geographic and environmental dissimilarity influence genetic differentiation among populations. This alternative analysis uses the raw climatic variables rather than the axes from a PCA analysis. We assessed the 19 bioclimatic variables for multicolinearity...
Data
List of species and corresponding GenBank numbers used to infer the Pristimantis phylogeny. (DOCX)
Article
Globally distributed groups may show regionally distinct rates of diversification, where speciation is elevated given timing and sources of ecological opportunity. However, for most organisms, nearly complete sampling at genomic-data scales to reduce topological error in all regions is unattainable, thus hampering conclusions related to biogeograph...