A Dataset of Amphibian Species in U.S. National Parks.

National parks and other protected areas are important for preserving landscapes and biodiversity worldwide. An essential component of the mission of the United States (U.S.) National Park Service (NPS) requires understanding and maintaining accurate inventories of species on protected lands. We describe a new, national-scale synthesis of amphibian species occurrence in the NPS system. Many park units have a list of amphibian species observed within their borders compiled from various sources and available publicly through the NPSpecies platform. However, many of the observations in NPSpecies remain unverified and the lists are often outdated. We updated the amphibian dataset for each park unit by collating old and new park-level records and had them verified by regional experts. The new dataset contains occurrence records for 292 of the 424 NPS units and includes updated taxonomy, international and state conservation rankings, hyperlinks to a supporting reference for each record, specific notes, and related fields which can be used to better understand and manage amphibian biodiversity within a single park or group of parks.

Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype.

Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.

A systematic revision of the Shovel-nosed Salamander (Plethodontidae: Desmognathus marmoratus), with re-description of the related D. aureatus and D. intermedius.

Shovel-nosed Salamanders, Desmognathus marmoratus (Moore, 1899), were long thought to represent a single species from the southern Appalachian Mountains of the eastern United States, ranging from northeastern Georgia to extreme southwestern Virginia. These populations have a highly derived ecomorphology, being fully aquatic with a specialized flattened and elongated phenotype adapted to rocky riffle zones in fast-flowing, high-gradient mountain streams. Because of this, they were originally described in a separate genus, Leurognathus Moore, 1899. Four additional species or subspecies were described from 1928-1956 based on regional geographic variation in phenotype before being synonymized with L. marmoratus in 1962, which was reassigned to Desmognathus in 1996. Molecular analyses subsequently revealed four distinct candidate lineages in two distantly related clades, which were recently re-delimited into three species. These are D. aureatus (Martof, 1956) from northeastern Georgia, D. intermedius (Pope, 1928) from western North Carolina, and D. marmoratus from northwestern North Carolina. We provide a systematic revision of these taxa, which do not represent a natural group but instead exhibit convergent phenotypes across multiple species, potentially driven by ancient episodes of adaptive introgression between ancestral lineages. Our recent fieldwork revealed an astonishingly disjunct and morphologically distinct population of D. marmoratus in the New River Gorge of West Virginia, which were previously confused with D. kanawha Pyron and Beamer, 2022. This locality is ~120 airline km away from the nearest populations of D. marmoratus in Virginia. No Shovel-nosed Salamanders have ever been found in the New River drainage during our extensive previous explorations or credibly reported in museum specimens or the literature. Additional cryptic populations of these taxa may remain.

Systematic revision of the Spotted and Northern Dusky Salamanders (Plethodontidae: Desmognathus conanti and D. fuscus), with six new species from the eastern United States.

Spotted and Northern Dusky Salamanders (Desmognathus conanti and D. fuscus) have a long and complex taxonomic history. At least 10 other currently recognized species in the genus were either described from populations previously considered D. fuscus, described as or later considered subspecies thereof, or later considered synonyms thereof, before ultimately being recognized as distinct. Recent molecular analyses have also revealed extensive cryptic diversity within both species, which are polyphyletic assemblages of 13 distinct mitochondrial lineages with 5.7-10.3% uncorrected 'p' distances in the COI barcode locus. Based on phylogenomic data and population-clustering analyses considering admixture between lineages, 11 candidate species were circumscribed by recent authors. Those within D. conanti are also ecomorphologically variable, comprising both large, robust, keel-tailed populations, and small, gracile, round-tailed forms. Evaluating their distinctiveness based on genetic, geographic, and morphological evidence, we conclude that six of the candidates represent new species: Desmognathus anicetus sp. nov., D. bairdi sp. nov., D. campi sp. nov., D. catahoula sp. nov., D. lycos sp. nov., and D. tilleyi sp. nov. Consequently, we recognize eight total species from populations formerly associated with the nominal species D. conanti and D. fuscus, the re-delimited concepts of which also contain additional phylogeographic lineage diversity that may represent further distinct species. In addition to existing mitochondrial and nuclear phylogenetic, network, and clustering results, we present preliminary analyses of linear morphometrics to bolster diagnostic specificity based on phenotypic characteristics. These changes stabilize the previously paraphyletic taxonomy of species-level lineages within Desmognathus, though additional cryptic diversity may exist both within the species considered here, and elsewhere in the genus.

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

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 hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large data sets. Integrative taxonomy can, therefore, reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We discover 2 geographic genetic clusters, for which demographic and spatial models of ecology and gene flow provide robust support for ecogeographic speciation despite limited phenotypic divergence. These data are integrated under evolutionary mechanisms (e.g., spatially localized gene flow with reduced migration) and reflected in emergent properties expected under models of reinforcement (e.g., ethological isolation and selection against hybrids). Their genetic divergence is prima facie evidence for species-level distinctiveness, supported by speciation models and divergence along axes such as behavior, geography, and climate that suggest an ecological basis with subsequent reinforcement through prezygotic isolation. As data sets grow more comprehensive, species-delimitation models can be tested, rejected, or corroborated as explicit speciation hypotheses, providing for reciprocal illumination of evolutionary processes and integrative taxonomies. [Desmognathus; integrative taxonomy; machine learning; species delimitation.].

A nomenclatural and taxonomic review of the salamanders (Urodela) from Holbrooks North American Herpetology.

John Edwards Holbrook published North American Herpetology in 11 volumes from 18361842, 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 (Philadelphia), Museum of Comparative Zoology (Cambridge), and Musum national dHistoire naturelle (Paris), six of which are types. We identified four other specimens figured by Holbrook in the MNHN and National Museum of Natural History (Washington), all of which are types from descriptions by other authors. We designate lectotypes for S. porpyhritica Green, 1827 (USNM 3840; reversing neotype MCZ A-35778), Salamandra gutto-lineata Holbrook, 1838a (ANSP 716), S. auriculata Holbrook, 1838b (MNHN-RA 0.4675), S. maculo-quadrata Holbrook, 1840 (ANSP 821), S. granulata De Kay in Holbrook, 1842e (USNM 3981), S. quadridigitata Holbrook, 1842e (ANSP 490; reversing neotype UF 178833), and Plethodon variolosum Dumril, Bibron, and Dumril, 1854 (MNHN-RA 0.4666). Allocation of S. auriculata Holbrook, 1838b, S. Haldemani Holbrook, 1840, and P. variolosum Dumril, Bibron, and Dumril, 1854 is still ambiguous. We consider S. maculo-quadrata Holbrook, 1840 to be a junior subjective synonym of S. fusca Green, 1818; no valid name has ever been applied to Black-bellied Salamanders (Desmognathus sp. quadramaculatus) at the species level, and up to five candidate species require new names. Additional discoveries of data and specimens pertaining to Holbrooks names may remain to be made among his surviving papers and collections.

A new, narrowly endemic species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus) from the Gulf Coastal Plain of Mississippi and Alabama.

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. Some populations of the new species were historically referred to as D. auriculatus, a polyphyletic assemblage of at least three species in the Atlantic and Gulf Coastal Plain from Texas to North Carolina. Populations of D. auriculatus from the Gulf Coastal Plain in Louisiana and Mississippi were recently described as D. valentinei. The new species includes populations that were tentatively referred to D. valentinei, but we find it is morphologically, genetically, and geographically distinct. It is smaller, has a more defined dorsal color pattern, more irregular whitish portholes in up to three rows on the lateral surfaces of the body and tail, and a brighter orange or yellowish orange postocular stripe. At present, the new species is known from only six extant populations in the lower Pascagoula, Escatawpa, and Mobile drainages. The latter represents a distinct phylogeographic lineage. We also refer a historical collection from the northeastern side of the Mobile-Tensaw River Delta to this species, suggesting a much broader range in the past. We suspect that more populations remain to be discovered in the area, and their potential species-level distinctiveness should be tested further. This discovery increases knowledge of the biodiversity in the southeastern United States Coastal Plain, a candidate region meeting the global criteria for a biodiversity hotspot, and underscores the amount of cryptic diversity likely remaining to be discovered and described in Nearctic salamanders.

Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones.

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 groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding (i) species-level diversity, (ii) hybridization and admixture, and (iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early-diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation.

Allocation of Salamandra auriculata Holbrook, 1838, with a new species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus) from the Atlantic Coastal Plain.

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 that could not be located by later authors. Recent workers have been unable to locate or verify swamp-dwelling populations from east Texas and western Louisiana, which appear to be extirpated and may not have represented a distinct taxon from co-occurring lineages of D. conanti. Recent molecular phylogenies have supported at least four distinct species-level taxa within D. auriculatus. Populations from the Gulf Coastal Plain in eastern Louisiana, Mississippi, and southwestern Alabama were recently described as D. valentinei Means, Lamb, and Bernardo, 2017 and D. pascagoula Pyron, O'Connell, Lamb, and Beamer, 2022. This leaves two remaining species-level lineages with uncertain taxonomy and nomenclature: D. auriculatus A (Alabama, Florida, and Georgia), and D. auriculatus B/C (Georgia, South Carolina, and North Carolina), both of which occur near the type locality. We recently located a specimen at the Muséum national d'Histoire naturelle in Paris (MNHN 0.4675) that we concluded is one of Holbrook's syntypes and designated it as the lectotype, but without allocation. Here, we use linear morphometrics to confidently allocate it to D. auriculatus A, bolstered by examination of three historical topotypic collections. This requires a new name for D. auriculatus B/C, which we describe as D. valtos sp. nov. (suggested common name: Carolina Swamp Dusky Salamander) from Otter Creek, Craven County, North Carolina. Other related and sympatric species of Desmognathus remain to be described from the Atlantic Coastal Plain and adjacent Piedmont of the southeastern United States.

Systematics of the Ocoee Salamander (Plethodontidae: Desmognathus ocoee), with description of two new species from the southern Blue Ridge Mountains.

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. abditus, D. carolinensis, D. ochrophaeus, D. ocoee, and D. orestes, which do not form a clade but are instead scattered across the phylogeny of Desmognathus. A Coastal Plain species with a mountain dusky phenotype (D. apalachicolae) is also nested within a lineage related to D. ocoee. Within the current concept of D. ocoee, there are up to 8 genetically distinct geographic lineages which display significantly different but substantially overlapping morphologies. Recent studies have suggested that as many as six species could reasonably be delimited based on genetic data. We evaluate the strength of that evidence here and find support for five species in the D. apalachicolae + D. ocoee group. The first is D. apalachicolae in essentially its originally described form from the Coastal Plain. The second and third are D. adatsihi sp. nov. and D. balsameus sp. nov., endemic to the Great Smoky/Plott Balsam and Great Balsam Mountains, respectively. The fourth corresponds to the resurrected D. perlapsus for populations from the Alarka and Cowee Mountains in North Carolina, through the Chattahoochee River drainage to the Fall Line in the Piedmont of Georgia and Alabama. The fifth is D. ocoee, here restricted to populations in the Nantahala and Unicoi Mountains and southernmost Blue Ridge escarpment, along with previously recognized populations from the Cumberland Escarpment and Cumberland Plateau of south-central Tennessee and northeastern Alabama. This taxon concept of D. ocoee includes three deeply divergent geographic genetic segments that hybridize across two contact zones, while D. apalachicolae may be nested within some southern Blue Ridge populations of D. ocoee. The resurrected form of D. perlapsus also exhibits some admixture with the newly restricted D. ocoee. While this taxonomic arrangement is robust and stably derived from mitochondrial, morphological, and nuclear data, more sophisticated future analyses sampling additional populations and loci to estimate relationships may reach more subtle conclusions regarding the identity of some lineages within D. ocoee.

The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders.

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 a series of nine papers on lizards, salamanders, and snakes, authoring the original description of several well-known species of salamanders from the eastern United States. Many of his names are ambiguous; some have been adjudicated by the ICZN, while others are currently treated as nomina dubia. Here, we review all of Green's publications, report on newly re-discovered or re-interpreted material from several major natural history collections, and resolve most if not all remaining issues through a series of taxonomic actions. In particular, we first designate a neotype for Salamandra nigra Green, 1818. We then place S. sinciput-albida Green, 1818 and S. frontalis Gray in Cuvier, 1831 in synonymy with S. scutata Temminck in Temminck Schlegel, 1838 and invoke Reversal of Precedence under Article 23.9 to designate them nomina oblita. We also designate a lectotype for S. bislineata Green, 1818. Finally, we resurrect the name S. fusca Green, 1818 as the valid name for the species Desmognathus fuscus, assuming priority over Triturus fuscus Rafinesque, 1820, designating S. fusca Laurenti, 1768 a nomen oblitum, and placing S. nigra Green, 1818 in synonymy. While Green's herpetological legacy is not as expansive as that of some of his successors such as Holbrook, he is nonetheless a foundational early worker in salamanders, having described some of the most-studied species in the world.

Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades.

Dusky salamanders (Desmognathus) constitute a large, species-rich group within the family Plethodontidae, and though their systematic relationships have been addressed extensively, most studies have centered on particular species complexes and therefore offer only piecemeal phylogenetic perspective on the genus. Recent work has revealed Desmognathus to be far more clade rich-35 reciprocally monophyletic clades versus 22 recognized species-than previously imagined, results that, in turn, provide impetus for additional survey effort within clades and across geographic areas thus far sparsely sampled. We conceived and implemented a sampling regime combining level IV ecoregions and independent river drainages to yield a geographic grid for comprehensive recovery of all genealogically exclusive clades. We sampled over 550 populations throughout the distribution of Desmognathus in the eastern United States of America and generated mitochondrial DNA sequence data (mtDNA; 1,991 bp) for 536 specimens. A Bayesian phylogenetic reconstruction of the resulting haplotypes revealed forty-five reciprocally monophyletic clades, eleven of which have never been included in a comprehensive phylogenetic reconstruction, and an additional three not represented in any molecular systematic survey. Although general limitations associated with mtDNA data preclude new species delineation, we profile each of the 45 clades and assign names to 10 new clades (following a protocol for previous clade nomenclature). We also redefine several species complexes and erect new informal species complexes. Our dataset, which contains topotypic samples for nearly every currently recognized species and most synonymies, will offer a robust framework for future efforts to delimit species within Desmognathus.

Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus).

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 behavior. Only 22 species are described, 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 "candidate species" and multiple paraphyletic taxa presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods do not estimate fully resolved relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in Desmognathus may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.

Digits lost or gained? Evidence for pedal evolution in the dwarf salamander complex (Eurycea, Plethodontidae).

Change in digit number, particularly digit loss, has occurred repeatedly over the evolutionary history of tetrapods. Although digit loss has been documented among distantly related species of salamanders, it is relatively uncommon in this amphibian order. For example, reduction from five to four toes appears to have evolved just three times in the morphologically and ecologically diverse family Plethodontidae. Here we report a molecular phylogenetic analysis for one of these four-toed lineages--the Eurycea quadridigitata complex (dwarf salamanders)--emphasizing relationships to other species in the genus. A multilocus phylogeny reveals that dwarf salamanders are paraphyletic with respect to a complex of five-toed, paedomorphic Eurycea from the Edwards Plateau in Texas. We use this phylogeny to examine evolution of digit number within the dwarf-Edwards Plateau clade, testing contrasting hypotheses of digit loss (parallelism among dwarf salamanders) versus digit gain (re-evolution in the Edwards Plateau complex). Bayes factors analysis provides statistical support for a five-toed common ancestor at the dwarf-Edwards node, favoring, slightly, the parallelism hypothesis for digit loss. More importantly, our phylogenetic results pinpoint a rare event in the pedal evolution of plethodontid salamanders.

Dusky salamanders (Desmognathus, Plethodontidae) from the Coastal Plain: multiple independent lineages and their bearing on the molecular phylogeny of the genus.

Recent phylogenetic reassessment of the lungless salamanders (Plethodontidae) confirmed a major life-history reversal-from direct development to an aquatic larval stage-in the dusky salamanders (Desmognathus) of eastern North America. This reversal initiated high rates of lineage accumulation, reputedly generating the species richness and ecological breath that now characterize Desmognathus. Certain important aspects of the radiation, e.g., ecomorphological evolution, have been identified through intense sampling effort of Appalachian Highland lineages. However, the research preoccupation on montane species has left overlooked a significant component of dusky salamander distribution-the Coastal Plain. We present the first molecular phylogeny for Desmognathus to incorporate extensive coverage from the Atlantic and Gulf coastal plains. We examined 38 Coastal Plain populations in conjunction with 45 additional populations, representing 16 of the 19 nominal species. Bayesian analysis of 88 mitochondrial cox1 haplotypes diagnosed eight independent population lineages within the Coastal Plain, a number at odds with the region's three currently recognized species. Desmognathus has apparently experienced a complex biogeographic history in this physiographic region, one involving multiple invasions and several ecological transitions from lotic to lentic habitats.