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Eurycea chamberlaini (Chamberlain's Dwarf Salamander) is a small spelerpine salamander with scant reproductive and life-history data available. Therefore, the objectives of our study were to examine the reproductive life history and population structure of E. chamberlaini from a North Carolina population. From February 2008 to February 2009, monthly collections were made in Craven County, North Carolina. All specimens (n=392) were histologically examined for reproductive life history and population characteristics by month. Overall, male and female E. chamberlaini follow a reproductive cycle similar to other spelerpine species with sperm in the Wolffian ducts of specimens from September to February; however, spermatidogenesis was delayed until August and September with the presence of mature sperm in testes from August through November. We captured 201 female salamanders of which 36 were considered immature. We caught 191 males of which 27 were considered immature. The mean snout-vent length (SVL61 SD) of mature females (27.1362.33 mm) and males (25.8462.03 mm) was statistically different from one another. Females tended to be larger than males from our monthly samples, with a greater proportion of the largest specimens being female. Overall, population structure of E. chamblerlaini appears similar to other coastal plain salamander species. [ABSTRACT FROM AUTHOR]

Aim: A limitation of species distribution models (SDMs) is that species with low sample sizes are difficult to model. Yet, it is often important to know the habitat associations of poorly known species to guide conservation efforts. Techniques have been proposed for modelling species' distributions from a few records, but their performance relative to one another has not been compared. Because these models are built and evaluated with small data sets, sampling error could cause severely biased sampling in environmental space. As a result, SDMs are likely to underpredict geographic distributions given small sample sizes. We perform the first comparison of methods explicitly promoted or developed for predicting the geographic ranges of species with very low sample sizes. Location: North Carolina, USA. Taxon: South Mountains Grey‐cheeked Salamander (Plethodon meridianus). Methods: Using the sparse, existing georeferenced records of P. meridianus, we built SDMs using a range of methods that previous researchers have argued should work for low sample sizes. We then tested each SDM's ability to accurately predict independent survey data that were not georeferenced prior to our study. We compared SDMs using omission error and AUC. Results: Roughly half of the models successfully predicted survey records in the range centre, and all models had high omission error rates in the range exterior. In the range of interior or exterior, the 'ensemble of small models' technique produced SDMs with high omission error rates. Spatial filtering had a negligible impact on model performance. Most, but not all, models outperformed predictions using distance from known populations. Using one of the best‐performing methods, we developed an improved range map of P. meridianus. Main Conclusions: Geographically peripheral populations were difficult to predict for all SDMs, though some methods were clearly inferior for our data set. We recommend that when sample sizes are low, researchers use Maxent with species‐specific model settings. [ABSTRACT FROM AUTHOR]

The Eurycea bislineata complex ("two-lined salamanders") of eastern North America contains six described species, of which three have very similar morphologies and relatively broad geographic distributions, and three have more divergent morphologies with narrow geographic distributions. Recent molecular phylogenetic analyses found that four of the six species in the complex contain deep genetic structure, and that two of the species (E. cirrigera and E. wilderae) are paraphyletic in mitochondrial and nuclear DNA, inferring that current taxonomy does not reflect actual species boundaries in the complex. The member of this complex in the Sandhills physiographic region of south-central North Carolina, USA, is notable for its distinctive coloration and ecology, and a study on allozymic variation published over 30 years ago demonstrated that it is genetically distinct but clustered within the paraphyletic E. cirrigera. This study investigates the taxonomic status of the Sandhills population using morphology, mitochondrial DNA, and a 21-locus nuclear DNA data set to test if the Sandhills taxon represents a local ecomorph that is conspecific with adjacent populations of E. cirrigera, or if it represents a divergent evolutionary lineage that warrants taxonomic recognition. Mitochondrial and nuclear DNA revealed that the Sandhills taxon is genetically distinct and phylogenetically unrelated to adjacent populations of E. cirrigera. Principal components analysis of 316 adult specimens of the Sandhills taxon and the three morphologically similar species in the complex found considerable overlap among these taxa, but pairwise comparisons of heavily loading morphological characters showed that the Sandhills taxon usually has a shorter body, shorter tail, and narrower head. Based on these corroborated lines of evidence, the hypothesis that the Sandhills taxon represents only a local ecomorph is rejected and it is described as a new species. Clarification of the extent of its geographic range (including its possible presence in South Carolina), differentiation of larvae from other members of the complex, and verification of hypothesized narrow zones of hybridization with E. cirrigera at the peripheries of its geographic range are needed. The description of the Sandhills taxon brings the number of endemic salamander species in North Carolina to seven. Integrative taxonomic revisions of the E. bislineata complex, particularly E. cirrigera and E. wilderae, are needed to estimate species diversity and distributions of these salamanders more accurately. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The article focuses on the discovery of a population of Shovel-nosed Salamanders (Desmognathus marmoratus) in Glade Creek, West Virginia, which is a new finding for the Kanawha/New River drainage. Topics include the visual and genetic identification of the salamander species, the unique characteristics of the population, and the possibility of its occurrence in other creeks in the region.

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 dwarf2Edwards 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. [ABSTRACT FROM AUTHOR]

Abstract: 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. [Copyright &y& Elsevier]

This paper addresses the issues raised by McNyset and Blackburn (2006 ) in their response to Stockman et al. (2006 ). Re-evaluation of our published GARP analyses by McNyset and Blackburn showed that a much improved ecological niche model is obtained for predicting the distribution of the trapdoor spider genus Promyrmekiaphila in central/northern California. The improved niche model results in a substantially reduced omission error rate and a predictive model comparable to models obtained using other methods (GLM and BIOCLIM). However, the improved GARP models have a high commission error rate (> 0.75); consequently, the inferences regarding difficulties in modelling non-vagile taxa drawn by Stockman et al. remain valid. Finally, we discuss other relatively minor criticisms of our study raised by McNyset and Blackburn and issues related to the peer review of our original paper. [ABSTRACT FROM AUTHOR]

One of the primary goals of any systematic, taxonomic or biodiversity study is the characterization of species distributions. While museum collection data are important for ascertaining distributional ranges, they are often biased or incomplete. The Genetic Algorithm for Rule-set Prediction (GARP) is an ecological niche modelling method based on a genetic algorithm that has been argued to provide an accurate assessment of the spatial distribution of organisms that have dispersal capabilities. The primary objective of this study is to evaluate the accuracy of a GARP model to predict the spatial distribution of a non-invasive, non-vagile invertebrate whose full distributional range was unknown. A GARP predictive model based on seven environmental parameters and 42 locations known from historical museum records for species of the trapdoor spider genus Promyrmekiaphila was produced and subsequently used as a guide for ground truthing the model. The GARP model was neither a significant nor an accurate predictor of spider localities and was outperformed by more simplistic BIOCLIM and GLM models. The isolated nature of Promyrmekiaphila populations mandates that environmental layers and their respective resolutions are carefully chosen for model production. Our results strongly indicate that, for modelling the spatial distribution of low vagility organisms, one should employ a modelling method whose results are more conducive to interpretation than models produced by a ‘black box’ algorithm such as GARP. [ABSTRACT FROM AUTHOR]

Besides studies on mental glands, research regarding cranial integumentary glands potentially involved in courtship of plethodontid salamanders is scarce. In this study, we examined the cranial glands of Eurycea chamberlaini. Scattered amongst typical mucous and serous glands of the integument, we found simple alveolar glands that reacted positively with the periodic acid-Schiff procedure along the lateral sides of the heads of only male E. chamberlaini during the putative mating season. These glands were identical to the lateral head courtship glands previously described in E. bislineata. External nasal glands of E. chamberlaini were also identical in morphology and histology to those previously described in E. bislineata, with the bulk of the secretory terminals residing behind the orbital cavities and extending anteriorly to where their excretory ducts empty through the integument dorsal to the external nares. We measured external nasal gland length, width, height, and volume and found that the means were greater in males when compared to females except for width, which was not sexually dimorphic. We compared external nasal gland tubular diameter to mental gland tubular diameter (a known secondary sexual structure) throughout the year and found a direct correlation that was significant in males but not for females; thus, hypertrophy of external nasal glands occurs at the same time pheromone production increases in mental glands, supporting a previously proposed hypothesis that external nasal glands are also secondary sexual structures in Eurycea. In culmination, Eurycea from two different complexes possess the same suite of cranial integumentary glands that may be involved in courtship, providing evidence that these glands are possibly ubiquitous across Eurycea. [ABSTRACT FROM AUTHOR]

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.] [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

• Desmognathus contains at least 49 candidate species. • Many traditional morphospecies are polyphyletic. • Many relationships are best described as networks. 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. [ABSTRACT FROM AUTHOR]