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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]

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]