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opencc-zeroJul 2022View details →

Resolving higher-level phylogenetic networks with repeated hybridization in a complex of polytypic salamanders (Plethodontidae: Desmognathus)

Repeated hybridization between incipient lineages is a common feature of ecological speciation and ecomorphological diversification. However, computational constraints currently limit our ability to reconstruct network radiations from gene-tree data. Available methods are limited to level-1 networks wherein reticulations do not share edges, and higher-level networks may be non-identifiable in many cases. We present a heuristic method to recover information from higher-level networks across a range of potentially identifiable empirical scenarios, supported by a theorem and success in simulated data. When extrinsic information indicating the location and direction of recent or ancestral hybridization events is available, our method can yield successful estimates of non-level-1 networks, or at least a reduced possible set thereof. We apply this technique to the Pisgah clade of Desmognathus salamanders, which contains four to seven species exhibiting two discrete phenotypes, aquatic "shovel-nosed" and semi-aquatic "black-bellied" forms in the southern Appalachian Mountains of the eastern United States. Phylogenomic data strongly support a single backbone topology with up to five overlapping hybrid edges. These results suggest an unusual mechanism of ecomorphological hybrid speciation, wherein a binary threshold trait causes hybrids to shift between two microhabitat niches, promoting ecological divergence between sympatric hybrids and parentals. This contrasts with other well-known systems in which hybrids exhibit intermediate, novel, or transgressive phenotypes. Geographically proximate populations of both phenotypes exhibit admixture, and at least two black-bellied lineages have been produced via reticulations between shovel-nosed parentals, suggesting complex transmission dynamics. The genetic basis of these phenotypes is unclear and further data are needed to clarify the nature of selection and speciation in the group.

opencc-zeroJul 2022View details →

Salamanders reveal novel trajectories of amphibian MHC evolution

Genes of the Major Histocompatibility Complex (MHC) code for immune proteins that are crucial for pathogen recognition in vertebrates. MHC research in non-model taxa has long been hampered by its genomic complexity that makes the locus-specific genotyping challenging. The recent progress in sequencing and genotyping methodologies allows an extensive phylogenetic coverage in studies of MHC evolution. Here, we analysed the peptide-binding region of MHC class I in 30 species of salamanders from six families representative of Urodela phylogeny. This extensive dataset revealed an extreme diversity of MHC-I in salamanders, both in terms of sequence diversity (ca. 3000 variants) and architecture (2-22 gene copies per species). The signal of positive selection was moderate and consistent between both peptide binding domains, but varied greatly between genera. Positions of positively selected sites mostly coincided with human Peptide Binding Sites, suggesting similar structural properties of MHC-I molecules across distant vertebrate lineages. Finally, we provided evidence for the common intra-exonic recombination at MHC-I and for the role of life-history traits in the processes of MHC-I expansion/contraction. Our study revealed novel evolutionary trajectories of amphibian MHC and it contributes to the understanding of the mechanisms that generated extraordinary MHC diversity throughout vertebrate evolution.

opencc-zeroAug 2022View details →

Data for: Modeling the distribution of the endangered Jemez Mountains salamander (Plethodon neomexicanus) in relation to geology, topography, and climate

The Jemez Mountains salamander (Plethodon neomexicanus; hereafter JMS) is an endangered salamander restricted to the Jemez Mountains in north-central New Mexico, United States. This strictly terrestrial species requires moist surface conditions for mating and foraging. Threats to its current habitat include fire suppression and ensuing severe fires, changes in forest composition, habitat fragmentation, and climate change. Forest composition changes resulting from reduced fire frequency and increased tree density suggest that its current aboveground habitat does not mirror its historically successful habitat regime. We hypothesized that geology and topography might play a significant role in the current distribution of the salamander. We modeled the distribution of the JMS using a machine learning algorithm to assess how geology, topography, and climate variables influence its distribution. Our habitat suitability map reveals low uncertainty in model predictions, and we found slight discrepancies between the designated critical habitat and the most suitable areas for the JMS. Because geological features are important to its distribution, we recommend that geological and topographical data are considered, both during survey design and in the description of localities of JMS records once detected.

opencc-zeroDec 2021View details →

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.

opencc-zeroMay 2024View details →

Hard edges, soft edges, and species range evolution: A genomic analysis of the Cumberland Plateau salamander

Aim: Gene flow from central to edge populations is thought to limit population growth at range edges by constraining local adaptation. In this study, we explore the thesis that range edges can differ in their dynamics and be either "hard" (e.g. a river) or "soft" (e.g. ecological gradients). We hypothesize that soft edge populations will have smaller effective population sizes than central populations and that gene flow will be greater from the center to the edge than vice versa. Conversely, we hypothesize that hard edge populations should have similar effective population sizes to central populations and that gene flow will be equal between the two. Location: Kentucky, West Virginia, and Virginia, USA. Taxon: Plethodon kentucki (Caudata: Plethodontidae). Methods: We evaluated landscape suitability using an ecological niche model, then we compared gene flow and effective population sizes between edge and central populations and quantified gene flow between populations. Finally, we characterized landscape genetic variation, testing for isolation by distance and isolation by environment. Results: We found continuously decreasing habitat quality along soft edges, with hard edges more variable. Additionally, we found that soft edges had lower effective population sizes than central populations and that gene flow was greater from the center of the range to the soft edges than the reverse. In hard edges, by contrast, we found effective population sizes in edge populations were similar to central populations, with relatively equal gene flow in both directions. Main conclusions: Understanding why species have range limits is central to investigations of the structure of biodiversity, yet the evolutionary dynamics of range edges remain poorly understood. We show that within a single species with a small range, the evolutionary dynamics operating at range boundaries may depend on the nature of the boundary.

opencc-by-4.0Dec 2018View details →

Fig. 2 in New sites of the endangered Marmaris Salamander, Lyciasalamandra flavimembris (Mutz and Steinfartz 1995), (Caudata: Salamandridae) from Muğla, Turkey

Fig. 2. General view of new site habitats. [A]. Arıcılar, [B,C]. Selimiye [D]. Taşlıca.

opencc-by-4.0Mar 2022View details →

Fig. 5. MaxEnt habitat suitability maps for L in Distribution and habitat suitability of two neighboring Lycian salamanders

Fig. 5. MaxEnt habitat suitability maps for L. flavimembris (a) and L. fazilae (b).

opencc-by-4.0Mar 2022View details →

Fig. 1 in Distribution and habitat suitability of two neighboring Lycian salamanders

Fig. 1. Study area and distributions of presence data for L. flavimembris and L. fazilae.

opencc-zeroDec 2016View details →

Data from: Natural history constrains the macroevolution of foot morphology in European plethodontid salamanders

The natural history of organisms can have major effects on the tempo and mode of evolution, but few examples show how unique natural histories affect rates of evolution at macroevolutionary scales. European plethodontid salamanders (Plethodontidae: Hydromantes) display a particular natural history relative to other members of the family. Hydromantes commonly occupy caves and small crevices, where they cling to the walls and ceilings. On the basis of this unique and strongly selected behavior, we test the prediction that rates of phenotypic evolution will be lower in traits associated with climbing. We find that, within Hydromantes, foot morphological traits evolve at significantly lower rates than do other phenotypic traits. Additionally, Hydromantes displays a lower rate of foot morphology evolution than does a nonclimbing genus, Plethodon. Our findings suggest that macroevolutionary trends of phenotypic diversification can be mediated by the unique behavioral responses in taxa related to particular attributes of their natural history.

opencc-zeroOct 2019View details →

Data from: Mortality and morphology in egg masses of unisexual and Jefferson Salamanders

Unisexual Ambystoma salamander egg masses have often been observed to exhibit very high rates of embryo mortality. The ecological consequences and underlying mechanisms are of great concern to researchers and managers studying these and other members of the species complex, all of which are listed as rare species throughout much of their range. Substantial embryo mortality is commonly used by field ecologists as an indicator that unisexual salamanders are present in a pond; egg masses of unisexual salamanders appear otherwise very similar to those of A. jeffersonianum (Jefferson Salamander). Early researchers suggested that elevated mortality among unisexual salamanders was due to lack of fertilization caused by sperm limitation. However, recent work has suggested that embryo failure is due to genetic errors particular to the unisexual salamander lineage. Our goals in this study were to (1) identify when during development embryonic mortality occurs in unisexual salamanders, and (2) to develop a morphological metric to distinguish egg masses of unisexual and Jefferson salamanders. Collecting from sites across western Massachusetts, we reared 356 eggs from 11 egg masses of known species identity in the laboratory, examined field photographs of 96 egg masses of known species identity (based on mitochondrial sequencing and 6 microsatellite alleles), and examined 757 field photographs of egg masses of unknown species identity. We developed a simple, scale-independent metric to distinguish Jefferson Salamander egg masses from those of co-occurring unisexual salamanders. Among developing embryos beyond the earliest stages, we found no difference in mortality rates between unisexual salamanders and Jefferson Salamanders. However, we observed a large pulse of embryo mortality in the earliest stages of development, followed by a trickle of additional mortality at later stages. Our results suggest that the primary cause of embryo mortality in Massachusetts populations of unisexual salamanders involves failure of embryos to initiate development.

opencc-zeroJul 2021View details →

Microgeographic divergence of functional responses among salamanders under antagonistic selection from apex predators

A predator's functional response determines predator–prey interactions by describing the relationship between the number of prey available and the number eaten. Its shape and parameters fundamentally govern the dynamic equilibrium of predator–prey interactions and their joint abundances. Yet, estimates of these key parameters generally assume stasis in space and time and ignore the potential for local adaptation to alter feeding responses and the stability of trophic dynamics. Here, we evaluate if functional responses diverge among populations of spotted salamander ( Ambystoma maculatum ) larvae that face antagonistic selection on feeding strategies based on their own risk of predation. Common garden experiments revealed that spotted salamander from ponds with varying predation risks differed in their functional responses, suggesting an evolutionary response. Applying mechanistic equations, we discovered that the combined changes in attack rates, handling times and shape of the functional response enhanced feeding rate in environments with high densities of gape-limited predators. We suggest how these parameter changes could alter community equilibria and other emergent properties of food webs. Community ecologists might often need to consider how local evolution at fine scales alters key relationships in ways that alter local diversity patterns, food web dynamics, resource gradients and community responses to disturbance.

Figure 71 in The Palaeozoic Ancestry of Salamanders, Frogs and Caecilians

Figure 71. Nested synapomorphies leading from primitive temnospondyls to crown-group anurans.

Figure 61 in The Palaeozoic Ancestry of Salamanders, Frogs and Caecilians

Figure 61. Nested synapomorphies leading to crown-group urodeles.

Figure 20 in The Palaeozoic Ancestry of Salamanders, Frogs and Caecilians

Figure 20. Diagram of the anuran auditory system. Reproduced from Duellman & Trueb (1986).

Figure 35 in The Palaeozoic Ancestry of Salamanders, Frogs and Caecilians

Figure 35. Phylogeny of extant caecilian families. Reproduced from Pough et al. (2004).

Figure 5 in The Palaeozoic Ancestry of Salamanders, Frogs and Caecilians

Figure 5. Phylogeny of salamanders. Reproduced from Wiens et al. (2005).

opencc-zeroDec 2022View details →

Population genomic analyses support sympatric origins of parapatric morphs in a salamander

In numerous clades, divergent sister species have largely non-overlapping geographic ranges. This pattern presumably arises because species diverged in allopatry or parapatry, prior to subsequent contact. Here we provide population-genomic evidence for the opposite scenario: previously sympatric ecotypes that have spatially separated into divergent monomorphic populations over large geographic scales (reverse sympatric scenario). We analyzed a North American salamander (Plethodon cinereus) with two color morphs that are broadly sympatric: striped (redback) and unstriped (leadback). Sympatric morphs can show considerable divergence in other traits, and many Plethodon species are fixed for a single morph. Long Island (New York) is unusual in having many pure redback and leadback populations that are spatially separated, with pure redback populations in the west and pure leadbacks in the east. Previous work showed that these pure-morph populations were genetically, morphologically, and ecologically divergent. Here, we performed a coalescent-based analysis of new data from 88,696 single-nucleotide polymorphisms to address the origins of these populations. This analysis strongly supports the monophyly of Long Island populations and their subsequent divergence into pure redback and pure leadback populations. Taken together, these results suggest that the formerly sympatric mainland morphs separated into parapatric populations on Long Island, reversing the conventional speciation scenario.

opencc-zeroDec 2022View details →

Salamander skin microbiome sample metadata: Variation in amphibian skin microbes

These data are associated with a study that explores variation in microbial communities on western tiger salamander skin (Ambystoma mavortium) through space, time, and across life history stages. Lake water and lake substrate microbiome samples were collected to observe microbial taxa which were disproportionately abundant between salamander skin and the environment. Microbiome samples were collected at two lakes during the summer and fall of 2018, and sampling occurred at each lake every other week. During each sampling event, water quality data were collected at four or five locations within the lake and are associated with microbiome samples collected in the lake's respective regions. For each sample, bacterial and fungal communities were examined through metabarcoding of the 16S and ITS metabarcoding regions, respectively, using Illumina next-generation sequencing. The dataset includes negative control samples to aid in detecting contamination, and the dataset includes mock community samples to aid in validating our bioinformatics methods. Each sample received spike-ins of cross-contamination oligos and synthetic genes to observe cross-contamination during library preparation and to allow for the estimation of absolute microbial abundances, respectively. This dataset includes spatiotemporal, ontogenetic, morphometric, and water quality metadata for microbiome samples along with essential information for processing the DNA sequence data.

opencc-zeroApr 2023View details →

Filial cannibalism leads to chronic nest failure of eastern hellbender salamanders (Cryptobranchus alleganienesis)

These data and code support the results in our accompanying manuscript. In species that provide parental care, parents will sometimes cannibalize their own young. Here, we quantified the frequency of whole-clutch filial cannibalism in a species of giant salamander (eastern hellbender; Cryptobranchus alleganienesis) that has experienced precipitous population declines with unknown causes. We used underwater, artificial nesting shelters deployed across a gradient of upstream forest cover to assess the fates of 182 nests at 10 sites over 8 years. We found strong evidence that nest failure rates increased at sites with low riparian forest cover in the upstream catchment. At several sites, reproductive failure was 100%, mainly due to cannibalism by the caring male. The high incidence of filial cannibalism at degraded sites was not explained by evolutionary hypotheses for filial cannibalism based on adult body condition or low reproductive value of clutches. Instead, larger clutches at degraded sites were most vulnerable to cannibalism. We hypothesize that high frequencies of filial cannibalism of large clutches in areas with low forest cover could be related to changes in water chemistry or siltation that influence parental physiology or that reduce viability of eggs. Importantly, our results identify a possible mechanism contributing to population declines and observed geriatric age structure in this imperiled species.