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opencc-zeroAug 2020View details →

Datasets for Mixed support for gene flow as a constraint to local adaptation and contributor to the limited geographic range of an endemic salamander

Understanding mechanisms that underlie species range limits is at the core of evolutionary ecology. Asymmetric gene flow between larger core populations and smaller edge populations can swamp local adaptation at the range edge and inhibit further range expansion. However, empirical tests of this theory are exceedingly rare. We tested the hypothesis that asymmetric gene flow can constrain local adaptation and thereby species' range limits in an endemic US salamander (Ambystoma barbouri) by determining if gene flow is asymmetric between the core and peripheries of the species' geographic distribution and testing whether local adaptation is swamped at range edges with a reciprocal transplant experiment. Using putatively neutral loci from populations across three core-to-edge transects that covered nearly the entire species' geographic range, we found evidence for asymmetric, core-to-edge gene flow along western and northern transects, but not along a southern transect. Subsequently, the reciprocal transplant experiment suggested that northern and western edge populations are locally adapted despite experiencing asymmetric gene flow yet have lower fitness in their respective home regions than center populations do. Conversely, southern populations exhibit low deme quality, experiencing high mortality regardless of where they were reared, likely due to harsher edge habitat conditions. Consequently, we provide rare species-wide evidence that local adaptation can occur despite asymmetric gene flow, though migration from the core may prohibit range expansion by reducing fitness in edge populations. Further, our multi-transect study shows that multiple, non-mutually exclusive mechanisms can lead to range limits within a single species.

opencc-zeroSep 2020View details →

Bioaccumulation of the pesticide Imidacloprid in stream organisms and sublethal effects in salamanders in West Virginia

Dataset for the article "Bioaccumulation of the Pesticide Imidacloprid in Stream Organisms and Sublethal Effects on Salamanders." Contains imidacloprid and metabolite concentrations for Desmognathus spp., benthic macroinvertebrates, and stream water. Also contains corticosterone concentration data for Desmognathus spp. and body condition indices for 5 species of stream salamander in relation to water imidacloprid concentrations.Dataset for the article "Bioaccumulation of the Pesticide Imidacloprid in Stream Organisms and Sublethal Effects on Salamanders." Contains imidacloprid and metabolite concentrations for Desmognathus spp., benthic macroinvertebrates, and stream water. Also contains corticosterone concentration data for Desmognathus spp. and body condition indices for 5 species of stream salamander in relation to water imidacloprid concentrations.

opencc-zeroNov 2020View details →

Water-borne and plasma corticosterone are not correlated in spotted salamanders

Water-borne hormone measurement is a noninvasive method suitable for amphibians of all sizes that are otherwise difficult to sample. For this method, containment-water is assayed for hormones released by the animal. Originally developed in fish, the method has expanded to amphibians, but requires additional species-specific validations. We wanted to determine physiological relevance of water-borne corticosterone in spotted salamanders (Ambystoma maculatum) by comparing concentrations to those taken using established corticosterone sampling methods, such as plasma. Using a mixture of field and laboratory studies, we compared water-borne corticosterone levels to other traditional methods of sampling corticosterone for spotted salamander larvae, metamorphs, and adults. Despite multiple attempts, and detecting differences between age groups, we found no correlations between water-borne and plasma corticosterone levels in any age group. Water-borne sampling measures a rate of release; whereas plasma is the concentration circulating in the blood. The unique units of measurement may inherently prevent correlations between the two. These two methods may also require different interpretations of the data and the physiological meaning. We also note caveats with the method, including how to account for differences in body size and life history stages. Collectively, our results illustrate the importance of careful validation of water-borne hormone levels in each species in order to understand its physiological significance.

FIGURE 7 in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 7. Newly recognized holotype (ANSP 1228) of Salamandra fusca Green, 1818 in dorsal (a) and ventral (b) view. Recorded in the ANSP catalogue as "P. cinereus" from "New Jersey" originating with "Dr. Bache, Green Collection." No specimens have been associated with this name historically. In particular, we note 14 apparent costal grooves, hind limbs more robust than forelimbs, and apparently partially healed broken tail, linking it to Green (1818)'s description. Primary type of Desmognathus fuscus (Green, 1818).

FIGURE 9 in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 9. Green (1827a)'s figure (Pls. 1, 2) of the preserved holotypes of Salamandra jeffersoniana Green, 1827a (USNM 3968; see Fig. 10) and S. porphyritica Green, 1827a (unknown disposition; possibly USNM 3840), drawn by T.R Peale and engraved by P.E. Hamm. Notes and legend cropped from original.

FIGURE 4 in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 4. Green (1827a)'s figure (third unnumbered plate) of a "variety" of Salamandra glutinosa Green, 1818, from Washington County, Pennsylvania, drawn by W. Mason and engraved by P.E. Hamm.

FIGURE 3. A in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 3. A poorly preserved specimen (USNM 3738) that we are nevertheless comfortable in assigning to Salamandra bislineata Green, 1818. Referred to by Cope (1889) as the "alcoholic type" from "Western Pennsylvania" collected by "Dr. J. Green," which was followed by Stejneger and Barbour (1917, 1933), but not by Cochran (1961) in her list of USNM type material. Based on Green's collections in western Pennsylvania primarily occurring after 1826, we do not consider this part of the original type series.

FIGURE 6 in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 6. Newly designated lectotype (ANSP 1238) of Salamandra bislineata Green, 1818. Recorded in the ANSP catalogue as "P. cinereus" from "New Jersey" originating with "Dr. Bache, Green Collection." Fowler and Dunn (1917) considered ANSP 695–698 the syntypes, which we here designate as paralectotypes.

FIGURE 2. A in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 2. A specimen (ANSP 900) of Triturus fuscus Rafinesque, 1820 from "Dr. Bache, Green coll.," locality "near Phila.," here designated as the neotype of Salamandra nigra Green, 1818. This name is thus a senior subjective synonym of Triturus fuscus Rafinesque, 1820.

FIGURE 10. A in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 10. A poorly preserved specimen (USNM 3968; ventral view) listed as the "alleged holotype" of Salamandra jeffersoniana Green, 1827. Cope (1868) states that it was received from "Dr. F. Bache," while Yarrow (1882) records it as the "alc. type." from "Dr. J. Green," locality "Western Pennsylvania," which was reiterated by Cope (1889). Comparison with Peale's drawing of the holotype (Green 1827a, Pl. 2; Fig. 9) confirms its identity.

FIGURE 5. A in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 5. A poorly preserved specimen (ANSP 1229) that we are nevertheless comfortable in assigning to Plethodon cinereus (Green, 1818). Fowler (1907) and Fowler and Dunn (1917) had considered the series ANSP 1227–38 from "Dr. Bache, Green Collection," locality "New Jersey" as the syntypes of Salamandra cinerea Green, 1818, but Highton (1962) restricted this to 1232–34 & 37, designating 1232 as the lectotype, rendering the remaining specimens paralectotypes. Thus, this specimen no longer has any name-bearing function.

FIGURE 8. A in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 8. A pencil sketch we suggest is of Salamandra tigrina Green, 1825a by Titian Peale, dated 1819 (Mss.B.P31.15d.150b). This may represent the holotype, which was a living pet of Peale's, and of which Green 1825a notes Peale "has made a very accurate drawing." Courtesy of the American Philosophical Society.

FIGURE 1. A in The herpetological legacy of Jacob Green and the nomenclature of some North American lizards and salamanders

FIGURE 1. A watercolor painting of Salamandra longicauda Green, 1818 by Titian Peale, dated 1819 (Mss.B.P31.15d.149b). This may represent one of Green's original specimens. The margin notes in pencil (cropped from the original) read "4 ¾ inches long," "Pittsg [Pittsburg?] May 1st 1819," and "n° 4." Courtesy of the American Philosophical Society.

opencc-zeroJan 2021View details →

Data from: Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies

Landscape features shape patterns of gene flow among populations, ultimately determining where taxa lay along the continuum between panmixia to complete reproductive isolation. Gene flow can be restricted leading to population differentiation in two non-exclusive ways: "physical isolation", in which geographic distance in combination with the landscape features restricts movement of individuals promoting genetic drift, and "ecological isolation", in which adaptive mechanisms constrain gene flow between different environments via divergent natural selection. In central Iberia, two fire salamander subspecies occur in parapatry across elevation gradients along the Iberian Central System mountains, while in adjacent Mountains of Toledo Region only one of them occurs. By integrating population and landscape genetic analyses, we show a ubiquitous role of physical isolation between and within mountain ranges, with unsuitable landscapes increasing differentiation between populations. However, across the Iberian Central System, we found strong support for a significant contribution of ecological isolation, with low genetic differentiation in environmentally homogeneous areas, but high differentiation across sharp transitions in precipitation seasonality. These patterns are consistent with a significant contribution of ecological isolation in restricting gene flow among subspecies. Overall, our results suggest that ecological divergence contributes to reduce genetic admixture, creating an opportunity for lineages to follow distinct evolutionary trajectories.

opencc-zeroDec 2015View details →

Data from: Cryptic sex? Estimates of genome exchange in unisexual mole salamanders (Ambystoma sp.)

Cryptic sex has been argued to explain the exceptional longevity of certain parthenogenetic vertebrate lineages, yet direct measurements of genetic exchange between sexual and apparently parthenogenetic forms are rare. Female unisexual mole salamanders (Ambystoma sp.) are the oldest known unisexual vertebrate lineage (~5 million years), and one hypothesis for their persistence is that allopolyploid female unisexuals periodically exchange haploid genomes 'genome exchange' during gynogenetic reproduction with males from sympatric sexual species. We test this hypothesis by using genome-specific microsatellite DNA markers to estimate the rates of genome exchange between sexual males and unisexual females in two ponds in NE Ohio. We also test the prediction that levels of gene flow should be higher for 'sympatric' (sexual males present) genomes in unisexuals compared to 'allopatric' (sexual males absent) unisexual genomes. We used a model testing framework in the coalescent-based program MIGRATE-N to compare models where unidirectional gene flow is present and absent between sexual species and unisexuals. As predicted, our results show higher levels of gene flow between sexuals and sympatric unisexual genomes compared to lower (likely artefactual) levels of gene flow between sexuals and allopatric unisexual genomes. Our results provide direct evidence that genome exchange between sexual and unisexual Ambystoma occurs and demonstrate that the magnitude depends on which sexual species are present. The relatively high levels of gene flow suggest that unisexuals must be at a selective advantage over sexual forms so as to avoid extinction due to genetic swamping through genome exchange.

opencc-zeroDec 2014View details →

Data from: The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long-toed salamander (Ambystoma macrodactylum Baird)

The relative importance of ecological versus non-ecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages—such as the distinct genetic groups that make up the ranges of many northern species—represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in maintaining the contact zones between them. In this study, we used tests of niche overlap in combination with ecological niche models to explore the extent of niche divergence between lineages of the long-toed salamander (Ambystoma macrodactylum Baird) species complex and to determine whether contact zones correspond to (divergent) niche limits. We found limited evidence for niche divergence between the different long-toed salamander lineages, substantial overlap in the predicted distribution of suitable climatic space for all lineages and range limits that are independent of niche limits. These results raise questions as to the importance of ecological divergence to the development of this widespread species complex and highlight the potential for non-ecological factors to play a more important role in the maintenance of northern taxa.

opencc-zeroDec 2017View details →

Data from: Salamander climbing behavior varies among species and is correlated with community composition

Species coexistence is often facilitated by behavioral strategies that minimize competition for limited resources. Terrestrial, lungless salamanders (genus Plethodon) coexist in predictable assemblages of body size guilds, but little is known about the behavioral mechanisms that promote such coexistence. Here, we considered the hypothesis that Plethodon salamanders use climbing behavior to reduce competitive interactions, thereby promoting coexistence through spatial partitioning. To explore this hypothesis, we quantified the frequency of climbing behavior at field sites where small-bodied (P. cinereus) and large-bodied (P. glutinosus) species are always present, but an intermediate-bodied species (P. montanus) is either absent, introduced, or native. We observed that climbing behavior varied among size guilds so that the smallest species climbed most frequently, followed by the intermediate, and then the large species. Further, we identified several correlates of climbing behavior that may be shaped by intraspecific and interspecific competition. Climbing frequency was positively correlated with intraspecific competition and negatively correlated with interspecific competition in the small species, unrelated to competition in the intermediate species, and positively correlated with interspecific competition in the large species. Our results suggest that Plethodon size guilds might differentially utilize climbing behavior to facilitate spatial partitioning in dense populations and communities. Further, we show how competition intensity can shape the behavior of cohabitating species, and ultimately provide insight into how behavioral plasticity and microhabitat partitioning can promote species coexistence.

opencc-zeroDec 2012View details →

Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci

The analysis of diverse data sets can yield different phylogenetic estimates that challenge systematists to explain the source of discordance. The mole salamanders (family Ambystomatidae) are a classic example of this phylogenetic conflict. Previous attempts to resolve the ambystomatid species tree using allozymic, morphological, and mitochondrial sequence data have yielded different estimates, making it unclear which data source best approximates ambystomatid phylogeny and which ones yield phylogenetically inaccurate reconstructions. To shed light on this conflict, we present the first multi-locus DNA sequence-based phylogenetic study of the Ambystomatidae. We utilized a range of analyses, including coalescent-based methods of species-tree estimation that account for incomplete lineage sorting within a locus and concordance-based methods that estimate the number of sampled loci that support a particular clade. We repeated these analyses with the removal of individual loci to determine if any locus has a disproportionate effect on our phylogenetic results. Collectively, these results robustly resolved many deep and relatively shallow clades within Ambystoma, including the placement of A. gracile and A. talpoideum as the sister clade to a clade containing all remaining ambystomatids, and the placement of A. maculatum as the sister lineage to all remaining ambystomatids excluding A. gracile and A. talpoideum. Both Bayesian coalescent and concordance methods produced similar results, highlighting strongly supported branches in the species tree. Furthermore, coalescent-based analyses that excluded loci produced overlapping species-tree posterior distributions, suggesting that no particular locus – including mtDNA – disproportionately contributed to our species-tree estimates. Overall, our phylogenetic estimates have greater similarity with previous allozyme and mitochondrial sequence-based phylogenetic estimates. However, intermediate depths of divergence in the ambystomatid species tree remain unresolved, potentially highlighting a region of rapid species radiation or a hard polytomy, which limits our ability to comment on previous morphologically-based taxonomic groups.

opencc-zeroDec 2014View details →

Data from: Effects of mountaintop removal mining and valley filling on the occupancy and abundance of stream salamanders

Human-induced land-use changes are among the primary causes of ecosystem degradation and biodiversity loss. Across central Appalachia (USA), mountaintop removal mining and valley filling (MTR/VF) is the prevailing form of land-use change and represents a stressor to stream ecosystems. Salamanders are the dominant vertebrate in Appalachian headwater streams. Thus, we addressed the question: Is salamander occupancy and conditional abundance reduced in streams impacted by MTR/VF? We conducted repeated counts of adult and larval salamanders within 10-m reaches in 11 valley-filled streams and 12 reference streams in south-eastern Kentucky. Relationships between occupancy, conditional abundance, and site type (MTR/VF vs. reference) were modelled using the hurdle model (Ecology, 94, 2013 and 1472), where occupancy is modelled separately from abundance while accounting for differences in per-individual detection probabilities among groups. We found mean occupancy probabilities were >0·85 for all groups in reference reaches, whereas mean occupancy probabilities were relatively lower in MTR/VF reaches (ranging from 0·23 to 0·66). Posterior means of the difference in occupancy between site types were negative across all groups, although MTR/VF stream reaches were at least 95% less likely to be occupied by spring salamander Gyrinophilus porphyriticus, adult southern two-lined salamander Eurycea cirrigera and larval dusky salamanders Desmognathus compared to reference reaches. Posterior means of the difference in conditional abundance between MTR/VF and reference stream reaches were negative across all groups; 95% credible interval for difference in conditional abundance covered zero for only one species (red salamander Pseudotriton ruber). After adjusting for goodness-of-fit, point estimates of differences in occupancy and conditional abundance still remained below zero for most species. Additionally, MTR/VF reaches had higher ion concentrations, total organic carbon and specific conductance compared to reference reaches. Synthesis and applications. Our study concludes that mountaintop removal mining and valley filling (MTR/VF) reduces salamander occupancy and conditional abundance. Although the potential mechanisms responsible for reduction are numerous, our findings suggest a change in the current regulatory framework is needed to offset the impacts of MTR/VF on stream ecosystems and biota. Reclamation techniques that enhance conditions for vegetative succession within catchments may improve habitat on reclaimed surface mines.