Polymorphic tetranucleotide microsatellites for Cope's giant salamander (Dicamptodon copei) and Pacific giant salamander (Dicamptodon tenebrosus)

We present primers and amplification conditions for 15 microsatellite loci developed for the Cope's giant salamander (Dicamptodon copei), 14 of which are tetranucleotide repeats. Cross-species amplification revealed 10 of these loci to also be polymorphic in the Pacific giant salamander (Dicamptodon tenebrosus). Several loci produced nonoverlapping allelic ranges between the two species and may be useful in species identification. These polymorphic microsatellite loci are potentially useful for future studies of population genetics in dicamptodontid salamanders.     

Scale‐dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks

The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho giant salamander, Dicamptodon aterrimus, in stream networks of Idaho and Montana, USA. We used microsatellite data to test population structure models by (i) examining hierarchical partitioning of genetic variation in stream networks; and (ii) testing for genetic isolation by distance along stream corridors vs. overland pathways. Replicated sampling of streams within catchments within three river basins revealed that hierarchical scale had strong effects on genetic structure and gene flow. amova identified significant structure at all hierarchical scales (among streams, among catchments, among basins), but divergence among catchments had the greatest structural influence. Isolation by distance was detected within catchments, and in‐stream distance was a strong predictor of genetic divergence. Patterns of genetic divergence suggest that differentiation among streams within catchments was driven by limited migration, consistent with a stream hierarchy model of population structure. However, there was no evidence of migration among catchments within basins, or among basins, indicating that gene flow only counters the effects of genetic drift at smaller scales (within rather than among catchments). These results show the strong influence of stream networks on population structure and genetic divergence of a salamander, with contrasting effects at different hierarchical scales.     

Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae)

Giant salamanders of the genus Dicamptodon are members of the mesic forest ecosystem that occurs in the Pacific Northwest of North America. We estimate the phylogeny of the genus to test several hypotheses concerning speciation and the origin of current species distributions. Specifically, we test competing a priori hypotheses of dispersal and vicariance to explain the disjunct inland distribution of the Idaho giant salamander (D. aterrimus) and to test the hypothesis of Pleistocene speciation of Cope's giant salamander (D. copei) using Bayesian hypothesis testing. We determined that available outgroups were too divergent to root the phylogeny effectively, and we calculated Bayesian posterior probabilities for each of the 15 possible root placements for this four-taxon group. This analysis placed the root on the branch leading to D. aterrimus, indicating that current distribution and speciation of D. aterrimus fit the ancient vicariance hypothesis and are attributable to the orogeny of the Cascade Mountains rather than recent inland dispersal. Furthermore, test results indicate that D. copei is distantly related to other coastal lineages and likely originated much earlier than the Pleistocene. These results suggest that speciation within the genus is attributable to ancient geologic events, while more recent Pleistocene glaciation has shaped genetic variation and distributions within the extant species.     

Postglacial dispersal patterns and mitochondrial genetic structure of the Pyrenean desman (Galemys pyrenaicus) in the northwestern region of the Iberian Peninsula

The genetic structure of small semiaquatic animals may be influenced by dispersal across both rivers and land. The relative importance of these two modes of dispersal may vary across different species and with ecological conditions and evolutionary periods. The Pyrenean desman (Galemys pyrenaicus) is an endemic mammal of the Iberian Peninsula with a strong phylogeographic structure and semiaquatic habits, thus making it an ideal model to study the effects of river and overland dispersal on its genetic structure. Thanks to different types of noninvasive samples, we obtained an extensive sampling of the Pyrenean desman from the northwestern region of the Iberian Peninsula and sequenced two mitochondrial DNA fragments. We then analyzed, using an isolation‐by‐distance approach, the correlation between phylogenetic distances and geographical distances measured along both river networks and land to infer the relative importance of river and overland dispersal. We found that the correlations in the whole area and in a large basin were consistent with an effect of overland dispersal, which may be due to the postglacial colonization of new territories using terrestrial corridors and, possibly, a more extensive fluvial network that may have been present during the Holocene. However, in a small basin, likely to be less influenced by the impact of ancient postglacial dispersal, the correlations suggested significant overall effects of both overland and river dispersal, as expected for a semiaquatic mammal. Therefore, different scales and geographical regions reflect different aspects of the evolutionary history and ecology of this semiaquatic species using this isolation‐by‐distance method. The results we obtained may have crucial implications for the conservation of the Pyrenean desman because they reinforce the importance of interbasin dispersal for this species in the studied area and the need to protect the whole riverine ecosystem, including rivers, upland streams and terrestrial corridors between basins.     

Phylogeographic incongruence of codistributed amphibian species based on small differences in geographic distribution

Codistributed species may display either congruent phylogeographic patterns, indicating similar responses to a series of shared climatic and geologic events, or discordant patterns, indicating independent responses. This study compares the phylogeographic patterns of two similarly distributed salamander species within the Pacific Northwest of the United States: Cope's giant salamander (Dicamptodon copei) and Van Dyke's salamander (Plethodon vandykei). Previous studies of P. vandykei support two reciprocally monophyletic lineages corresponding to coastal populations, located from the Olympic Mountains to the mouth of the Columbia River, and inland populations within the Cascade Mountains. We hypothesized that D. copei would have a congruent phylogeographic pattern to P. vandykei due to similarity in distribution and dependence upon similar stream and stream-side habitats. We test this hypothesis by estimating the phylogeny of D. copei using approximately 1800bp of mitochondrial DNA and comparing it to that of P. vandykei. Sympatric populations of D. copei and of P. vandykei display an identical phylogeographic pattern, suggesting similar responses within their shared distribution. Populations of D. copei occurring outside the range of P. vandykei displayed high levels of genetic divergence from those sympatric to P. vandykei. Overall, phylogeographic patterns between the two species were ultimately incongruent due to the high divergence of these allopatric populations. These results provide an example of codistributed species displaying overall incongruent phylogeographic patterns while simultaneously displaying congruent patterns within portions of their shared geographic distribution. This pattern demonstrates that a simple dichotomy of congruent and incongruent phylogeographic patterns of codistributed species may be too simplistic and that more complex intermediate patterns can result even from minor differences in species' ranges.     

HYBRIDIZATION AND CRYPTIC SPECIES IN DICAMPTODON (CAUDATA: DICAMPTODONTIDAE)

The salamander genus Dicamptodon consists of at least four genetically divergent groups of populations with 10–19 fixed allelic differences (out of 31 loci scored) between populations in alternative groups. One of these groups corresponds to D. copei; the other three until now usually have been considered to belong to the single morphologically homogeneous species D. ensatus. Two instances of geographic contact between genetic units occur in the genus, one between D. copei and “D. ensatus” in northern Oregon and the other between two highly divergent types of “D. ensatus” in coastal northern Calfornia. In the former case no hybridization occurs, while in the latter a narrow hybrid zone has been observed. There appears to be selection against hybrids within this hybrid zone, and introgression beyond the zone is apparently nonexistent. The population groups therefore appear to be genetically independent units, and Dicamptodon is best considered to consist of four species: D. copei, D. ensatus, D. tenebrosus, and D. aterrimus.     

Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations

With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus) in two core regions (Washington State, United States) versus the species' northern peripheral region (British Columbia, Canada) where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a 'flat' landscape), but at the periphery, topography (slope and elevation) had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management.     

Streams over mountains: influence of riparian connectivity on gene flow in the Pacific jumping mouse (Zapus trinotatus)

In species affiliated with heterogeneous habitat, we expect gene flow to be restricted due to constraints placed on individual movement by habitat boundaries. This is likely to impact both individual dispersal and connectivity between populations. In this study, a GIS-based landscape genetics approach was used, in combination with fine-scale spatial autocorrelation analysis and the estimation of recent intersubpopulation migration rates, to infer patterns of dispersal and migration in the riparian-affiliated Pacific jumping mouse (Zapus trinotatus). A total of 228 individuals were sampled from nine subpopulations across a system of three rivers and genotyped at eight microsatellite loci. Significant spatial autocorrelation among individuals revealed a pattern of fine-scale spatial genetic structure indicative of limited dispersal. Geographical distances between pairwise subpopulations were defined following four criteria: (i) Euclidean distance, and three landscape-specific distances, (ii) river distance (distance travelled along the river only), (iii) overland distance (similar to Euclidean, but includes elevation), and (iv) habitat-path distance (a least-cost path distance that models movement along habitat pathways). Pairwise Mantel tests were used to test for a correlation between genetic distance and each of the geographical distances. Significant correlations were found between genetic distance and both the overland and habitat-path distances; however, the correlation with habitat-path distance was stronger. Lastly, estimates of recent migration rates revealed that migration occurs not only within drainages but also across large topographic barriers. These results suggest that patterns of dispersal and migration in Pacific jumping mice are largely determined by habitat connectivity.     

Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)

Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species' phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20,000 years ago), mid-Pleistocene (800,000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and 'g' distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.     

A geographic mosaic of passive dispersal: population structure in the endemic Hawaiian amber snail Succinea caduca (Mighels, 1845)

We used 276 cytochrome c oxidase subunit I (COI, 645 bp) and a subset of 84 16S large ribosomal subunit (16S, 451 bp) sequences to evaluate geographic patterns of genetic variation in 24 populations of the endemic Hawaiian land snail Succinea caduca spanning its range on six islands. Haplotype networks, gene tree topologies, pairwise molecular divergence and F _ST matrices suggest substantial geographic genetic structuring and complex dispersal patterns. Low nucleotide diversity and low pairwise molecular divergence values within populations coupled with higher between population values suggest multiple founder events. High overall haplotype diversity suggests diversification involving rare interpopulation dispersal, fragmentation by historical lava flows and variation in habitat structure. Within-island rather than between-island population comparisons accounted for the majority of molecular variance. Although 98% of 153 COI haplotypes were private by population, a Mantel test showed no evidence for isolation by distance. Mismatch distributions and population partitioning patterns suggest that genetic fragmentation has been driven by punctuated, passive dispersal of groups of closely related haplotypes that subsequently expanded and persisted in isolation for long periods (average > 2 million years ago), and that Pleistocene island connections may have been important in enhancing gene flow. Historical availability of mesic coastal habitat, together with effective dispersal may explain the long-term persistence and unusual multi-island distribution of this species, contrasting with the single-island endemism of much of the Hawaiian biota.     

New microsatellite markers for examining genetic variation in peripheral and core populations of the Coastal Giant Salamander (Dicamptodon tenebrosus)

The Coastal Giant Salamander (Dicamptodon tenebrosus) is classified as threatened at the northern periphery of its range in British Columbia (BC), Canada, primarily due to forestry practices and habitat fragmentation. Characterising dispersal behaviour and population connectivity is therefore a priority for this region, while genetic differentiation in core versus peripheral locations remains unstudied in this wide-ranging species. We present seven new polymorphic microsatellite markers for use in population genetic analyses of D. tenebrosus. We examine locus characteristics and genetic variation in 12 streams at the species' northern range limit in BC, and within two regions representing sub-peripheral (North Cascades) and core localities (South Cascades) in Washington State, United States. In BC, the number of alleles per locus ranged from 2-5 and observed heterozygosity ranged from 0.044-0.825. Genetic differentiation was highest between BC and the South Cascades, and intermediate between BC and the North Cascades. Across loci, mean allelic richness was similar across regions, while private allelic richness was highest in the core locality (corrected for sample size). These new microsatellite loci will be a valuable addition to existing markers for detailed landscape and population genetic analyses of D. tenebrosus across its range.     

Influence of landscape on the population genetic structure of the alpine butterfly parnassius smintheus (Papilionidae)

Four microsatellite DNA markers were developed which were used to examine the relationship between landscape and population genetic structure among a set of populations of the butterfly Parnassius smintheus located in the foothills of the Canadian Rockies. Detailed information on the dispersal of adult butterflies among this same set of populations was available. Simple and partial Mantel tests were used to examine the relationships between genetic distances, predicted rates of dispersal, and a number of landscape variables, all measured pairwise for 17 sample sites. Nei's standard genetic distance was negatively correlated with predicted dispersal. We observed a significant pattern of isolation by distance at a very small spatial scale. The distance between sites that was through forest was a stronger predictor of genetic distance than the distance through open meadow, indicating a significant effect of landscape on population genetic structure beyond that of simple isolation by distance. Our results suggest that rises in the tree-line in alpine areas, caused by global warming, will lead to reduced gene flow among populations of P. smintheus.     

In-stream and overland dispersal across a river network influences gene flow in a freshwater insect, Calopteryx splendens

Gene flow in riverine species is constrained by the dendritic (branching) structure of the river network. Spatial genetic structure (SGS) of freshwater insects is particularly influenced by catchment characteristics and land use in the surroundings of the river. Gene flow also depends on the life cycle of organisms. Aquatic larvae mainly drift downstream whereas flying adults can disperse actively overland and along watercourses. In-stream movements can generate isolation by distance (IBD) at a local scale and differentiation between subcatchments. However, these patterns can be disrupted by overland dispersal. We studied SGS across the Loire River in the damselfly Calopteryx splendens which is able to disperse along and between watercourses. Our sampling design allowed us to test for overland dispersal effects on genetic differentiation between watercourses. Amplified fragment length polymorphism markers revealed high genetic differentiation at the catchment scale but the genetic structure did not reflect the geographical structure of sampling sites. We observed IBD patterns when considering the distance following the watercourse but also the Euclidean distance, i.e. the shortest distance, between pairs of sites. Altogether, our results support the hypothesis of overland dispersal between watercourses. From a conservation perspective, attention should be paid to the actual pathways of gene flow across complex landscapes such as river networks.     

Clinal genetic variation and isolation by distance in the European eel Anguilla anguilla (L.)

The genetic variability and structure of the European eel ( Anguilla anguilla L.) in populations throughout Europe was reassessed using 15 allozymic loci, seven of which were polymorphic. Seven sites were sampled on a latitudinal gradient across the natural continental range, extending from southern France to southern Norway. Heterozygosity ( H _e = 0.05) and level of polymorphism (P = 0.43) were comparable to other marine fish. Populations were poorly differentiated ( G _ST = 0.014, F _ST = 0.002), which is not surprising considering the high dispersal capability of the European eel. However, a significant geographical cline was detected at two alleles ( IDH-1 * 100 and GPI-1 * 110 ), and genetic distances ( D _CE) were concordant with geographical coastal distances. Mantel tests, pairwise F _ST's and multidimensional scaling analyses identify three distinct groups: Northern Europe, Western Europe and the Mediterranean Sea. We propose that the clinal genetic structure in the European eel may be due to (1) isolation by distance (as recently detected with microsatellites), (2) temporal reproductive separation, (3) post-larval selective forces, (4) contact between formerly separated groups or (5) some combination thereof.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 509–521     

Landscape influences on dispersal behaviour: a theoretical model and empirical test using the fire salamander,Salamandra infraimmaculata

When populations reside within a heterogeneous landscape, isolation by distance may not be a good predictor of genetic divergence if dispersal behaviour and therefore gene flow depend on landscape features. Commonly used approaches linking landscape features to gene flow include the least cost path (LCP), random walk (RW), and isolation by resistance (IBR) models. However, none of these models is likely to be the most appropriate for all species and in all environments. We compared the performance of LCP, RW and IBR models of dispersal with the aid of simulations conducted on artificially generated landscapes. We also applied each model to empirical data on the landscape genetics of the endangered fire salamander, Salamandra infraimmaculata, in northern Israel, where conservation planning requires an understanding of the dispersal corridors. Our simulations demonstrate that wide dispersal corridors of the low-cost environment facilitate dispersal in the IBR model, but inhibit dispersal in the RW model. In our empirical study, IBR explained the genetic divergence better than the LCP and RW models (partial Mantel correlation 0.413 for IBR, compared to 0.212 for LCP, and 0.340 for RW). Overall dispersal cost in salamanders was also well predicted by landscape feature slope steepness (76 %), and elevation (24 %). We conclude that fire salamander dispersal is well characterised by IBR predictions. Together with our simulation findings, these results indicate that wide dispersal corridors facilitate, rather than hinder, salamander dispersal. Comparison of genetic data to dispersal model outputs can be a useful technique in inferring dispersal behaviour from population genetic data.     

Testing Pleistocene refugia theory: phylogeographical analysis of Desmognathus wrighti,a high-elevation salamander in the southern Appalachians

During the colder climates of the Pleistocene, the ranges of high-elevation species in unglaciated areas may have expanded, leading to increased gene flow among previously isolated populations. The phylogeography of the pygmy salamander, Desmognathus wrighti, an endemic species restricted to the highest mountain peaks of the southern Appalachians, was examined to test the hypothesis that the range of D. wrighti expanded along with other codistributed taxa during the Pleistocene. Analyses of genetic variation at 14 allozymic loci and of the 12S rRNA gene in the mtDNA genome was conducted on individuals sampled from 14 population isolates throughout the range of D. wrighti. In contrast to the genetic patterns of many other high-elevation animals and plants, genetic distances derived from both molecular markers showed significant isolation by distance and genetic structuring of populations, suggesting long-term isolation of populations. Phylogeographical analyses revealed four genetically distinct population clusters that probably remained fragmented during the Pleistocene, although there was also evidence supporting recent gene flow among some population groups. Support for isolation by distance is rare among high-elevation species in unglaciated areas of North and Middle America, although not uncommon among Plethodontid Salamanders, and this pattern suggests that populations of D. wrighti did not expand entirely into suitable habitat during the Pleistocene. We propose that intrinsic barriers to dispersal, such as species interactions with other southern Appalachian plethodontid salamanders, persisted during the Pleistocene to maintain the fragmented distribution of D. wrighti and allow for significant genetic divergence of populations by restricting gene flow.     

Marked genetic structuring and extreme dispersal limitation in the Pyrenean brook newt Calotriton asper (Amphibia: Salamandridae) revealed by genome-wide AFLP but not mtDNA

Direct estimation of dispersal rates at large geographic scales can be technically and logistically challenging, especially in small animals of low vagility like amphibians. The use of molecular markers to reveal patterns of genetic structure provides an indirect way to infer dispersal rates and patterns of recent and historical gene flow among populations. Here, we use mitochondrial DNA (mtDNA) sequence data and genome-wide amplified fragment length polymorphism markers to examine population structure in the Pyrenean brook newt ( Calotriton asper ) across four main drainages in the French Pyrenees. mtDNA sequence data (2040 bp) revealed three phylogroups shallowly differentiated and with low genetic diversity. In sharp contrast, variation in 382 amplified fragment length polymorphism loci was high and revealed a clear pattern of isolation by distance consistent with long-term restriction of gene flow at three spatial scales: (i) among all four main drainages, (ii) between sites within drainages, and (iii) even between adjacent populations separated by less than 4 km. The high pairwise F _ST values between localities across numerous loci, together with the high frequency of fixed alleles in several populations, suggests a combination of marked geographic isolation, small population sizes and very limited dispersal in C. asper . The contrasting lack of variation detected in mtDNA sequence data is intriguing and underscores the importance of multilocus approaches to detect true patterns of gene flow in natural populations of amphibians.     

The effect of ant association on the population genetics of the Australian butterfly Jalmenus evagoras (Lepidoptera: Lycaenidae)

Populations of the myrmecophilous lycaenid Jalmenus evagoras Donovan were assessed for genetic structure at three hierarchical spatial scales: sites, geographically-defined subpopulations, and subpopulations defined by species of mutualistic ant-associate. Estimates of Wright's FST generated from multilocus electrophoretic data revealed low, though significant, amounts of genetic structure. Most structure was observed at the level of geographic subpopulations, suggesting that adult butterflies do not exhibit preferential mating and oviposition along the lines of ant associate. The genetic structure data, together with estimates of Nei's genetic distance (D) for pairwise site and subpopulation comparisons, suggest that J. evagoras populations are spatially and temporally dynamic. These patterns are considered in the context of extinction and recolonization models. The extreme patchiness of J. evagoras populations stems from the stringent requirements of both host plant and host ant, contributing to an extinction/ recolonization process. We discuss the key parameters influencing genetic cohesion versus differentiation under an extinction/recolonization regime, including mode of butterfly dispersal, site turnover rate, and the effects of host dispersal and phenology. This system provides a model of population-level consequences of certain mutualistic interactions as well as of a class of patterns arising from an extinction/recolonization process.     

Population Graphs: the graph theoretic shape of genetic structure

Patterns of intraspecific genetic variation result from interactions among both historical and contemporary evolutionary processes. Traditionally, population geneticists have used methods such as F-statistics, pairwise isolation by distance models, spatial autocorrelation and coalescent models to analyse this variation and to gain insight about causal evolutionary processes. Here we introduce a novel approach (Population Graphs) that focuses on the analysis of marker-based population genetic data within a graph theoretic framework. This method can be used to estimate traditional population genetic summary statistics, but its primary focus is on characterizing the complex topology resulting from historical and contemporary genetic interactions among populations. We introduce the application of Population Graphs by examining the range-wide population genetic structure of a Sonoran Desert cactus (Lophocereus schottii). With this data set, we evaluate hypotheses regarding historical vicariance, isolation by distance, population-level assignment and the importance of specific populations to species-wide genetic connectivity. We close by discussing the applicability of Population Graphs for addressing a wide range of population genetic and phylogeographical problems.     

Using stable isotopes to test for trophic niche partitioning: a case study with stream salamanders and fish

1. Stream salamanders and fish often co‐occur even though fish prey on and outcompete salamanders. However, the mechanisms that allow palatable salamanders to coexist with fish are unknown. 2. We tested mechanisms in the field that promote coexistence between Idaho giant salamanders (Dicamptodon aterrimus) and stream salmonid fishes in headwater streams. Previous research in this system indicated that salamander dispersal did not promote coexistence with fish. We tested the hypothesis that D. aterrimus shift their diet when they occur with fish, facilitating coexistence through local niche partitioning. 3. We used nitrogen and carbon stable isotopes to describe the trophic niche of D. aterrimus and fish in three co‐occurring populations of salamanders and fish and three populations of salamanders without fish. We used two approaches to quantify trophic niche partitioning with stable isotopes: 95% kernel density estimators and isotopic mixing models. 4. We found that salamanders and fish were generalists that consumed aquatic invertebrates primarily, but both species were also cannibalistic and predatory on one another. We also found no support for trophic niche partitioning as a coexistence mechanism because there were no differences in the trophic niche metrics among salamander populations with and without fish. 5. Although we did not identify mechanisms that facilitate salamander and fish coexistence, our empirical data and use of novel approaches to describe the trophic niche did yield important insights on the role of predator–prey interactions and cannibalism as alternative coexistence mechanisms. In addition, we found that 95% kernel estimators are a simple and robust method to describe population‐level measure of trophic structure.