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Model-based analyses are common in phylogeographic inference because they parameterize processes such as population division, gene flow and expansion that are of interest to biologists. Approximate Bayesian computation is a model-based approach that can be customized to any empirical system and used to calculate the relative posterior probability of several models, provided that suitable models can be identified for comparison. The question of how to identify suitable models is explored using data from Plethodon idahoensis, a salamander that inhabits the North American inland northwest temperate rainforest. First, we conduct an ABC analysis using five models suggested by previous research, calculate the relative posterior probabilities and find that a simple model of population isolation has the best fit to the data (PP=0.70). In contrast to this subjective choice of models to include in the analysis, we also specify models in a more objective manner by simulating prior distributions for 143 models that included panmixia, population isolation, change in effective population size, migration and range expansion. We then identify a smaller subset of models for comparison by generating an expectation of the highest posterior probability that a false model is likely to achieve due to chance and calculate the relative posterior probabilities of only those models that exceed this expected level. A model that parameterized divergence with population expansion and gene flow in one direction offered the best fit to the P. idahoensis data (in contrast to an isolation-only model from the first analysis). Our investigation demonstrates that the determination of which models to include in ABC model choice experiments is a vital component of model-based phylogeographic analysis., (© 2014 John Wiley & Sons Ltd.)

Theory suggests that source-sink dynamics can allow coexistence of intraguild predators and prey, but empirical evidence for this coexistence mechanism is limited. We used capture-mark-recapture, genetic methods, and stable isotopes to test whether source-sink dynamics promote coexistence between stream fishes, the intraguild predator, and stream salamanders (Dicamptodon aterrimus), the intraguild prey. Salamander populations from upstream reaches without fish were predicted to maintain or supplement sink populations in downstream reaches with fish. We found instead that downstream reaches with fish were not sinks even though fish consumed salamander larvae-apparent survival, recruitment, and population growth rate did not differ between upstream and downstream reaches. There was also no difference between upstream and downstream reaches in net emigration. We did find that D. aterrimus moved frequently along streams, but believe that this is a response to seasonal habitat changes rather than intraguild predation. Our study provides empirical evidence that local-scale mechanisms are more important than dispersal dynamics to coexistence of streams salamanders and fish. More broadly, it shows the value of empirical data on dispersal and gene flow for distinguishing between local and spatial mechanisms of coexistence.

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.

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.

Several theoretical studies have demonstrated the importance of accounting for coalescent stochasticity in phylogeographical studies, however, there are few empirical examples that do so in the context of explicit hypothesis testing. Here, we provide an example from the Idaho giant salamander (Dicamptodon aterrimus) using 118 mtDNA sequences, nearly 2 kb in length. This species is endemic to mesic forests in northern and central Idaho, and several a priori hypotheses have been erected based both on palaeoclimatic grounds and from phylogeographical studies of codistributed amphibians. Phylogenetic analysis of the D. aterrimus data suggests an expansion from a single refugium south of the Salmon River, whereas the inference from nested clade analysis is one of expansion from a single refugium in the Clearwater drainage. Explicit testing of these hypotheses, using geographically structured coalescent simulations to erect null distributions, indicates we can reject expansion from the Clearwater drainage (pCLW = 0.089), but not expansion from the South Fork of the Salmon drainage (pSAL = 0.329). Furthermore, data from codistributed amphibians suggest that there may have been two refugia, and an amova shows that most of the molecular variance partitioned between the Clearwater and the Salmon drainages (54.40%; P < 0.001) and within drainages (43.61%; P < 0.001). As a result, we also tested three a priori hypotheses which predicted that both the Clearwater and Salmon drainages functioned as refugia during the late Pleistocene; we could reject (PCORD = 0.019) divergence dates during the Cordilleran glacial maxima [c. 20 000 years before present (ybp)], during the Sangamon interglacial (c. 35 000 ybp; pSANG = 0.032), as well as pre-Pleistocene divergence (c. 1.7 Ma; ppP < 0.001). Mismatch distributions and Tajima's D within the individual drainages provide further support to recent population expansion. This work demonstrates coalescent stochasticity is an important phenomenon to consider in testing phylogeographical hypotheses, and suggests that analytical methods which fail to sufficiently quantify this uncertainty can lead to false confidence in the conclusions drawn from these methods.