California Tiger Salamander Ambystoma Californiense Research Articles

The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi.

In this paper, we report on the scaffold-level assembled genome for the federally endangered, California endemic crustacean Lepidurus packardi (the Vernal Pool Tadpole Shrimp). L. packardi is a key food source for other conserved California species including the California Tiger Salamander Ambystoma californiense. It faces significant habitat loss and fragmentation as vernal pools are threatened by urbanization, agricultural conversion, and climate change. This resource represents the first scaffold-level genome of any Lepidurus species. The assembled genome spans 108.6 Mbps, with 6 chromosome-length scaffolds comprising 71% of total genomic length and 444 total contigs. The BUSCO score for this genome is 97.3%, suggesting a high level of completeness. We produced a predicted gene set for this species trained on the Daphnia magna set of genes and predicted 17,650 genes. These tools can aid researchers in understanding the evolution and adaptive potential of alternative reproductive modes within this species.

Using Environmental DNA to Monitor the Spatial Distribution of the California Tiger Salamander

AbstractGlobal efforts to conserve declining amphibian populations have necessitated the development of rapid, reliable, and targeted survey methods. Environmental DNA surveys offer alternative or complementary methods to traditional amphibian survey techniques. The California tiger salamander Ambystoma californiense (CTS) is endemic to California, where it breeds in vernal pools. In the past 25 y, CTS has faced a 21% loss of known occurrences, largely through habitat loss, and it is threatened by hybridization with an introduced congener. Protecting and managing remaining CTS populations rely on accurately monitoring changes in their spatial distribution. Current monitoring practices typically use dip-net surveys that are time-consuming and prone to false negative errors. To provide a new resource for monitoring and surveying larval CTS, we designed an assay and tested it on water samples collected from 29 vernal pools at two locations in California. We compared environmental DNA results to contemporaneous dip-net surveying results and found the assay agreed with positive dip-net results in 100% of cases. In several instances, we also detected the presence of CTS genetic material in the early spring before larvae hatched, potentially offering a new, earlier detection option for this imperiled species. This assay provides a valuable, noninvasive molecular tool for monitoring the spatial distribution of the CTS in vernal pools.

Determinants of size at metamorphosis in an endangered amphibian and their projected effects on population stability

Roughly 80% of animal species have complex life cycles spanning a major habitat shift, and delayed life history effects play an important role in their population dynamics. Through their effect on size at metamorphosis, factors in the pre‐ metamorphic environment often have profound effects upon survival and fecundity in the post‐metamorphic environment. Here, we adopted a combined experimental and field observational approach to investigate the factors that determine size at metamorphosis in pond‐breeding amphibians, and to predict some of their downstream effects on population stability. We set up ecologically realistic mesocosm communities for the endangered California tiger salamander Ambystoma californiense to test the effects of larval density, prey density and hydroperiod on mean size at metamorphosis. We found significant effects for all three factors, with mean size at metamorphosis negatively correlated with larval density and positively correlated with prey density and hydroperiod. We also used six years of field survey data to identify the most informative model explaining mean size at metamorphosis and thus validate our mesocosm results. The optimal three‐term model identified terms that were roughly analogous to each of the mesocosm treatments and with similar effect sizes, providing strong field confirmation of our experimental results. The field data also provide correlations between each factor and the number of metamorphs recruited to the population, allowing us to predict the effect of each factor on population stability. Finally, we show that these populations of the endangered A. californiense are strongly resource limited, which has important implications for their management and recovery as an endangered taxon.

Field validation supports novel niche modeling strategies in a cryptic endangered amphibian

Many studies employ ecological niche models (ENMs) to predict species’ occurrences in undersampled regions, generally without field confirmation. Here, we use field surveys to test the relative utility of four potential refinements to the standard ENM approach: 1) altering model complexity based on AICc, 2) selecting background points from a biologically informed region, 3) using target‐group background to account for sampling bias in existing localities, and 4) using many rangewide localities (global model) versus fewer proximal localities (local model) to construct geographically restricted range predictions. We used Maxent to predict new localities for the California tiger salamander Ambystoma californiense, an endangered species that often goes undocumented due to its cryptic lifestyle. We followed this with a field survey of 260 previously unsampled potential breeding sites in Solano County, CA and used the resulting presence/absence data to compare all factorial combinations of the four model refinements using a new application of the Kruskal–Wallis test for ENM outputs. Our field surveys led to the discovery of 81 previously undocumented breeding localities for the California tiger salamander and demonstrated that ENMs could be significantly improved by utilizing target‐group background to account for spatial sampling bias and local models to focus model output on the subregion of the range being surveyed. Our results clearly demonstrate the potential for local models to outperform global models, and we recommend supplementing traditional Maxent global models that utilize all known localities with local models, particularly when species occupy geographically structured, heterogeneous habitat types. We also recommend using target‐group background since the improvement we observed when including it in our models was significant and very similar to that documented by previous studies. Most importantly, we emphasize the importance of field verification to enable rigorous statistical comparisons among models.

Cautious optimism for applied conservation genetics and metapopulation viability analysis

Among conservation biologists there is little argument that habitat loss and fragmentation are the greatest threats to future biodiversity. We know from elementary population ecology that, if isolated, even large populations will ultimately be driven to extinction by demographic stochasticity, and that this will occur more rapidly for small populations in small fragments. Theory and observations also show that post-fragmentation species losses can occur slowly, sometimes requiring more than a century for the total ‘extinction debt’ to be realized (Tilman et al., 1994; Vellend et al., 2006). For long-lived animals, such as ambystomatid salamanders, isolated populations doomed to demographic irrelevance and ultimate extinction may persist for decades or longer (Greenwald, 2010). I think of the animals occupying these isolated habitats with little chance of long-term survival as ‘zombie’ populations. As imperfect as our population models are, they represent our best chance for understanding the threats to populations at risk and possibly recovering them from zombie status. Population and metapopulation viability analyses are valuable tools for illustrating, in an understandable way, the risk of extinctions, and for exploring probabilities of local and regional persistence under different scenarios (Morris & Doak, 2002; Marsh, 2008). I see the greatest value of these modeling exercises in their ability to help land managers to evaluate alternative management actions and appreciate their relative costs and likely benefits. As Greenwald (2010) shows, actions to promote connectivity can enhance population viability. Restoring connectivity to fragmented landscapes is often extremely costly (think wildlife overpasses), and avoiding fragmentation completely may be even more controversial (think not building the freeway at all). So, models evaluating the importance of habitat connectivity must be convincing to those people on the hook for making big decisions. The greatest barrier to constructing convincing models is obtaining parameter estimates in which we have confidence, which traditionally means laborand time-intensive mark–recapture studies. Fortunately, the recent work of Greenwald (2010) in addition to others indicates that molecular tools may be surprisingly robust to the challenge of more rapidly and painlessly estimating at least some demographic parameters needed for landscape-scale population modeling. As someone who has invested years in the field marking and recapturing animals, I am optimistic at the promise these methods potentially hold (Trenham et al., 2000; Trenham, Koenig & Shaffer, 2001). The ability of genetic assignment tests to accurately reveal residents and immigrants in samples could change the study of dispersal. My caution in getting too excited about the current abilities of these methods stems from my understanding of several issues that can substantially bias the results. The author addressed the issue of unsampled ‘ghost’ populations. This is a real issue for animals like ambystomatid salamanders where large fractions of the adult population commonly skip breeding and are completely undetectable, thus samples from a single year are unlikely to accurately represent the standing genetic variation present in a population. Despite these issues, one recent study is very encouraging. A detailed study with marked skinks, occupying and dispersing among patches of rocky habitat, showed that assignment tests usually recognized immigrants with high confidence. And further, using skink tissues collected over 3months, the assignment tests yielded estimates of interpatch dispersal rates essentially identical to those estimated over 7 years of mark–recapture efforts (Berry, Tocher & Sarre et al., 2004). At this point, I think there is still need for more cross validation of these methods with mark–recapture studies in other taxa and landscapes, especially if we are to use these data predicting metapopulation viability. If these methods produce robust predictions they have the potential to greatly assist conservation planners. For example, the California tiger salamander Ambystoma californiense is the species about which I know the most, and one whose management would benefit greatly from the types of genetic data and the coupled modeling approach explored