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When invasive and endangered native taxa hybridize, the resulting admixture introduces novel conservation challenges. Across a large region of central California, a hybrid swarm consisting of admixed endangered California tiger salamanders (CTS) (Ambystoma californiense) and introduced barred tiger salamanders (BTS) (Ambystoma mavortium) has replaced native populations, threatening the genetic integrity of CTS and the vernal pool systems they inhabit. We employed a large‐scale, genomically informed field experiment to test whether shortening breeding pond hydroperiod would favor native CTS genotypes. We constructed 14 large, seminatural ponds to evaluate the effect of hydroperiod duration on larval survival and mass at metamorphosis. We tracked changes in non‐native allele frequencies with a 5237‐gene exon capture array and employed a combination of custom Bayesian and generalized linear models to quantify the effect of pond duration on salamander fitness. Earlier work on this system showed hybrid superiority under many conditions and suggested that hybrids are favored in human‐modified ponds with artificially long hydroperiods. Consistent with these earlier studies, we found overwhelming evidence for hybrid superiority. Very short hydroperiods substantially reduced the mass (1.1–1.5 fold) and survival probability (10–13 fold) of both native and hybrid larvae, confirming that hydroperiod likely exerts a strong selective pressure in the wild. We identified 86 genes, representing 1.8% of 4723 screened loci, that significantly responded to this hydroperiod‐driven selection. In contrast to earlier work, under our more natural experimental conditions, native CTS survival and size at metamorphosis were always less than hybrids, suggesting that hydroperiod management alone will not shift selection to favor native larval genotypes. However, shortening pond hydroperiod may limit productivity of hybrid ponds, complementing other strategies to remove hybrids while maintaining vernal pool ecosystems. This study confirms and expands on previous work that highlights the importance of hydroperiod management to control invasive aquatic species. [ABSTRACT FROM AUTHOR]

Copyright of Molecular Ecology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Integral projection models (IPMs) can estimate the population dynamics of species for which both discrete life stages and continuous variables influence demographic rates. Stochastic IPMs for imperiled species, in turn, can facilitate population viability analyses (PVAs) to guide conservation decision‐making. Biphasic amphibians are globally distributed, often highly imperiled, and ecologically well suited to the IPM approach. Herein, we present a stochastic size‐ and stage‐structured IPM for a biphasic amphibian, the U.S. federally threatened California tiger salamander (CTS) (Ambystoma californiense). This Bayesian model reveals that CTS population dynamics show greatest elasticity to changes in juvenile and metamorph growth and that populations are likely to experience rapid growth at low density. We integrated this IPM with climatic drivers of CTS demography to develop a PVA and examined CTS extinction risk under the primary threats of habitat loss and climate change. The PVA indicated that long‐term viability is possible with surprisingly high (20%–50%) terrestrial mortality but simultaneously identified likely minimum terrestrial buffer requirements of 600–1000 m while accounting for numerous parameter uncertainties through the Bayesian framework. These analyses underscore the value of stochastic and Bayesian IPMs for understanding both climate‐dependent taxa and those with cryptic life histories (e.g., biphasic amphibians) in service of ecological discovery and biodiversity conservation. In addition to providing guidance for CTS recovery, the contributed IPM and PVA supply a framework for applying these tools to investigations of ecologically similar species. [ABSTRACT FROM AUTHOR]

Dispersal drives invasion dynamics of nonnative species and pathogens. Applying knowledge of dispersal to optimize the management of invasions can mean the difference between a failed and a successful control program and dramatically improve the return on investment of control efforts. A common approach to identifying optimal management solutions for invasions is to optimize dynamic spatial models that incorporate dispersal. Optimizing these spatial models can be very challenging because the interaction of time, space, and uncertainty rapidly amplifies the number of dimensions being considered. Addressing such problems requires advances in and the integration of techniques from multiple fields, including ecology, decision analysis, bioeconomics, natural resource management, and optimization. By synthesizing recent advances from these diverse fields, we provide a workflow for applying ecological theory to advance optimal management science and highlight priorities for optimizing the control of invasions. One of the striking gaps we identify is the extremely limited consideration of dispersal uncertainty in optimal management frameworks, even though dispersal estimates are highly uncertain and greatly influence invasion outcomes. In addition, optimization frameworks rarely consider multiple types of uncertainty (we describe five major types) and their interrelationships. Thus, feedbacks from management or other sources that could magnify uncertainty in dispersal are rarely considered. Incorporating uncertainty is crucial for improving transparency in decision risks and identifying optimal management strategies. We discuss gaps and solutions to the challenges of optimization using dynamic spatial models to increase the practical application of these important tools and improve the consistency and robustness of management recommendations for invasions. [ABSTRACT FROM AUTHOR]

The article discusses the discovery of a previously unrecorded population of the Ivallda Arctic butterfly (Oeneis chryxus ivallda) at the summit of Mount Whitney, the highest mountain in the conterminous US. This observation marks what is believed to be the highest extant butterfly population in North America. The article highlights the challenges faced by alpine butterflies in the Sierra Nevada due to warming temperatures and suggests that proactive conservation practices, such as translocation and assisted migration, may be necessary to prevent extinction. The California Conservation Genomics Project (CCGP) is mentioned as a source of detailed population genomic data that can inform these conservation efforts. [Extracted from the article]

Globally endangered ecosystems, such as ephemeral wetlands, are often critical habitat for multiple interacting imperilled species. To conserve this biodiversity, managers must consider both species‐specific resource requirements and mechanisms for endangered species coexistence under variable habitat conditions.We examined communities native to California playa pools, ephemeral wetlands that have declined by >90% from their historic extent. Specifically, we describe the diet of a federally Threatened amphibian (Ambystoma californiense), and characterise interactions between this amphibian and two federally Endangered macrocrustaceans (Branchinecta conservatio and Lepidurus packardi) across three rain years to understand how these imperilled species coexist. We examined the dietary preferences of A. californiense larvae, metamorphs, juveniles, and breeding adults, and determined how prey electivity by larval A. californiense differs between natural playa pools and human‐modified stock ponds.Within playa pools, both breeding adult and larval A. californiense preyed extensively on L. packardi, whereas fully terrestrial juveniles had relatively empty stomachs. We provide evidence for size‐moderated optimal foraging by larval A. californiense, and show that larval prey differed dramatically between playa pools and stock ponds. Additionally, an ontogenetic progression from smaller to larger prey gave the relatively large, endangered macrocrustaceans an early‐season temporal refuge, during which they reached maturity in all three rain years.Consistent with complex life cycle theory, our results suggest that ephemeral wetland habitat offers abundant food resources for A. californiense relative to terrestrial habitat. Our findings also suggest that diet flexibility facilitates the persistence of this imperilled amphibian in human‐modified stock ponds. Temporal offsets in prey maturation rates and ontogenetic shifts in predator diets are likely to facilitate coexistence among the focal endangered species.We highlight the importance of accounting for spatial and temporal variation in interspecific interactions when predicting the effects of environmental change on biodiversity, particularly in highly threatened ecosystems. [ABSTRACT FROM AUTHOR]

Hybridization between native and non‐native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue‐specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele‐specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures. [ABSTRACT FROM AUTHOR]

Genomic data are increasingly used for high resolution population genetic studies including those at the forefront of biological conservation. A key methodological challenge is determining sequence similarity clustering thresholds for RADseq data when no reference genome is available. These thresholds define the maximum permitted divergence among allelic variants and the minimum divergence among putative paralogues and are central to downstream population genomic analyses. Here we develop a novel set of metrics to determine sequence similarity thresholds that maximize the correct separation of paralogous regions and minimize oversplitting naturally occurring allelic variation within loci. These metrics empirically identify the threshold value at which true alleles at opposite ends of several major axes of genetic variation begin to incorrectly separate into distinct clusters, allowing researchers to choose thresholds just below this value. We test our approach on a recently published data set for the protected foothill yellow‐legged frog (Rana boylii). The metrics recover a consistent pattern of roughly 96% similarity as a threshold above which genetic divergence and data missingness become increasingly correlated. We provide scripts for assessing different clustering thresholds and discuss how this approach can be applied across a wide range of empirical data sets. [ABSTRACT FROM AUTHOR]

Introductions of non‐native predators often reduce biodiversity and affect natural predator–prey relationships and may increase the abundance of potential disease vectors (e.g., mosquitoes) indirectly through competition or predation cascades. The Santa Monica Mountains (California, U.S.A.), situated in a global biodiversity hotspot, is an area of conservation concern due to climate change, urbanization, and the introduction of non‐native species. We examined the effect of non‐native crayfish (Procambarus clarkii) on an existing native predator, dragonfly nymphs (Aeshna sp.), and their mosquito larvae (Anopheles sp.) prey. We used laboratory experiments to compare the predation efficiency of both predators, separately and together, and field data on counts of dragonfly nymphs and mosquito larvae sampled from 13 local streams. We predicted a lower predation efficiency of crayfish compared with native dragonfly nymphs and a reduced predation efficiency of dragonfly nymphs in the presence of crayfish. Dragonfly nymphs were an order of magnitude more efficient predators than crayfish, and dragonfly nymph predation efficiency was reduced in the presence of crayfish. Field count data showed that populations of dragonfly nymphs and mosquito larvae were strongly correlated with crayfish presence in streams, such that sites with crayfish tended to have fewer dragonfly nymphs and more mosquito larvae. Under natural conditions, it is likely that crayfish reduce the abundance of dragonfly nymphs and their predation efficiency and thereby, directly and indirectly, lead to higher mosquito populations and a loss of ecosystem services related to disease vector control. Article impact statement: The efficiency of native predators to control potential disease vectors is diminished in the presence of non‐native predators. [ABSTRACT FROM AUTHOR]

Understanding the evolutionary history of diversifying lineages and the delineation of evolutionarily significant units and species remains major challenges for evolutionary biology. Low‐cost representational sampling of the genome for single nucleotide polymorphisms shows great potential at the temporal scales that are typically the focus of species delimitation and phylogeography. We apply these markers to a case study of a freshwater turtle, Emydura macquarii, whose systematics has so far defied resolution, to bring to light a dynamic system of substantive allopatric lineages diverging on independent evolutionary trajectories, but held back in the process of speciation by low level and episodic exchange of alleles across drainage divides on various timescales. In the context of low‐level episodic gene flow, speciation is often reticulate, rather than a bifurcating process. We argue that species delimitation needs to take into account the pattern of ancestry and descent of diverging lineages in allopatry together with the recent and contemporary processes of dispersal and gene flow that retard and obscure that divergence. Underpinned by a strong focus on lineage diagnosability, this combined approach provides a means for addressing the challenges of incompletely isolated populations with uncommon, but recurrent gene flow in studies of species delimitation, a situation likely to be frequently encountered. Taxonomic decisions in cases of allopatry often require subjective judgements. Our strategy, which adds an additional level of objectivity before that subjectivity is applied, reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation. [ABSTRACT FROM AUTHOR]

A critical consideration when using molecular ecological methods to detect trends and parameterize models at very fine spatial and temporal scales has always been the technical limits of resolution. Key landscape features, including most anthropogenic modifications, can cause biologically important, but very recent changes in gene flow that require substantial statistical power to detect. The problem is one of temporal scale: Human change is rapid and recent, while genetic changes accumulate slowly. We generated SNPs from thousands of nuclear loci to characterize the population structure of New York‐endangered eastern tiger salamanders (Ambystoma tigrinum) on Long Island and quantify the impacts of roads on population fragmentation. In stark contrast to a recent microsatellite study, we uncovered highly structured populations over an extremely small spatial scale (approximately 40 km2) in an increasingly human‐modified landscape. Geographic distance and the presence of roads between ponds were both strong predictors of genetic divergence, suggesting that both natural and anthropogenic factors contribute to the observed patterns of genetic variation. All ponds supported small to modest effective breeding populations, and pond surface area showed a strong positive correlation with population size. None of these patterns emerged in an earlier study of the same system using microsatellite loci, and we determined that at least 300–400 SNPs were needed to recover the fine‐scale population structure present in this system. Conservation assessments using earlier genetic techniques in other species may similarly lack the statistical power for small‐scale inferences and benefit from reassessments using genomic tools. [ABSTRACT FROM AUTHOR]

The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow, in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field-ecological studies. However, empirical assessments of the concordance between direct field-ecological and indirect population genetic studies of the same populations are uncommon in the literature. In this study, we investigate genetic isolation, rates of dispersal, and population sizes for the endangered California tiger salamander, Ambystoma californiense, across multiple breeding seasons in an intact vernal pool network. We then compare our molecular results to a previously published study based on multiyear, mark-recapture data from the same breeding sites. We found that field and genetic estimates of population size were only weakly correlated, but dispersal rates were remarkably congruent across studies and methods. In fact, dispersal probability functions derived from genetic data and traditional field-ecological data were a significant match, suggesting that either method can be used effectively to assess population connectivity. These results provide one of the first explicit tests of the correspondence between landscape genetic and field-ecological approaches to measuring functional population connectivity and suggest that even single-year genetic samples can return biologically meaningful estimates of natural dispersal and gene flow. [ABSTRACT FROM AUTHOR]

Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence data sets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large data sets is time-consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions. Here, we investigated how locus number and information content affect species delimitation results for an endangered Mexican salamander species, Ambystoma ordinarium. We compared results for an eight-locus, 137-individual data set and an 89-locus, seven-individual data set. For both data sets, we used species discovery methods to define delimitation models and species validation methods to rigorously test these hypotheses. We also used integrated demographic model selection tools to choose among delimitation models, while accounting for gene flow. Our results indicate that while cryptic lineages may be delimited with relatively few loci, sampling larger numbers of loci may be required to ensure that enough informative loci are available to accurately identify and validate shallow-scale divergences. These analyses highlight the importance of striking a balance between dense sampling of loci and individuals, particularly in shallowly diverged lineages. They also suggest the presence of a currently unrecognized, endangered species in the western part of A. ordinarium's range. [ABSTRACT FROM AUTHOR]

Gathering genomic-scale data efficiently is challenging for nonmodel species with large, complex genomes. Transcriptome sequencing is accessible for organisms with large genomes, and sequence capture probes can be designed from such mRNA sequences to enrich and sequence exonic regions. Maximizing enrichment efficiency is important to reduce sequencing costs, but relatively few data exist for exon capture experiments in nonmodel organisms with large genomes. Here, we conducted a replicated factorial experiment to explore the effects of several modifications to standard protocols that might increase sequence capture efficiency for amphibians and other taxa with large, complex genomes. Increasing the amounts of c0t-1 repetitive sequence blocker and individual input DNA used in target enrichment reactions reduced the rates of PCR duplication. This reduction led to an increase in the percentage of unique reads mapping to target sequences, essentially doubling overall efficiency of the target capture from 10.4% to nearly 19.9% and rendering target capture experiments more efficient and affordable. Our results indicate that target capture protocols can be modified to efficiently screen vertebrates with large genomes, including amphibians. [ABSTRACT FROM AUTHOR]

After decades of discussion, there is little consensus on the extent to which hybrids between endangered and nonendangered species should be protected by US law. As increasingly larger, genome-scale data sets are developed, we can identify individuals and populations with even trace levels of genetic admixture, making the 'hybrid problem' all the more difficult. We developed a decision-tree framework for evaluating hybrid protection, including both the processes that produced hybrids (human-mediated or natural) and the ecological impact of hybrids on natural ecosystems. We then evaluated our decision tree for four case studies drawn from our own work and briefly discuss several other cases from the literature. Throughout, we highlight the management outcomes that our approach provides and the nuances of hybridization as a conservation problem. [ABSTRACT FROM AUTHOR]

The use of taxon substitutes for extinct or endangered species is a controversial conservation measure. We use the example of the endangered California tiger salamander ( Ambystoma californiense; CTS), which is being replaced by hybrids with the invasive barred tiger salamander ( Ambystoma mavortium), to illustrate a strategy for evaluating taxon substitutes based on their position in a multivariate community space. Approximately one-quarter of CTS's range is currently occupied by 'full hybrids' with 70% nonnative genes, while another one-quarter is occupied by 'superinvasives' where a specific set of 3/68 genes comprising 4% of the surveyed genome is nonnative. Based on previous surveys of natural CTS breeding ponds, we stocked experimental mesocosms with field-verified, realistic densities of tiger salamander larvae and their prey, and used these mesocosms to evaluate ecological equivalency between pure CTS, full hybrids, and superinvasives in experimental pond communities. We also included a fourth treatment with no salamanders present to evaluate the community effects of eliminating Ambystoma larvae altogether. We found that pure CTS and superinvasive larvae were ecologically equivalent, because their positions in the multivariate community space were statistically indistinguishable and they did not differ significantly along any univariate community axes. Full hybrids were ecologically similar, but not equivalent, to the other two genotypes, and the no- Ambystoma treatment was by far the most divergent. We conclude that, at least for the larval stage, superinvasives are adequate taxon substitutes for pure CTS and should probably be afforded protection under the Endangered Species Act. The proper conservation status for full hybrids remains debatable. [ABSTRACT FROM AUTHOR]

Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Aim Ecological niche modelling is one of the main tools that allows for the incorporation of climate change effects into conservation planning. For example, ecological niche model predictions can be used to rank species by degree of predicted future habitat loss. While many studies have considered how different modelling decisions contribute to uncertainty in niche model outputs, here we evaluate how metrics used to rank species by conservation risk respond to the choice of global climate models, greenhouse gas emission scenarios, suitable versus unsuitable threshold values, and the degree of model complexity. Location California, USA. Methods We built ecological niche models for 153 species of reptiles and amphibians. Reduced complexity models were compared to default complexity models using AICc to select climate variables and tune Maxent' s built-in regularization parameter. We predicted the distribution of climatically suitable habitat under future (2041-2060) climate conditions according to 11 global climate models, four representative concentration pathways, and three threshold values. Two metrics to rank species by predicted future loss of climatically suitable habitat were calculated for each set of modelling decisions. To determine the effects of modelling decisions on rankings, we used mixed models. Results Our results indicate that while individual modelling decisions had relatively small effects on species ranks alone, in combination, they lead to very different conservation assessments. Main conclusions We recommend that a wide range of modelling decisions be explored and that variation in ranks across runs be reported as a first step in identifying the uncertainty in rank metrics used for assessing conservation risk under changing, but uncertain climate predictions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

As the field of phylogeography has matured, it has become clear that analyses of one or a few genes may reveal more about the history of those genes than the populations and species that are the targets of study. To alleviate these concerns, the discipline has moved towards larger analyses of more individuals and more genes, although little attention has been paid to the qualitative or quantitative gains that such increases in scale and scope may yield. Here, we increase the number of individuals and markers by an order of magnitude over previously published work to comprehensively assess the phylogeographical history of a well-studied declining species, the western pond turtle ( Emys marmorata). We present a new analysis of 89 independent nuclear SNP markers and one mitochondrial gene sequence scored for rangewide sampling of >900 individuals, and compare these to smaller-scale, rangewide genetic and morphological analyses. Our enlarged SNP data fundamentally revise our understanding of evolutionary history for this lineage. Our results indicate that the gains from greatly increasing both the number of markers and individuals are substantial and worth the effort, particularly for species of high conservation concern such as the pond turtle, where accurate assessments of population history are a prerequisite for effective management. [ABSTRACT FROM AUTHOR]

Aim Ecological niche models are increasingly being used to aid in predicting the effects of future climate change on species distributions. Complex models that show high predictive performance on current distribution data may do a poor job of predicting new data due to overfitting. In addition, model performance is often evaluated using techniques that are sensitive to spatial sampling bias. Here, we explore the effects of model complexity and spatial sampling bias on niche models for 90 vertebrate taxa of conservation concern. Location California, USA. Methods We used Akaike information criterion ( AICc) to select variables and tune Maxent's built-in regularization parameter (β) to constrain model complexity. In addition, we incorporated several estimates of spatial sampling bias based on interpolations of target group data. Ensemble forecasts were developed for future conditions from two emission scenarios and three climate change models for the year 2050. Results Reducing the number of predictors and tuning β resulted in a reduction in the number of parameters in models built with sample sizes greater than approximately 10 occurrence points. Reducing the number of predictors had a substantially higher impact on the relative prioritization of different grid cells than did increasing regularization. There was little difference in prioritization of habitat when comparing models built using different spatial sampling bias estimates. Over half of the taxa were predicted to experience >80% reductions in environmental suitability in currently occupied cells, and this pattern was consistent across taxonomic groups. Main Conclusions Our results demonstrate that reducing the number of correlated predictor variables tends to decrease the breadth of models, while tuning regularization using AICc tends to increase it. These two strategies may provide a reasonable bracketing strategy for assessing climate change impacts. [ABSTRACT FROM AUTHOR]

Delayed life history effects (DLHEs) occur when fitness in one life stage affects fitness in subsequent life stages. Given their biphasic life cycle, pond-breeding amphibians provide a natural system for studying DLHEs, although these effects are not restricted to species with biphasic life histories. In this study, we used multiple mark-recapture techniques enabled by a large trapping array to monitor components of fitness and resulting DLHEs in a population of the endangered California tiger salamander (Ambystoma californiense). We found that DLHEs are prominent across all life stage transitions and that there is variation in whether selection acts primarily at the individual or cohort level. We also demonstrated that there is more than an order of magnitude variation in mean cohort fitness, providing tremendous variation for DLHEs to act upon. We documented an evolutionary trade-off between mass at emergence and date of emergence, which may play a role in maintaining the variation in mass (fitness) at emergence. A literature review revealed that such high levels of intercohort variation occur in many other pond-breeding amphibians, and that appropriately documenting the magnitude of intercohort variation requires long-term studies (roughly two population turnovers). Given the profound effect that DLHEs can have on population dynamics, quantifying intercohort variation in mean fitness and the level(s) at which selection acts will be very important for developing accurate models of population dynamics. In general, when developing models of population dynamics, more attention should be paid to variation in mean fitness and not just variation in total numbers. [ABSTRACT FROM AUTHOR]

ABSTRACT Tissue samples used for genetic analyses are increasingly necessary for proper management of rare or endangered species, yet growing evidence suggests that traditional methods used to sample or mark amphibians have detrimental fitness effects. We used a semi-natural mesocosm experiment to determine the effect of larval tail-clipping on growth and survival of the endangered California tiger salamander. Even with relatively extreme levels of tail loss, we found no effect on survival, mass, or snout-vent length. We recommend larval tail-clipping as a low-impact method for collecting tissue samples from pond-breeding amphibians. © 2013 The Wildlife Society. [ABSTRACT FROM AUTHOR]

Copyright of Conservation Biology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome-wide loci are analysed. We present the results of an initial application of parallel tagged sequencing ( PTS) on a next-generation platform to sequence thousands of barcoded PCR amplicons generated from 95 nuclear loci and 93 individuals sampled across the range of the tiger salamander ( Ambystoma tigrinum) species complex. To manage the bioinformatic processing of this large data set (344 330 reads), we developed a pipeline that sorts PTS data by barcode and locus, identifies high-quality variable nucleotides and yields phased haplotype sequences for each individual at each locus. Our sequencing and bioinformatic strategy resulted in a genome-wide data set with relatively low levels of missing data and a wide range of nucleotide variation. structure analyses of these data in a genotypic format resulted in strongly supported assignments for the majority of individuals into nine geographically defined genetic clusters. Species tree analyses of the most variable loci using a multi-species coalescent model resulted in strong support for most branches in the species tree; however, analyses including more than 50 loci produced parameter sampling trends that indicated a lack of convergence on the posterior distribution. Overall, these results demonstrate the potential for amplicon-based PTS to rapidly generate large-scale data for population genetic and phylogenetic-based research. [ABSTRACT FROM AUTHOR]

The article discusses the tissue baits decomposition and the termites density in gradient of human land-use intensification in western Kenya. It states that there was a comparison of density and functional composition of termites with cellulose removal of undisturbed forest and farmlands. It mentions that no termite abundance was found in the gradient of human land-use intensification but the soil feeders density in the forest and farmlands decreased.

Quantifying the influence of the landscape on the genetic structure of natural populations remains an important empirical challenge, particularly for poorly studied, ecologically cryptic species. We conducted an extensive microsatellite analysis to examine the population genetics of the southern long-toed salamander ( Ambystoma macrodactylum sigillatum) in a naturally complex landscape. Using spatially explicit modelling, we investigated the influence of the Sierra Nevada topography on potential dispersal corridors between sampled populations. Our results indicate very high-genetic divergence among populations, high within-deme relatedness, and little evidence of recent migration or population admixture. We also discovered unexpectedly high between-year genetic differentiation ( FST) for breeding sites, suggesting that breeding groups vary over localized space and time. While environmental factors associated with high-elevation montane habitats apparently play an important role in shaping population differentiation, additional, species-specific biological processes must also be operating to account for observed deviations from temporal, among-year panmixia. Our study emphasizes the population-level insights that can be gained from high-density sampling in space and time, and the highly substructured population biology that may characterize amphibians in extreme montane habitats. [ABSTRACT FROM AUTHOR]

The historical biogeography of California’s taxa has been the focus of extensive research effort. The western pond turtle ( Emys marmorata) is an example of a wide-ranging taxon that spans several well-known California diversity hotspots. Using a dataset comprised of one mitochondrial and five nuclear loci, we elucidate the major biogeographic patterns of the western pond turtle across the California landscape. By employing a combination of phylogenetic and network-based approaches, we recovered a relatively ancient ( c. 2–8 Ma) north/south split among populations of E. marmorata and find an area of intergradation centred in the Central Coast Ranges of California. In addition, discordant mitochondrial/nuclear genetic patterns suggest subsequent gene flow from northern populations and from San Joaquin Valley populations into the Central Coast Ranges after the Pliocene-Pleistocene marine embayment of the Great Central Valley subsided. Our results emphasize the utility of nuclear DNA phylogeography for recovering the impact of relatively ancient biogeographic events, and suggest that the Central Coast Ranges of California have played a major role in the geographic structuring of the western pond turtle, and possibly other co-distributed taxa. [ABSTRACT FROM AUTHOR]

Current conservation mitigation plans often fail to ensure full in-kind habitat replacement for endangered species, which suggests the need for improved methods for calculating mitigation credits. A simple, yet biologically meaningful method for calculating mitigation credits would be to let the number of mitigation credits assigned to a parcel of land scale with the reproductive value of the individuals occupying that parcel. This can be accomplished by dividing the population into 2 or more subdivisions with different reproductive values, calculating the densities of these subdivisions as a function of one or more habitat parameters, and then forming a weighted sum of these densities such that each density distribution is weighted by the reproductive value of its respective subdivision of the population. This weighted sum is the density distribution of reproductive value, and by integrating it over a particular parcel, one can determine the mitigation value of that parcel. We carried out this procedure for a population of California tiger salamanders (Ambystoma californiense ), with distance from breeding site as our habitat parameter and the 3 visually identifiable age classes (adults, juveniles, and metamorphs) as our population subdivisions. This led to a density distribution of reproductive value that decreased exponentially with increasing distance from a breeding site. Mitigation strategies derived from this function will be more likely to ensure the persistence of California tiger salamander populations than current approaches, which assign all land within 1.6 km of a breeding site the same mitigation value. Use of the density distribution of reproductive value as a basis for mitigation plans is a procedure that can be applied to all endangered species, and it should improve the quality of mitigation decisions. [ABSTRACT FROM AUTHOR]

The article focuses on a study related to the extent of introgression between California tiger salamanders and introduced barred tiger salamanders. Ancestry informative markers (AIMs) were used to characterize the degree of introgression, keeping factors such as habitat, distance from introduction sites and watershed boundaries, under consideration. The markers showed that different chromosomal segments introgress at constant rates. According to the researchers, highly modified perennial breeding ponds showed higher introduced allele frequencies than natural seasonal ponds, which suggests greater invasion in perennial breeding ponds.

Well-supported, congruent phylogeographic and biogeographic patterns permit the development of a priori phylogeographic and distributional predictions. In the southeastern Coastal Plain of the United States, the common discovery of east–west disjunctions (phylogeographic breaks and species’ distributional boundaries) suggests that similar disjunctions should occur in codistributed taxa. Despite the near ubiquity of these disjunctions, the most recent morphological analyses of the flatwoods salamander, Ambystoma cingulatum, indicate that none occur in this low-vagility, Coastal Plain endemic. We conducted molecular and morphological analyses to test whether the flatwoods salamander is an exception to this common biogeographic pattern. Assessing geographic variation in this species is also an important management tool for this threatened, declining amphibian. We demonstrate that flatwoods salamanders, as predicted by comparisons to codistributed taxa, are polytypic with a major disjunction at the Apalachicola River. This drainage is a common site for east–west phylogeographic breaks, probably because repeated marine embayments during the Pliocene and Pleistocene interglacials generated barriers to gene flow. Based on mitochondrial DNA, morphology, and allozymes, we recognize two species of flatwoods salamanders —  Ambystoma cingulatum to the east of the Apalachicola drainage and Ambystoma bishopi to the west. Given this increased diversity, the conservation status of these two taxa may warrant re-evaluation. More generally, these results emphasize that in the absence of taxon-specific data, established comparative patterns can provide strong expectations for designing management units for unstudied species of conservation concern. [ABSTRACT FROM AUTHOR]

Delimiting the boundaries of species involved in radiations is critical to understanding the tempo and mode of lineage formation. Single locus gene trees may or may not reflect the underlying pattern of population divergence and lineage formation, yet they constitute the vast majority of the empirical data in species radiations. In this study we make use of an expressed sequence tag (EST) database to perform nuclear (nDNA) and mitochondrial (mtDNA) genealogical tests of species boundaries in Ambystoma ordinarium, a member of an adaptive radiation of metamorphic and paedomorphic salamanders (the Ambystoma tigrinum complex) that have diversified across terrestrial and aquatic environments. Gene tree comparisons demonstrate extensive nonmonophyly in the mtDNA genealogy of A. ordinarium, while seven of eight independent nuclear loci resolve the species as monophyletic or nearly so, and diagnose it as a well-resolved genealogical species. A differential introgression hypothesis is supported by the observation that western A. ordinarium localities contain mtDNA haplotypes that are identical or minimally diverged from haplotypes sampled from a nearby paedomorphic species, Ambystoma dumerilii, while most nDNA trees place these species in distant phylogenetic positions. These results provide a strong example of how historical introgression can lead to radical differences between gene trees and species histories, even among currently allopatric species with divergent life history adaptations and morphologies. They also demonstrate how EST-based nuclear resources can be used to more fully resolve the phylogenetic history of species radiations. [ABSTRACT FROM AUTHOR]

The article focuses on the effects of habitat alteration on population size and viability of amphibians. Many amphibians breed in wetland habitats and spend the vast majority of their lives in nearby upland habitats. To estimate the upland distribution of subadult and adult California tiger salamanders, the researchers used a novel trapping approach that allowed them to model the spatial variation in capture rates in the landscape surrounding an isolated breeding pond. To investigate the population-level consequences of reducing the amount of suitable upland habitat around breeding ponds, they used a stage-based stochastic population model with subadult and adult survival parameters modified according to their empirical observations of upland distribution. Model simulations suggested that substantial reductions in population size are less likely if upland habitats extending at least 600 meters from the pond edge are maintained. Model elasticities indicated that quasi-extinction probabilities are more sensitive to reductions in subadult and adult survivorship than reproductive parameters.

We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas,E. marmoratacontains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspeciesEmys marmorata marmorata(Washington–central California). However, no clade is congruent with the distribution of the southern subspeciesEmys marmorata pallidafrom central California–Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Ouramovaand phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation. [ABSTRACT FROM AUTHOR]

The red-legged frog, Rana aurora, has been recognized as both a single, polytypic species and as two distinct species since its original description 150 years ago. It is currently recognized as one species with two geographically contiguous subspecies, aurora and draytonii; the latter is protected under the US Endangered Species Act. We present the results of a survey of 50 populations of red-legged frogs from across their range plus four outgroup species for variation in a phylogenetically informative, ∼400 base pairs (bp) fragment of the mitochondrial cytochrome b gene. Our mtDNA analysis points to several major results. (1) In accord with several other lines of independent evidence, aurora and draytonii are each diagnosably distinct, evolutionary lineages; the mtDNA data indicate that they do not constitute a monophyletic group, but rather that aurora and R. cascadae from the Pacific northwest are sister taxa; (2) the range of the draytonii mtDNA clade extends about 100 km further north in coastal California than was previously suspected, and corresponds closely with the range limits or phylogeographical breaks of several codistributed taxa; (3) a narrow zone of overlap exists in southern Mendocino County between aurora and draytonii haplotypes, rather than a broad intergradation zone; and (4) the critically endangered population of draytonii in Riverside County, CA forms a distinct clade with frogs from Baja California, Mexico. The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California. [ABSTRACT FROM AUTHOR]

Wind-borne pesticides have long been suggested as a cause of amphibian declines in areas without obvious habitat destruction. In California, the transport and deposition of pesticides from the agriculturally intensive Central Valley to the adjacent Sierra Nevada is well documented, and pesticides have been found in the bodies of Sierra frogs. Pesticides are therefore a plausible cause of declines, but to date no direct links have been found between pesticides and actual amphibian population declines. Using a geographic information system, we constructed maps of the spatial pattern of declines for eight declining California amphibian taxa, and compared the observed patterns of decline to those predicted by hypotheses of wind-borne pesticides, habitat destruction, ultraviolet radiation, and climate change. In four species, we found a strong positive association between declines and the amount of upwind agricultural land use, suggesting that wind-borne pesticides may be an important factor in declines. For two other species, declines were strongly associated with local urban and agricultural land use, consistent with the habitat-destruction hypothesis. The patterns of decline were not consistent with either the ultraviolet radiation or climate-change hypotheses for any of the species we examined. [ABSTRACT FROM AUTHOR]

Presents a study that evaluated the spatial population structure of California tiger salamanders in a network of breeding ponds. Background on metapopulation dynamics; Methods used; Results and discussion.

Abstract We present a comprehensive survey of genetic variation across the range of the narrowly distributed endemic Yosemite toad Bufo canorus, a declining amphibian restricted to the Sierra Nevada of California. Based on 322 bp of mitochondrial cytochrome b sequence data, we found limited support for the monophyly of B. canorus and its closely related congener B. exsul to the exclusion of the widespread western toad B. boreas. However, B. exsul was always phylogenetically nested within B. canorus, suggesting that the latter may not be monophyletic. SSCP (single-strand conformation polymorphism) analysis of 372 individual B. canorus from 28 localities in Yosemite and Kings Canyon National Parks revealed no shared haplotypes among these two regions and lead us to interpret these two parks as distinct management units for B. canorus. Within Yosemite, we found significant genetic substructure both at the level of major drainages and among breeding ponds. Kings Canyon samples show a different pattern, with substantial variation among breeding sites, but no substructure among drainages. Across the range of B. canorus as well as among Yosemite ponds, we found an isolation-by-distance pattern suggestive of a stepping stone model of migration. However, in Kings Canyon we found no hint of such a pattern, suggesting that movement patterns of toads may be quite different in these nearby parklands. Our data imply that management for B. canorus should focus at the individual pond level, and effective management may necessitate reintroductions if local extirpations occur. A brief review of other pond-breeding anurans suggests that highly structured populations are often the case, and thus that our results for B. canorus may be general for other species of frogs and toads. [ABSTRACT FROM AUTHOR]