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The Provincelands of Cape Cod National Seashore, Barnstable County, Massachusetts, USA. The reddish vegetation in the center of the photo is a cranberry (Vaccinium macrocarpon) bog, a wetland used for breeding by the Fowler's toad. The surrounding landscape is ideal for the Fowler's toad and supports one of the largest populations of this species in the United States. The landscape contains a patchwork of sand, pitch pine (Pinus rigida), scrub oak (Quercus ilicifolia), and dune grass (Ammophila breviligulata). Photo by Rebecca Flaherty. in Fowler's Toad (Anaxyrus fowleri) occupancy in the southern mid-Atlantic, USA

The Provincelands of Cape Cod National Seashore, Barnstable County, Massachusetts, USA. The reddish vegetation in the center of the photo is a cranberry (Vaccinium macrocarpon) bog, a wetland used for breeding by the Fowler's toad. The surrounding landscape is ideal for the Fowler's toad and supports one of the largest populations of this species in the United States. The landscape contains a patchwork of sand, pitch pine (Pinus rigida), scrub oak (Quercus ilicifolia), and dune grass (Ammophila breviligulata). Photo by Rebecca Flaherty.

Fig. 3 in Fowler's Toad (Anaxyrus fowleri) occupancy in the southern mid-Atlantic, USA

Fig. 3. Accumulation curve showing the maximum agricultural pesticide application rates at occupied sites. The maximum amount of pesticides applied at 90% of occupied sites was 165 kg/km2.

Fig. 1 in Fowler's Toad (Anaxyrus fowleri) occupancy in the southern mid-Atlantic, USA

Fig. 1. Map of calling anuran surveys conducted in Maryland and Virginia. Closed circles indicate sites occupied by A. fowleri and open circles indicate unoccupied sites.

Fig. 2 in Fowler's Toad (Anaxyrus fowleri) occupancy in the southern mid-Atlantic, USA

Fig. 2. Accumulation curve showing the maximum proportions of habitat variables found at each occupied site. Ninety-percent of occupied sites were covered by less than 0.25 development, 0.35 hay, and 0.50 deciduous forest cover.

Fig. 4 in Fowler's Toad (Anaxyrus fowleri) occupancy in the southern mid-Atlantic, USA

Fig. 4. Mean site occupancy and confidence intervals of A. fowleri in Virginia and Maryland from 1999–2012. Time series analysis indicates a 53% decrease in site occupancy, from 55.3% in 1999 to 29.5% in 2012.

opencc-zeroOct 2019View details →

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus) Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this "glacial pulse" model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including novel admixed ("fused") lineages. We tested for patterns of glacial pulse lineage diversification in the Yosemite toad (Anaxyrus [Bufo] canorus), an alpine endemic tied to glacially influenced meadow environments. Using double-digest RADseq on populations densely sampled from a portion of the species range, we identified nine distinct lineages with divergence times ranging from 18–724 ka, coinciding with multiple Sierra Nevada glacial events. Three lineages have admixed origins, and demographic models suggest these fused lineages have persisted throughout past glacial cycles. Directionality indices supported the hypothesis that some lineages recolonized Yosemite from east of the ice sheet, whereas other lineages remained in western refugia. Finally, refugial niche reconstructions suggest that low- and high-elevation lineages have convergently adapted to similar climatic niches. Our results suggest glacial cycles and refugia may be important crucibles of adaptive diversity across deep evolutionary time. Gene pool boundaries for the Yosemite toad (Anaxyrus canorus) reveal asymmetrical migration within meadow neighborhoods The Yosemite toad (Anaxyrus [Bufo] canorus) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well documented, and is reputed to remain in low abundance throughout its range. Recent phylogeographic work has demonstrated that Pleistocene toad lineages diverged and then admixed to differing extents across an elevational gradient. Although lineage divisions may have significant effects on evolutionary trajectories over large spatial and temporal scales, present-day population dynamics must be delineated in order to manage and conserve the species effectively. In this study, we used a double-digest RADseq dataset to address three primary questions: (1) Are single meadows or neighborhoods of nearby meadows most correlated with population boundaries? (2) Does asymmetrical migration occur among neighborhoods of nearby meadows? (3) What topographic or hydrological variables predict such asymmetrical migration in these meadow neighborhoods? Hierarchical STRUCTURE and AMOVA analyses suggested that populations are typically circumscribed by a single meadow, although 84% of meadows exist in neighborhoods of at least two meadows connected by low levels of migration, and over half (53%) of neighborhoods examined display strong asymmetrical migration. Meadow neighborhoods often contain one or more large and flat "hub" meadows that experience net immigration, surrounded by smaller and topographically rugged "satellite" meadows with net emigration. Hubs tend to contain more genetic diversity and could be prioritized for conservation and habitat management and as potential sources for reestablishment efforts. Landscape genetics of a sub-alpine toad: Climate change predicted to induce upward range shifts via asymmetrical migration corridors Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the 21st century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park. ** Note: Multiple articles are associated with this dataset

zenodo36/100

Data from a study on the role of the American toad (Anaxyrus americanus) in vegetable pest management in Pennsylvania

Datasets associated with a manuscript on the role of the American toad (Anaryxus americanus) in pest management in vegetable production in Pennsylvania, USA. The datasets derive from three distinct studies that shed light on the ecological role of the toad: (1) gut contents of field-collected individuals from a small diversified vegetable farm, (2) outcomes from a laboratory experiment on toad foraging behavior toward a range of prey, and (3) outcomes from a field mesocosm experiment in which different densities of toads were enclosed with kale plants.  Please see the file <code>toad_column_key.xlsx</code> for the definitions of fields in all data files.

opencc-by-4.0Jul 2024View details →

opencc-zeroNov 2022View details →

Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite Toad (Anaxyrus canorus)

An essential goal in conservation biology is delineating population units that maximize the probability of species persisting into the future and adapting to future environmental change. However, future-facing conservation concerns are often addressed using retrospective patterns that could be irrelevant. We recommend a novel landscape genomics framework for delineating future "Geminate Evolutionary Units" (GEUs) in a focal species: (1) identify loci under environmental selection, (2) model and map adaptive conservation units that may spawn future lineages, (3) forecast relative selection pressures on each future lineage, and (4) estimate their fitness and likelihood of persistence using geo-genomic simulations. Using this process, we delineated conservation units for the Yosemite toad (Anaxyrus canorus), a U.S. federally threatened species that is highly vulnerable to climate change. We used a genome-wide dataset, redundancy analysis, and Bayesian association methods to identify 24 candidate loci responding to climatic selection (R2 ranging from 0.09–0.52), after controlling for demographic structure. Candidate loci included genes such as MAP3K5, involved in cellular response to environmental change. We then forecasted future genomic response to climate change using the multivariate machine learning algorithm Gradient Forests. Based on all available evidence, we found three GEUs in Yosemite National Park, reflecting contrasting adaptive optima: YF-North (high winter snowpack with moderate summer rainfall), YF-East (low to moderate snowpack with high summer rainfall), and YF-Low-Elevation (low snowpack and rainfall). Simulations under the RCP 8.5 climate change scenario suggest that the species will decline by 29% over 90 years, but the highly diverse YF-East lineage will be least impacted for two reasons: (1) geographically it will be sheltered from the largest climatic selection pressures, (2) its standing genetic diversity will promote a faster adaptive response. Our approach provides a comprehensive strategy for protecting imperiled non-model species with genomic data alone and has wide applicability to other declining species.

publicNov 2022View details →

Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite Toad (Anaxyrus canorus)

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publicMar 2024View details →

Yosemite Toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression

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publicOct 2022View details →

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

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dryad32/100

Data from: Temporal population genetic instability in range edge Western Toads, Anaxyrus boreas

In this article, we address the temporal stability of population genetic structure in a range-edge population that is undergoing continual, short-distance colonization events. We sampled western toad, Anaxyrus boreas, breeding populations over 2 seasons near their northern range limit in southeast Alaska. We sampled 20 ponds each during the summers of 2008 and 2009, with 14 ponds sampled in both summers. We found considerable turnover in the population genetic relationships among ponds in those 2 seasons, as well as biologically meaningful genetic differentiation between years within some ponds. We found relatively consistent relationships between major population centers, whereas the relationships between the central ponds and smaller, outlying populations differed year to year. This finding indicates that multiple years of genetic sampling may be important for understanding the genetic landscape of some populations.

opencc-zeroDec 2013View details →

dryad32/100

Annotated transcriptome data from: Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri

Briefly considered extinct in the wild, the future of the wild population of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in the host immune response represents an important conservation need. Population decline may have reduced immunogenetic diversity sufficiently to increase the vulnerability of the species to infectious diseases. Here we use comparative transcriptomics to examine the diversity of toll-like receptors and major histocompatibility complex (MHC) sequences across three individual Wyoming toads. We find reduced diversity at MHC genes compared to bufonid species with a similar history of bottleneck events. Our data provide a foundation for future studies that seek to evaluate the genetic diversity of Wyoming toads, identify biomarkers for infectious disease outcomes, and guide breeding strategies to increase genomic variability and wild release successes.

opencc-zeroJan 2022View details →

FIGURE 1 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada

FIGURE 1. Sampling localities of populations included for morphological (a) and DNA (b) collections within the hydrological Great Basin and surrounding states. a) Colors indicate species-specific populations measured for morphological analysis. b) Colors correspond with localized species and B. boreas colors correspond with major mtDNA haplotype clades (ONV- Oregon- NW Nevada (yellow), HL-Humboldt-Lahontan (blue), M-Mojave (aqua)) identified in Tracy et al. (in progress) molecular study of B. boreas diversity. Maps created using ArcGIS software by ESRI (2011: Release 10).

FIGURE 5 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada

FIGURE 5. Discriminant function analysis (DFA). Cross validated DFA using 14 size corrected morphological characters measured from 380 live adult toads (Fig. 1a) examined within the hydrological Great Basin Bufo (Anaxyrus) boreas species complex. Species identified as B. boreas (red circle), B. nelsoni (blue diamond), B. exsul (green circle), and B. williamsi (yellow square).

FIGURE 4 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada

FIGURE 4. Photographs of Bufo (Anaxyrus) williamsi sp. nov. holotype (CAS 259271). Adult male toad presented live: (a) dorsal view and (b) ventral view; and preserved: (c) dorsal view and (d) ventral view. Photographs taken by M.R.Gordon.

FIGURE 3 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada

FIGURE 3. Molecular examination of Bufo (Anaxyrus) boreas species complex.The TCS haplotype network was constructed using 246 sequences (1622 aligned sites) obtained from toad sampling (Fig.1b) resulting in 72 unique haplotypes, with circle sizes corresponding with the number of individuals of a particular haplotype. Haplotype colors correspond geographically (Fig. 1b) and to localized species (B. canorus (purple), B. exsul (green) and B. nelsoni (orange)) and highlight the genetic divergence of B. williamsi (red). The condensed phylogeny identifying Great Basin Bufo (Anaxyrus) boreas species complex major haplotype clades: maximum likelihood of 10 samples (1436 aligned sites) using GTR +G+I evolutionary model. The terminals are identified by taxon name and followed by locality of collection for B. boreas. Bufo williamsi, noted with a red circle, is sister to boreas of the HL clade. Heavy bars correspond with major haplotype clades.

FIGURE 2 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada

FIGURE 2. Bufo (Anaxyrus) boreas species complex distribution. a) Bufo (Anaxyrus) boreas distribution (shown in brown) across the Western United States with hydrological Great Basin shown with black outline and hash mark interior; b) Bufo (Anaxyrus) boreas species complex and ranges for toads including new species, illustrating the narrow distribution of localized endemics. Spatial data for all toads except B. williamsi provided by IUCN (2015). Images taken by M.R.Gordon except B. canorus with photo credit to G. Nafis.

FIGURE 6 in A diamond in the rough desert shrublands of the Great Basin in the Western United States: A new cryptic toad species (Amphibia: Bufonidae: Bufo (Anaxyrus)) discovered in Northern Nevada

FIGURE 6. Major and minor groups identified: Bayesian inference phylogenetic tree constructed from analyses from unique haplotype sequences of 1622bp fragment of the control region of the mitochondrial genome (Fig. 1b; n = 308). Posterior probabilities are shown. Haplotype number (n = 72) and sampling locality comprise terminal ends of tree and two haplotypes of the root are shown. Minor groups include localized species: Bufo (Anaxyrus) nelsoni (green), B. exsul (orange), B. canorus (purple), B. williamsi (red) and undescribed divergent species (black). Large bars identify major groups, which include populations of B. boreas, sampled within the hydrological Great Basin (Fig. 1b).