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Data and code for Winter conditions structure extratropical patterns of species richness of amphibians, birds, and mammals globally
<p>This repository contains the dataset analyzed in 'Winter conditions structure extratropical patterns of species richness of amphibians, birds, and mammals globally' - published in the journal Global Ecology and Biogeography - and the R code used to generate the correlations, generalized additive models, and related figures presented in the manuscript. Column descriptions for the data can be found in the associated README.txt file. Please refer to the manuscript for further detail on the variables and how they were derived.</p> <p>The Winter Indices (WIs) were derived using satellite remote sensing data from optical (MODIS, snow cover) and microwave (MEaSUREs freeze/thaw, frozen ground) sensors. The species richness maps were derived using IUCN range maps for individual species of amphibians, birds, and mammals (data requests can be made here: <a href="https://www.iucnredlist.org/resources/spatial-data-download">https://www.iucnredlist.org/resources/spatial-data-download</a>). Climatic varibales were derived from WorldClim v2.0 data, elevation from USGS GMTED2010 data, and primary productivity from the cumulative dynamic habitat index available here: <a href="http://silvis.forest.wisc.edu/maps-data/">http://silvis.forest.wisc.edu/maps-data/</a>.</p>
Fig. 1. Study area. C1-5 in Helminth communities from amphibians inhabiting agroecosystems in the Pampean Region (Argentina)
Fig. 1. Study area. C1-5: crop sites, L1- 4: livestock sites (C1: 34°55'13''S; 58°06'33''O; C2: 34°55'54''S; 58°04'29''O; C3: 34°57'36''S; 58°04'57''O; C4: 35°01'42''S; 57°59'44''O; C5: 35°03'06''S; 57°58'35''O; L1: 35°04'27''S; 57°57'23''O; L2: 35°07'46''S; 57°53'11''O; L3: 35°02'22,94''S; 57°48'58,8''O; L4: 35°02'23,2''S; 57°48'58,2''O).
Genomics‐informed delineation of conservation units in a desert amphibian
<p>Delineating conservation units (CUs, e.g., evolutionarily significant units, ESUs, and management units, MUs) is critical to the recovery of declining species because CUs inform both listing status and management actions. Genomic data have strengths and limitations in informing CU delineation and related management questions in natural systems. We illustrate the value of using genomic data in combination with landscape, dispersal, and occupancy data, to inform CU delineation in Nevada populations of the Great Basin Distinct Population Segment of the Columbia spotted frog (<em>Rana luteiventris</em>). <em>R</em>. <em>luteiventris</em> occupies naturally fragmented aquatic habitats in this xeric region, but beaver removal, climate change, and other factors have put many of these populations at high risk of extirpation without management intervention. We addressed three objectives: (1) assessing support for ESUs within Nevada; (2) evaluating and revising, if warranted, the current delineation of MUs; and (3) evaluating genetic diversity, effective population size, adaptive differentiation, and functional connectivity to inform ongoing management actions. We found little support for ESUs within Nevada but did identify potential revisions to MUs based on unique landscape drivers of connectivity that distinguish these desert populations from those in the northern portion of the species range. Effective sizes were uniformly small, with low genetic diversity and weak signatures of adaptive differentiation. Our findings suggest that management actions, including translocations and genetic rescue, might be warranted. Our study illustrates how a carefully planned genetic study, designed to address priority management goals that include CU delineation, can provide multiple insights to inform conservation action.</p>
Figure 2 in Amphibians and reptiles as prey of Heteroctenus junceus (Scorpiones: Buthidae), with a summary of vertebrate predation by scorpions in the West Indies
Figure 2. Heteroctenus junceus, the largest species in the genus and one of the largest scorpions in the West Indies, male (2a) and female (2b).
Figure 1 in Amphibians and reptiles as prey of Heteroctenus junceus (Scorpiones: Buthidae), with a summary of vertebrate predation by scorpions in the West Indies
Figure 1. Partially digested Anolis ophiolepis found being preyed upon by an adult female Heteroctenus junceus at Loma La Carrera; the scorpion fled as soon as we turned the rock over.
Figure 3 in Amphibians and reptiles as prey of Heteroctenus junceus (Scorpiones: Buthidae), with a summary of vertebrate predation by scorpions in the West Indies
Figure 3. Live individuals of the species of amphibians and reptiles reported here as being preyed upon by Heteroctenus junceus: Osteopilus septentrionalis (3a), Anolis allisoni (3b), A. sagrei (3c), and A. ophiolepis (3d).
Fig. 2 in Patterns and progress of Malaysia's amphibian research in the 21 century
Fig. 2. Percentage and number of papers published (in parenthesis) by category between January 2000 and September 2021 (A); the number of papers published in the New Species and Taxonomy category, grouped by data type (B).
Fig. 4 in Patterns and progress of Malaysia's amphibian research in the 21 century
Fig. 4. Number of papers published by region (A) and state (B). Only studies that were explicitly conducted within a particular region or state were included.
Fig. 1 in Patterns and progress of Malaysia's amphibian research in the 21 century
Fig. 1. The number of amphibian research papers published between January 2000 and September 2021 (A); the years 2000–2010 (B); and the years 2011–2021 (C). Regression lines are shown in blue (local polynomial regression fitting method) and red (linear regression method). Grey shading represents the 95% confidence interval of the linear regression model. Numbers next to points represent the total number of papers published that year.
Fig. 3 in Patterns and progress of Malaysia's amphibian research in the 21 century
Fig. 3. Bar plots grouped by category and binned into 5-year periods. Numbers above bars represent the total number of papers published in each category.
Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis
<p>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 the first stochastic size- and stage-structured IPM for a biphasic amphibian, the U.S. federally threatened California tiger salamander (<em>Ambystoma</em> <em>californiense</em>; CTS). This Bayesian model reveals that CTS population dynamics show the 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 indicates 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.</p>
Supplementary material 1 from: Pontoppidan M, Nachman G (2013) Changes in behavioural responses to infrastructure affect local and regional connectivity – a simulation study on pond breeding amphibians. Nature Conservation 5: 13-28. https://doi.org/10.3897/natureconservation.5.4611
Full model description following the ODD-template suggested by Grimm et al. (2006, 2010) and model parameterisation. (doi: 10.3897/natureconservation.5.4611.app). File format: Adobe PDF document (pdf).:
Supplementary material 1 from: Pontoppidan M, Nachman G (2013) Spatial Amphibian Impact Assessment – a management tool for assessment of road effects on regional populations of Moor frogs (Rana arvalis). Nature Conservation 5: 29-52. https://doi.org/10.3897/natureconservation.5.4612
Full model description following the protocol suggested by Grimm et al. (2006, 2010) and model parameterisation. (doi: 10.3897/natureconservation.5.4612.app). File format: Adobe PDF document (pdf).:
FIGURE 16 in Herpetological Survey of Iona National Park and Namibe Regional Natural Park, with a Synoptic List of the Amphibians and Reptiles of Namibe Province, Southwestern Angola
FIGURE 16. Adult Dwarf Plated Lizard, Cordylosaurus subtessellatus (Smith, 1844), from near Espinheira. Photo by Edward Stanley.
FIGURE 19 in Herpetological Survey of Iona National Park and Namibe Regional Natural Park, with a Synoptic List of the Amphibians and Reptiles of Namibe Province, Southwestern Angola
FIGURE 19 – Adult Karoo Sand Snake, Psammophis notostictus Peters, 1867, from Espinheira. Photo by Luis Ceríaco.
FIGURE 8 in Herpetological Survey of Iona National Park and Namibe Regional Natural Park, with a Synoptic List of the Amphibians and Reptiles of Namibe Province, Southwestern Angola
FIGURE 8. Adult Barnard's Namib Day Gecko, Rhoptropus barnardi Hewitt, 1926, from Kamanjab, Kunene Region, Namibia. Photo courtesy of Johan Marais.
FIGURE 3 in Herpetological Survey of Iona National Park and Namibe Regional Natural Park, with a Synoptic List of the Amphibians and Reptiles of Namibe Province, Southwestern Angola
FIGURE 3. Anchieta's Ground Agama, Agama anchietae Bocage, 1866, from Sesfontein, Kunene Region, Namibia. Photo courtesy of Johan Marais.
FIGURE 2 in Herpetological Survey of Iona National Park and Namibe Regional Natural Park, with a Synoptic List of the Amphibians and Reptiles of Namibe Province, Southwestern Angola
FIGURE 2. Marbled Rubber Frog, Phrynomantis annectens Werner, 1910, from Palmwag, Kunene Region, Namibia. Photo courtesy of Randall Babb.
FIGURE 7 in Herpetological Survey of Iona National Park and Namibe Regional Natural Park, with a Synoptic List of the Amphibians and Reptiles of Namibe Province, Southwestern Angola
FIGURE 7. Juvenile Angolan Thick-toed Gecko, Pachydactylus angolensis (Loveridge, 1944), from Chimalavera, Benguela Province, Angola. Photo by Luis Ceríaco.
FIGURE 12 in Herpetological Survey of Iona National Park and Namibe Regional Natural Park, with a Synoptic List of the Amphibians and Reptiles of Namibe Province, Southwestern Angola
FIGURE 12. Adult Speckled Sand Skink, Trachylepis punctulata (Bocage, 1872), from Kamanjab, Kunene Region, Namibia. Photo courtesy of Johan Marais.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.