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Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis

Citation

Messerman, Arianne et al. (2022), Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis , Dryad, Dataset, https://doi.org/10.5061/dryad.59zw3r291

Abstract

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 (Ambystoma californiense; 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.

Methods

Please see the associated manuscript for full methodological details.

Usage Notes

Available files to conduct a Bayesian integral projection model (IPM) and population viability analysis (PVA) for the California tiger salamander (CTS) include:

-The preliminary frequentist CTS IPM and PVA script created by Christopher A. Searcy is:
    "CTS-Frequentist-IPM.R" -- Frequentist code to build the IPM and run the PVA.

-The primary scripts to run the IPM and PVA are:
    "CTS_SOURCE.R" -- Source code for the vital rate functions.
    "CTS_IPM_PVA.R' -- Code to build the IPM, conduct sensitivity and elasticity analyses, and run the PVA.

-The scripts used to build the vital rate functions that inform the IPM are:
    "CTS_Best_Survival.R" -- The best Cormack-Jolly-Seber model of metamorph and juvenile/adult CTS survival and recapture probabilities.
    "CTS_Growth.R" -- CTS metamorph and juvenile/adult growth functions.
    "CTS_Fertility.R" -- CTS fertility function.
    "CTS_Maturity.R" -- CTS maturity function.
    "CTS_Larval_Survival.R" -- CTS larval survival given egg density function.
    "CTS_Females_Precip.R" -- The proportion of CTS females breeding given annual December-January precipitation function.
    "CTS_Replacement.R" -- Adult-only replacement and reproductive success functions to construct piecewise environmental-dependency function.

-All necessary data files to run the CTS_IPM_PVA.R script and support the findings of our study are:

"adults-v2.txt" -- The adult CTS capture histories from the capture-mark-recapture study at Jepson prairie Preserve, CA.

"covariates-v2.txt" -- The CTS capture histories from the capture-mark-recapture study at Jepson prairie Preserve, CA specifying individual body masses (ln-transformed; g).

"metamorphs-v2.txt" -- The metamorph CTS capture histories from the capture-mark-recapture study at Jepson prairie Preserve, CA.

"precip.csv" -- Study rain year-specific November-February and October-June precipitation values (mm).

"density-distance.csv" -- Proportion of the post-metamorphic life stage individuals (from 0 to 1) found within 100-m distance radius increments from the pond shoreline.

"Larval-Survival-Density.csv" -- Ln-transformed larval survival and Ln-transformed egg density (eggs/m^3) data.

"meta-size-by-egg-density.csv" -- Study year-specific metamorph size and egg density (eggs/m^3) data.

"Olcott20**.txt" -- Body size distributions of each cohort of CTS from the mark-recapture study across the 122 body size bins, where "**" indicates study year in the file name.

"Stochastic_Climate_Pool.txt" -- Historic precipitation record from 1893-2012 (Vacaville and Nut Tree Airport station records).

"Stochastic_Climate_Pool_Rev.txt" -- Historic precipitation record from 1893-2008 (Nut Tree Airport-only station records).

"females-precip-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distribution of the function of female CTS breeding given December-January precipitation (mm).

"fertility-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distribution of the function of clutch size (# eggs) given female CTS body mass (g).

"growth-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distributions of the life stage-specific growth functions.

"larval-survival-posterior-samples.csv" -- The 500 random samples from the posterior distribution of the function of larval survival probability given egg density (eggs/m^3).

"maturity-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distribution of the function of maturity probabilitygiven CTS body mass (g).

"replace-success-infection-samples-CENTERED.csv" -- The 500 random samples of the inflection point from the posterior distribution of the function of probability of metamorph recruitment being above the replacement rate given October-June precipitation (mm).

"repro-success-infection-samples-CENTERED.csv" -- The 500 random samples of the inflection point from the posterior distribution of the function of probability of reproductive success given October-June precipitation (mm).

"survival-posterior-samples-CENTERED.csv" -- The 500 random samples from the posterior distribution of the Cormack-Jolly-Seber model of life stage-specific survival probabilities given body mass (g).

Scripts were developed and run using R version 4.0.0.

Funding

Bureau of Reclamation

California Department of Transportation

National Science Foundation

Solano County Water Agency

University of California, Davis

University of California Natural Reserve System