Optimizing Survey Design for Shasta Salamanders (Hydromantes spp.) to Estimate Occurrence in Little-Studied Portions of their Range
Shasta salamanders (collectively, Hydromantes samweli, H. shastae, and H. wintu; hereafter, Shasta salamander) are endemic to northern California in the general vicinity of Shasta Lake reservoir. Although generally associated with limestone, they have repeatedly been found in association with other habitats, calling into question the distribution of the species complex. Further limiting our knowledge of the species' distributions is that they are only active or available for sampling on the soil surface for a small portion of the year, and detection probabilities for the species have never been estimated. We developed and implemented a survey protocol designed to estimate detection, availability, and occurrence probabilities from December 2019 through March 2020. We provide inference on Shasta salamander occurrence in portions of their range that have received little survey effort. We found that Shasta salamander occurrence was positively associated with the percent cover of embedded rock, and the species' availability (i.e., probability of being active on the soil surface during sampling) was positively related to relative humidity. The probability of occurrence of Shasta salamanders in our study area was low, and our winter-to-spring survey protocol was effective for estimating detection, availability, and occurrence probabilities in the study area and at specific sites. We suggest that conducting replicate surveys that quantify animal availability and detection probabilities will facilitate a better understanding of the habitat associations of Shasta salamanders and other rare species that might often be unavailable for detection.Abstract
Location of the focal areas (large polygons) and surveyed sites (squares) relative to the estimated range of Shasta salamanders (collectively, Hydromantes samweli, H. shastae, and H. wintu) in northern California, 2019–2020. The inset shows the range of Shasta salamanders in northern California in black, with the study area (main map) outlined in red.
Effect of ambient relative humidity on the availability of Shasta salamanders (Hydromantes samweli and H. shastae) in northern California, 2019–2020. The bold line represents the posterior mode, light lines represent the 95% highest posterior density interval, and intensity of shading represents the posterior probability density. Tick marks represent observed values of relative humidity when salamanders were (y = 1) and were not (y = 0) detected.
Effect of percent cover of embedded rock on the probability of occurrence of Shasta salamanders (Hydromantes samweli and H. shastae) in northern California, 2019–2020. The bold line represents the posterior mode, light lines represent the 95% highest posterior density interval, and intensity of shading represents the posterior probability density. Tick marks represent observed values of percent cover of embedded rock where salamanders were (y = 1) and were not (y = 0) detected.
Posterior probability of occurrence of Shasta salamanders (Hydromantes samweli and H. shastae) at surveyed sites in northern California, 2019–2020, based on site and survey conditions and nondetection of salamanders. The color of the circles represents the posterior probability of occurrence. Black stars indicate sites where Shasta salamanders were detected. Polygons represent focal areas.
Number of secondary surveys (n*) required to declare Shasta salamanders (Hydromantes samweli and H. shastae) absent from a site with 95% certainty, given the percent cover of embedded rock at the site, the relative humidity at the time of the secondary surveys, and the number of tertiary surveys (q) per secondary survey. Note that availability (θ) increases with relative humidity and the probability of occurrence (ψ) increases with embedded rock cover. Sites with less embedded rock need fewer secondary surveys to declare absence than do sites with more rock because salamanders have a lower prior probability of occurrence at sites with less rock. Secondary surveys that are conducted when relative humidity is high provide more information about absence than do surveys conducted when relative humidity is low, so fewer surveys are necessary to declare absence when it is humid. Values in the figure are based on the posterior mean of ψ at the specified percent cover of embedded rock, the posterior mean of θ at the specified relative humidity, and the 0.05 quantile of detection probability (p = 0.51).
Number of secondary surveys (n*) required to declare Shasta salamanders (Hydromantes samweli and H. shastae) absent from a site with 95% certainty, given the percent cover of embedded rock at the site, the relative humidity at the time of the secondary surveys, detection probability (p), and the number of tertiary surveys (q) per secondary survey. Note that availability (θ) increases with relative humidity and the probability of occurrence (ψ) increases with embedded rock cover. Sites with less embedded rock need fewer secondary surveys to declare absence than do sites with more rock because salamanders have a lower prior probability of occurrence at sites with less rock. Secondary surveys that are conducted when relative humidity is high provide more information about absence than do surveys conducted when relative humidity is low, so fewer surveys are necessary to declare absence when it is humid. Values in the figure are based on the posterior mean of ψ at the specified percent cover of embedded rock and the posterior mean of θ at the specified relative humidity.
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