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Analytic dataset informing modeling of winter species distributions of North American bat species

Citation

Olson, Sarah et al. (2021), Analytic dataset informing modeling of winter species distributions of North American bat species, Dryad, Dataset, https://doi.org/10.5061/dryad.crjdfn32r

Abstract

The fungal pathogen Pseudogymnoascus destructans and resultant white-nose syndrome (WNS) continues to advance across North America, infecting new bat populations, species, and hibernacula. Western North America hosts the highest bat diversity in the U.S. and Canada, yet little is known about hibernacula and hibernation behavior in this region. An improved understanding of where bats hibernate and the conditions that create suitable hibernacula is critical if land managers are to anticipate and address the conservation needs of WNS-susceptible species in regions yet to be infected. We estimated suitability of potential winter hibernaculum sites across the ranges of five bat species occurring in western North America. We estimated winter survival capacity from a mechanistic survivorship model based on bat bioenergetics and climate conditions. Leveraging the Google Earth Engine platform for spatial data processing, we used boosted regression trees to relate these estimates, along with key landscape attributes, to bat occurrence data in a hybrid correlative-mechanistic approach. Winter survival capacity, topography, land cover, and access to caves and mines were important predictors of winter hibernaculum selection, but the shape and relative importance of these relationships varied among species. This suggests that the occurrence of bat hibernacula can, in part, be predicted from readily mapped above-ground features, and is not only dictated by below-ground characteristics for which spatial data are lacking. Furthermore, our mechanistic estimate of winter survivorship was, on average, the third strongest predictor of winter occurrence probability across focal species. Winter distributions of North American bat species were driven by their physiological capacity to survive winter conditions and duration in a given location, as well as selection for topographic and other landscape features, but in species-specific ways. The influence of winter survivorship on several species’ distributions, the underlying influence of climate conditions on winter survivorship, and the anticipated influence of WNS on bats’ hibernation physiology and survivorship together suggest that North American bat distributions may undergo future shifts as these species are exposed to not only WNS, but climate change. We anticipate that the models presented here may offer a valuable baseline for assessing the potential species-level impacts of these stressors.

Methods

Winter occurrence data

We selected five focal species for our analyses: Corynorhinus townsendii, Myotis californicus, Myotis lucifugus, Myotis velifer, and Perimyotis subflavus. These species were chosen because occurrence data and field-measured metabolic parameters were available for estimating survivorship, and because they were representative of variability in known habitat requirements among hibernating bats whose ranges lie in whole or in part in the West, defined here as west of the Mississippi River.

We compiled species occurrence data from multiple sources, including online databases of museum records (VertNet, Biodiversity Information Serving Our Nation [BISON]), online repositories of vetted public and scientific observations (Global Biodiversity Information Facility [GBIF], Bat Population Database [BPD]), data associated with published literature, data obtained from multiple Natural Heritage Programs (Montana NHP and via NatureServe), and data collected in our own field studies (unpublished data). We amassed thousands of occurrence records for each focal species, but the vast majority of records (>85%) were observed during summer or fall swarming, when bats are more readily observed. Even in bats that do not migrate seasonally, selection of hibernaculum microclimates and the surrounding habitat mosaic is expected to differ from selection of summer roosts. Moreover, due to the sensitivity of hibernaculum locations to disturbance or exploitation, along with the difficulty of detecting torpid bats in hibernacula, winter bat location data were difficult to come by and limited in number. See linked publication for further details. 

We included only in-hand or visual observations (i.e., no acoustic detections) since 1948 (to match the earliest availability of gridded climate data) with location error < 5 km. Because we were interested only in winter distributions associated with hibernaculum use, we filtered the compiled dataset to observations recorded during what we defined as winter in a spatially explicit manner. We first used a generalized linear model informed by the timing of M. lucifugus immergence and emergence observations at hibernacula throughout North America to estimate winter duration for each 1-km raster cell across the U.S. and Canada (see linked publication for further details). Then, to estimate the start and end date of winter hibernation at a given grid cell, we centered this model-based winter duration estimate on the winter solstice. Finally, we selected only occurrence records observed between these spatially explicit start and end dates. Lastly, we removed repeat observations (e.g., across multiple studies or survey dates), retaining a single record for a given site (with unique sites defined to the nearest thousandth of a degree of latitude and longitude).

Predictor variables

We identified landscape attributes that potentially influence hibernaculum selection from the published literature and our own knowledge. We selected publicly available datasets representing these predictors with sufficient spatial extent to encompass our compiled occurrence data (United States and Canada south of the Arctic Circle). Where multiple candidate datasets were available, we chose those with the highest spatial resolution and/or temporal range that best encompassed our occurrence data. The scale at which bats perceive and respond to landscape attributes may vary among species, attributes, and locales. We therefore derived predictor variables at multiple spatial scales (i.e., different neighborhood sizes, or the radius around each focal raster cell across which predictor values were smoothed) where applicable for comparison. Our selection of neighborhood sizes, which included 500 m, 5 km, and 25 km was guided by those to which bats were found to respond in previous studies of multiscale habitat selection (100 m – 10 km). However, these studies focused on response to the landscape during daily foraging bouts, and we felt it was important to consider a broader range of spatial scales for selection of a winter hibernaculum. All smoothing of predictor variables using each of the selected neighborhood sizes was performed at the native resolution of each variable prior to sampling. Thus, for a variable with native resolution of 30 m, we summarized values within 500 m, 5 km, and 25 km of each focal 30 m cell. Each layer was then aggregated to two scales, 1 km and 10 km, for sampling. This step offered a means of exploring the scale of bats’ response to those variables to which we could not reasonably apply the above range of neighborhood sizes, either due to the coarse native resolution of the variables or because application of varying neighborhood sizes did not make intuitive sense. All predictors were derived and/or sampled using Google Earth Engine, a cloud-based computing platform supporting large-scale analysis on an extensive catalog of remotely sensed, climatological, and other geospatial datasets. All final predictive maps were derived at a resolution of 1 km.

Survivorship. We estimated species-specific, spatially explicit winter survivorship relative to the duration of winter. These estimates were based on an existing bioenergetic model of bat winter survivorship, recently updated and parameterized for western bat species. Full details are elsewhere (see linked publication and references therein), but briefly, the model uses the hypothesized energetic requirements of bats in torpor to dynamically model torpor bouts for the duration of a predicted winter under specified hibernaculum conditions. For M. lucifugus, torpor consumes approximately eighty times less energy per unit time than euthermia, whereas the infrequent but periodic arousals to euthermic temperatures use the majority of energy stores, with each arousal consuming approximately 5% of total overwinter energetic costs. In this model, ambient temperature and relative humidity were drivers of arousal frequency. Using gridded spatial data, we applied the model to values of each 1-km grid cell across the study extent to predict the fat mass expected to remain at the end of winter given mean ambient temperature and winter duration at each 1-km2 raster cell. Higher, positive predicted values are expected to correspond to high survivorship, while low or negative values indicate areas where bats are unlikely to survive. Further details regarding the bioenergetic model and spatial parameters are described in the Supplemental Information.

Topography. We derived topographic covariates from the global ALOS Digital Surface Model (DSM version 2.2) at 30-m resolution, including elevation, topographic ruggedness, and topographic position. Topographic ruggedness was quantified as the standard deviation of elevation values within a given radius around each focal raster cell. Similarly, topographic position was quantified as the difference between the elevation of each focal raster cell and the mean of elevation values within a given radius, such that high values are associated with peaks and ridges and low values are associated with canyon bottoms. We also extracted Continuous Heat-Insolation Load Index, a surrogate for effects of solar insolation and topographic shading on evapotranspiration, also derived from the global ALOS DSM at 90-m resolution. We used a moving window approach to derive topographic ruggedness and position at three spatial scales (diameter = 500 m, 5 km, 25 km), then the resulting values were averaged to create ‘multiscale’ metrics. We took the focal mean of solar insolation values over these multiple scales as well. 

Surface attributes. We derived percent tree cover from the Terra MODIS Vegetation Continuous Fields product, which estimates sub-pixel-level surface vegetation cover globally, including percent tree cover, on an annual basis (250-m resolution; NASA). Because data were not available for the entire temporal range of our occurrence data, we used data for the most recent year available (2015). We estimated percent tree cover at two aggregated scales (diameter = 5 km, 25 km). We used global nighttime lights imagery from the Defense Meteorological Program Operational Line-Scan System (Radiance-Calibrated, V4) as a proxy for relative intensity of human development (30-arcsec resolution; NOAA). We estimated availability of surface water based on the Joint Research Center Yearly Water Classification History (V1), which maps the location and seasonality of surface water from Landsat 5, 7, and 8 imagery (30-m resolution). We estimated the percent cover of seasonal or permanent surface water at three spatial scales (diameter = 500 m, 5 km, 25 km), focusing on the most recent year for which data were available (2015) because the data do not span the entire temporal range of our occurrence dataset. We estimated the frequency of snow cover based on the MODIS Global Daily Snow Cover product (V6), which estimates percent snow cover of each 500-m pixel on a daily basis. We counted the average number of days per year with at least 10% snow cover over the 5-year period from July, 2013 to June, 2018. We quantified precipitation using the DayMet dataset (V3), which provides gridded daily precipitation data at 1-km resolution. We estimated mean annual total precipitation by summing daily values annually then averaging the most recent five years available (2013-2018) for consistency with the temporal range of other available predictor data. 

Below-ground attributes. To represent potential availability of karst features that may provide suitable hibernacula, we relied on a map of karst and pseudokarst features across the United States produced by Weary and Doctor (2014, USGS Open-File Report 2014–1156) derived from State geological survey maps and USGS integrated geologic map databases (1:24,000 to 1:500,000 resolution). We merged this with an equivalent dataset for British Columbia provided by the Ministry of Forests, Lands, Natural Resource Operations and Rural Development (1:250,000 resolution) (Forest Analysis and Inventory, 2019). We did not differentiate among karst types, and instead created a simple binary indicator of karst presence vs. absence in raster format (1-km resolution). We also estimated availability of mines as potential hibernacula, using mine site locations available from the USGS Prospect- and Mine-Related Features database (v4, available for all but northeastern states) and the Mineral Resources Data System (MRDS, used for northeastern states; USGS), and from the MINFILE Production Database for British Columbia (BC Geological Survey). We included only mineral resource sites classified as mines (Mine-Related Features and MRDS) or as producing at one time (MINFILE). We derived two measures of mine availability: distance to the nearest mine and density of mines within 50 km of each focal raster cell (1-km resolution), calculated using a Gaussian kernel density function (sigma = 25 km). Karst and mine data were not available for other Canadian provinces; these predictors were not included in models for M. lucifugus, whose range spans these areas. Finally, we estimated groundwater depth from a global water table depth model that gap-filled point observations with a mechanistic groundwater model (1-km resolution; Fan et al., 2013, Science 339:940). 

Model fitting

We estimated species-specific relative probability of occurrence during winter using boosted regression trees (BRT; De’Ath, 2007, Ecology 88(1):243; Elith et al., 2008, Journal of Animal Ecology 77:802). A BRT (a.k.a. gradient boosting machine or stochastic gradient boosting) is an ensemble approach that combines regression trees, which relate a response to predictors by recursive binary splits of the data, and boosting, in which inference is drawn from the relative strength of many possible models rather than fitting a single parsimonious model. This method offers advantages over more traditional linear regression approaches in that a variety of response data and model forms can be accommodated (e.g., Gaussian, binomial, Poisson); different types of predictor variables (e.g., continuous, ordinal, categorical) can be included with no need for transformation or outlier removal; nonlinear relationships are easily captured; and interactions between predictors are handled automatically. Furthermore, overfitting is well-controlled through the use of cross‐validation as BRT models are ‘grown’. Importantly, a number of studies (see linked publication and references therein) have shown strong BRT predictive performance relative to other SDM approaches (e.g., generalized linear models, generalized additive models, climatic envelope models, maximum entropy). 

We follow the approach detailed by Elith et al. (2008) for application of BRT to species distribution modeling. One key difference in our application is that we make use of presence-background data rather than presence-absence data. Use of presence-background data, in which sites where the focal species was absent are not known with certainty, requires a shift in model assumptions and inference. Presence-absence models compare landscape attributes of sites at which the species was known to be present and absent to estimate the absolute probability of occurrence at any unobserved site given its climate and/or landscape characteristics. Without absence data, attributes of presence locations must instead be compared to randomly-sampled ‘background’ locations. In this case, presence is assessed relative to availability and the species’ absence at sampled background locations is not guaranteed. This shift in comparison fundamentally alters the inferences that can be made from the model: we cannot estimate the absolute probability of focal species occurrence (i.e., 80% probability of occurrence at a given site), but we can estimate, or rank, the relative probability of occurrence.

We sampled ‘background’ locations from geographic areas extending well beyond each species’ known range in the US and Canada (16 western states and British Columbia for C. townsendii, M. californicus; all states and provinces for M. lucifugus; all US states for M. velifer, P. subflavus). This choice aimed to sufficiently capture the full range of environmental conditions limiting bats’ distributions. Because bats were more likely to have been observed in locations already known to harbor bats and that are more accessible (e.g., closer to population centers, accessible by roads, and in less rugged topography), we generated background points so as to replicate and thus control for this inherent spatial bias (after Hertzog et al., 2014, Diversity and Distributions 20:1403). We first created a bias grid based on the kernel density of occurrence locations using the MASS package for R, then generated background points with probability dictated by occurrence density, such that areas with high density of occurrences had high probability of background sampling, but all locations within the sampling extent had nonzero probability of sampling. Our background sample consisted of three background points per occurrence point as a balance between achieving good coverage of available habitat and not artificially inflating sample size. Finally, we sampled all candidate predictor variables at each presence and background location.

To identify the most appropriate scale for each predictor (i.e., the scale at which habitat selection was most evident), we first fit univariate generalized additive models (GAM) for each predictor. We chose GAM for this preliminary predictor selection step to not constrain the form of the response. We selected the best performing scale for each predictor based on a comparison of Akaike’s Information Criterion (AIC) scores across each scale at which the predictor was sampled. We then assessed pairwise correlations and variance inflation factors across the resulting set of predictors and excluded those causing standard thresholds of 0.7 and 4.0, respectively, to be exceeded to avoid multicollinearity. We also excluded mine density from further consideration due to its poorer AIC-based performance across all focal species compared to distance from mines. 

We fit and calibrated each BRT model using the stepwise cross-validation process detailed by Elith et al. (2008) and accompanying R scripts (Elith et al., 2008 Appendix S3). We adjusted the model learning rate to ensure that a minimum of 1000 trees were fit, then calibrated the tree complexity (range: 3-5) and bag fraction (range: 0.5-0.7) to minimize deviance. We tested for benefits of dropping uninformative model terms based on estimated reduction in deviance. We then used this ‘optimized’ model to assess the relative contribution of each predictor, plot the relationship between each predictor and relative occurrence probability, and evaluate model performance. We evaluated the model’s fit to the training data (iteratively partitioned in the cross-validation process) based on the mean proportion of deviance explained in each cross-validation iteration (D2), a pseudo-determination coefficient intended to be comparable to R2. We also assess predictive performance based on the cross-validated area under the receiver operating curve (AUC). Although use of this metric to evaluate presence-background models is flawed by ‘contamination’ of background sites with unobserved presence, we report it as an additional evaluation metric that supports comparison with other studies that frequently include it. As a final modeling step, we applied the optimized model to predictor values in each 1-km cell of the extent of interest for each species to predict and map relative probability of occurrence (Elith et al., 2008 Appendix S3). We summarized the percentile ranks of occurrence probability values predicted for presence and background locations as an additional assessment of predictive performance.  All model fitting and prediction were conducted in R (version 3.4.1).

Usage Notes

See uploaded ReadMe file.

Funding

U.S. Department of Defense, Award: W912HQ-16-C-0015

Royal Society Te Aparangi, Award: MAU1701