Through the North American Bat Monitoring Program, Bat Conservation International and U.S Geological Survey (USGS) provided technical and science support to assistance in U.S. Fish and Wildlife Service Species Status Assessment (“SSA”) for the northern long-eared bat (Myotis septentrionalis), little brown bat (Myotis lucifugus), and tri-colored bat (Perimyotis subflavus). USGS facilitated the SSA data call providing data archival for repeatable and transparent analyses, provided statistical support to assess the historical, current, an future population status for each of the three species, and developed a demographic projection tool to evaluate future viability of each species under multiple threat scenarios. We assessed population trends from count surveys of wintering colonies at hibernacula for these three bat species. Winter colony counts were downloaded from the database of the North American Bat Monitoring Program (U.S. Geological Survey North American Bat Monitoring Program. Accessed 2020-12-01. NABat Request Number 12. Database Version v5.4.0).

Through the North American Bat Monitoring Program, Bat Conservation International and U.S. Geological Survey (USGS) collaborated with the U.S. Fish and Wildlife Service to provided technical and science support to assistance in U.S. Fish and Wildlife Services’ Species Status Assessment (“SSA”) for the northern long-eared bat (Myotis septentrionalis), little brown bat (Myotis lucifugus), and tri-colored bat (Perimyotis subflavus). We conducted analyses to estimate changes in bat echolocation activity recorded during mobile transect surveys. Bat activity recorded during mobile acoustic transects provide an index of abundance and can be used to determine changes in populations over time (Roche et al. 2011, Jones et al. 2013). We hypothesized that mobile transect surveys would detect changes in populations for Myotis lucifugus, Myotis septentrionalis, and Perimyotis subflavus over the past decade related to two main stressors on North American bat populations: the emergence of White-nose Syndrome (WNS) and increases in installed wind energy facilities. We obtained data stored in the North American Bat Monitoring Program (NABat) (U.S. Fish and Wildlife Service, 3-Species Status Assessment - Mobile Transect Acoustic Monitoring Data Accessed 2020-11-23. NABat Request Number 11. Database Version v5.3.0), West Virginia (West Virginia Division of Natural Resources), and New York (New York State Department of Environmental Conservation). West Virginia and New York have mobile acoustic sampling programs that began in 2009 but their mobile acoustic data have not been contributed to the NABat Program database. These data were joined with stressor and habitat covariates (year of Pd arrival, wind energy risk index, habitat composition) with SSAmobile_04_combineData.R. A dataset for each species was created by filtering for grid cells within a species range (as defined by the USFWS). The following data were removed from final analyses: • Data from Canada were removed due to our inability to calculate a comparable wind energy index in Canada (see below) • Data collected from September to April as this does not represent the summer maternity season • Data where no observations of a species were recorded on any run at a site (i.e., all zeros) were removed to prevent zero inflation • Sites with only one run were removed due to the lack of information they provide for trend analysis. Note: Sites with multiple runs within a single year were retained for analysis because these data provide information on the effect of day of year and sampling variability. To determine changes in bat populations, we first modeled bat activity as counts of echolocation call sequences recorded along mobile acoustic transects. We used three categories of variables to model the count of call sequences along a transect: 1) Stressors to populations — We examined the influence of WNS and wind energy development over time 2) Spatial variation in activity — We used latitude, longitude, and habitat covariates to account for changes in activity across landscapes 3) Sampling variation — We accounted for day of year, sampled transect length, detector type, and ID software used. We then predicted the number of call sequences at each spatial scale and year. Finally, we derived the rate of change in population from the change in the predicted number of call sequences.

Through the North American Bat Monitoring Program, Bat Conservation International and U.S. Geological Survey (USGS) collaborated with the U.S. Fish and Wildlife Service to provided technical and science support to assistance in U.S. Fish and Wildlife Services’ Species Status Assessment (“SSA”) for the northern long-eared bat (Myotis septentrionalis), little brown bat (Myotis lucifugus), and tri-colored bat (Perimyotis subflavus). We conducted analyses to estimate changes in bat echolocation activity recorded during mobile transect surveys. Bat activity recorded during mobile acoustic transects provide an index of abundance and can be used to determine changes in populations over time (Roche et al. 2011, Jones et al. 2013). We hypothesized that mobile transect surveys would detect changes in populations for Myotis lucifugus, Myotis septentrionalis, and Perimyotis subflavus over the past decade related to two main stressors on North American bat populations: the emergence of White-nose Syndrome (WNS) and increases in installed wind energy facilities. We obtained data stored in the North American Bat Monitoring Program (NABat) (U.S. Fish and Wildlife Service, 3-Species Status Assessment - Mobile Transect Acoustic Monitoring Data Accessed 2020-11-23. NABat Request Number 11. Database Version v5.3.0), West Virginia (West Virginia Division of Natural Resources), and New York (New York State Department of Environmental Conservation). West Virginia and New York have mobile acoustic sampling programs that began in 2009 but their mobile acoustic data have not been contributed to the NABat Program database. These data were joined with stressor and habitat covariates (year of Pd arrival, wind energy risk index, habitat composition) with SSAmobile_04_combineData.R. A dataset for each species was created by filtering for grid cells within a species range (as defined by the USFWS). The following data were removed from final analyses: • Data from Canada were removed due to our inability to calculate a comparable wind energy index in Canada (see below) • Data collected from September to April as this does not represent the summer maternity season • Data where no observations of a species were recorded on any run at a site (i.e., all zeros) were removed to prevent zero inflation • Sites with only one run were removed due to the lack of information they provide for trend analysis. Note: Sites with multiple runs within a single year were retained for analysis because these data provide information on the effect of day of year and sampling variability. To determine changes in bat populations, we first modeled bat activity as counts of echolocation call sequences recorded along mobile acoustic transects. We used three categories of variables to model the count of call sequences along a transect: 1) Stressors to populations — We examined the influence of WNS and wind energy development over time 2) Spatial variation in activity — We used latitude, longitude, and habitat covariates to account for changes in activity across landscapes 3) Sampling variation — We accounted for day of year, sampled transect length, detector type, and ID software used. We then predicted the number of call sequences at each spatial scale and year. Finally, we derived the rate of change in population from the change in the predicted number of call sequences.

The dataset is comprised of historical observations and predictions of winter colony counts at known sites for three bat species (little brown bat, Myotis lucifugus; tricolored bat, Perimyotis subflavus; and big brown bat, Eptesicus fuscus). The dataset consists of two separate but related data files in tabular format (comma-separated values [.csv]). Each data set consists of predicted winter counts derived using winter status and trends modeling methods developed by the North American Bat Monitoring Program (NABat). These two predicted winter count data sets were used to inform NABat summertime status and trends analysis: 1) modeled abundance predictions for all hibernacula for all three species from 2010-2021, and 2) modeled abundance predictions for P. subflavus from 2010-2023 using updated monitoring data. Abundance predictions were derived with a combined modeling approach that applied an exponential linear interpolation model (when there were less than 4 observations per location) and a Bayesian hierarchical model (where there were 4 or more data points per location).

The dataset is comprised of historical observations and predictions of winter colony counts at known sites for three bat species (little brown bat, Myotis lucifugus; tricolored bat, Perimyotis subflavus; and big brown bat, Eptesicus fuscus). The dataset consists of two separate but related data files in tabular format (comma-separated values [.csv]). Each data set consists of predicted winter counts derived using winter status and trends modeling methods developed by the North American Bat Monitoring Program (NABat). These two predicted winter count data sets were used to inform NABat summertime status and trends analysis: 1) modeled abundance predictions for all hibernacula for all three species from 2010-2021, and 2) modeled abundance predictions for P. subflavus from 2010-2023 using updated monitoring data. Abundance predictions were derived with a combined modeling approach that applied an exponential linear interpolation model (when there were less than 4 observations per location) and a Bayesian hierarchical model (where there were 4 or more data points per location).

These data are the collection of generalized linear mixed models run for AIC comparison of the pre- and post-White-nose Syndrome bat mist-net captures and percent juveniles in capture by year, time since White-nose Syndrome at collection set, U.S Fish and Wildlife Service designated geographic units, states or NABAT grid cell, collection site mean temperature, collection site temperature range and collection site elevation. Models are inclusive of data from 1999-2019 for the little brown bat (Myotis lucifugus), northern long-eared bat (Myotis septentrionalis) and the tri-colored bat (Perimyotis subflavus).

These data are the collection of generalized linear mixed models run for AIC comparison of the pre- and post-White-nose Syndrome bat mist-net captures and percent juveniles in capture by year, time since White-nose Syndrome at collection set, U.S Fish and Wildlife Service designated geographic units, states or NABAT grid cell, collection site mean temperature, collection site temperature range and collection site elevation. Models are inclusive of data from 1999-2019 for the little brown bat (Myotis lucifugus), northern long-eared bat (Myotis septentrionalis) and the tri-colored bat (Perimyotis subflavus).

Our model is a full-annual-cycle population model {hostetler2015full} that tracks groups of bat surviving through four seasons: breeding season/summer, fall migration, non-breeding/winter, and spring migration. Our state variables are groups of bats that use a specific maternity colony/breeding site and hibernaculum/non-breeding site. Bats are also accounted for by life stages (juveniles/first-year breeders versus adults) and seasonal habitats (breeding versus non-breeding) during each year, This leads to four states variable (here depicted in vector notation): the population of juveniles during the non-breeding season, the population of adults during the non-breeding season, the population of juveniles during the breeding season, and the population of adults during the breeding season, Each vector's elements depict a specific migratory pathway, e.g., is comprised of elements, {non-breeding sites}, {breeding sites}The variables may be summed by either breeding site or non-breeding site to calculate the total population using a specific geographic location. Within our code, we account for this using an index column for breeding sites and an index column for non-breeding sides within the data table. Our choice of state variables caused the time step (i.e. \(t\)) to be 1 year. However, we recorded the population of each group during the breeding and non-breeding season as an artifact of our state-variable choice. We choose these state variables partially for their biological information and partially to simplify programming. We ran our simulation for 30 years because the USFWS currently issues Indiana Bat take permits for 30 years. Our model covers the range of the Indiana Bat, which is approximately the eastern half of the contiguous United States (Figure \ref{fig:BatInput}). The boundaries of our range was based upon the United States boundary, the NatureServe Range map, and observations of the species. The maximum migration distance was 500-km, which was based upon field observations reported in the literature \citep{gardner2002seasonal, winhold2006aspects}. The landscape was covered with approximately 33,000, 6475-ha grid cells and the grid size was based upon management considerations. The U.S.~Fish and Wildlife Service considers a 2.5 mile radius around a known maternity colony to be its summer habitat range and all of the hibernaculum within a 2.5 miles radius to be a single management unit. Hence the choice of 5-by-5 square grids (25 miles\(^2\) or 6475 ha). Each group of bats within the model has a summer and winter grid cell as well as a pathway connecting the cells. It is possible for a group to be in the cell for both seasons, but improbable for females (which we modeled). The straight line between summer and winter cells were buffered with different distances (1-km, 2-km, 10-km, 20-km, 100-km, and 200-km) as part of the turbine sensitivity and uncertainty analysis. We dropped the largest two buffer sizes during the model development processes because they were biologically unrealistic and including them caused all populations to go extinct all of the time. Note a 1-km buffer would be a 2-km wide path. An example of two pathways are included in Figure \ref{fig:BatPath}. The buffers accounts for bats not migrating in a straight line. If we had precise locations for all summer maternity colonies, other approaches such as Circuitscape \citep{hanks2013circuit} could have been used to model migration routes and this would have reduced migration uncertainty.

Our model is a full-annual-cycle population model {hostetler2015full} that tracks groups of bat surviving through four seasons: breeding season/summer, fall migration, non-breeding/winter, and spring migration. Our state variables are groups of bats that use a specific maternity colony/breeding site and hibernaculum/non-breeding site. Bats are also accounted for by life stages (juveniles/first-year breeders versus adults) and seasonal habitats (breeding versus non-breeding) during each year, This leads to four states variable (here depicted in vector notation): the population of juveniles during the non-breeding season, the population of adults during the non-breeding season, the population of juveniles during the breeding season, and the population of adults during the breeding season, Each vector's elements depict a specific migratory pathway, e.g., is comprised of elements, {non-breeding sites}, {breeding sites}The variables may be summed by either breeding site or non-breeding site to calculate the total population using a specific geographic location. Within our code, we account for this using an index column for breeding sites and an index column for non-breeding sides within the data table. Our choice of state variables caused the time step (i.e. \(t\)) to be 1 year. However, we recorded the population of each group during the breeding and non-breeding season as an artifact of our state-variable choice. We choose these state variables partially for their biological information and partially to simplify programming. We ran our simulation for 30 years because the USFWS currently issues Indiana Bat take permits for 30 years. Our model covers the range of the Indiana Bat, which is approximately the eastern half of the contiguous United States (Figure \ref{fig:BatInput}). The boundaries of our range was based upon the United States boundary, the NatureServe Range map, and observations of the species. The maximum migration distance was 500-km, which was based upon field observations reported in the literature \citep{gardner2002seasonal, winhold2006aspects}. The landscape was covered with approximately 33,000, 6475-ha grid cells and the grid size was based upon management considerations. The U.S.~Fish and Wildlife Service considers a 2.5 mile radius around a known maternity colony to be its summer habitat range and all of the hibernaculum within a 2.5 miles radius to be a single management unit. Hence the choice of 5-by-5 square grids (25 miles\(^2\) or 6475 ha). Each group of bats within the model has a summer and winter grid cell as well as a pathway connecting the cells. It is possible for a group to be in the cell for both seasons, but improbable for females (which we modeled). The straight line between summer and winter cells were buffered with different distances (1-km, 2-km, 10-km, 20-km, 100-km, and 200-km) as part of the turbine sensitivity and uncertainty analysis. We dropped the largest two buffer sizes during the model development processes because they were biologically unrealistic and including them caused all populations to go extinct all of the time. Note a 1-km buffer would be a 2-km wide path. An example of two pathways are included in Figure \ref{fig:BatPath}. The buffers accounts for bats not migrating in a straight line. If we had precise locations for all summer maternity colonies, other approaches such as Circuitscape \citep{hanks2013circuit} could have been used to model migration routes and this would have reduced migration uncertainty.