Enhancing animal movement analyses: spatiotemporal matching of animal positions with remotely sensed data using Google Earth Engine and R

Movement ecologists have witnessed a rapid increase in the amount of animal position data collected over the past few decades, as well as a concomitant increase in the availability of ecologically relevant remotely sensed data. Many researchers, however, lack the computing resources necessary to incorporate the vast spatiotemporal aspects of datasets available, especially in countries with less economic resources, limiting the scope of ecological inquiry. We developed an R coding workflow that bridges the gap between R and the multi-petabyte catalogue of remotely sensed data available in Google Earth Engine (GEE) to efficiently extract raster pixel values that best match the spatiotemporal aspects (i.e., spatial location and time) of each animal’s GPS position. We tested our approach using movement data freely available on Movebank (movebank.org). In a first case study, we extracted Normalized Difference Vegetation Index information from the MOD13Q1 data product for 12,344 GPS animal locations by matching the closest MODIS image in the time series to each GPS fix. Data extractions were completed in approximately 3 min. In a second case study, we extracted hourly air temperature from the ERA5-Land dataset for 33,074 GPS fixes from 12 different wildebeest (Connochaetes taurinus) in approximately 34 min. We then investigated the relationship between step length (i.e., the net distance between sequential GPS locations) and temperature and found that animals move less as temperature increases. These case studies illustrate the potential to explore novel questions in animal movement research using high-temporal-resolution, remotely sensed data products. The workflow we present is efficient and customizable, with data extractions occurring over relatively short time periods. While computing times to extract remotely sensed data from GEE will vary depending on internet speed, the approach described has the potential to facilitate access to computationally demanding processes for a greater variety of researchers and may lead to increased use of remotely sensed data in the field of movement ecology. We present a step-by-step tutorial on how to use the code and adapt it to other data products that are available in GEE

Political transition and emergent forest-conservation issues in Myanmar.

Political and economic transitions have had substantial impacts on forest conservation. Where transitions are underway or anticipated, historical precedent and methods for systematically assessing future trends should be used to anticipate likely threats to forest conservation and design appropriate and prescient policy measures to counteract them. Myanmar is transitioning from an authoritarian, centralized state with a highly regulated economy to a more decentralized and economically liberal democracy and is working to end a long-running civil war. With these transitions in mind, we used a horizon-scanning approach to assess the 40 emerging issues most affecting Myanmar's forests, including internal conflict, land-tenure insecurity, large-scale agricultural development, demise of state timber enterprises, shortfalls in government revenue and capacity, and opening of new deforestation frontiers with new roads, mines, and hydroelectric dams. Averting these threats will require, for example, overhauling governance models, building capacity, improving infrastructure- and energy-project planning, and reforming land-tenure and environmental-protection laws. Although challenges to conservation in Myanmar are daunting, the political transition offers an opportunity for conservationists and researchers to help shape a future that enhances Myanmar's social, economic, and environmental potential while learning and applying lessons from other countries. Our approach and results are relevant to other countries undergoing similar transitions

Political transition and emergent forest-conservation issues in Myanmar.

Political and economic transitions have had substantial impacts on forest conservation. Where transitions are underway or anticipated, historical precedent and methods for systematically assessing future trends should be used to anticipate likely threats to forest conservation and design appropriate and prescient policy measures to counteract them. Myanmar is transitioning from an authoritarian, centralized state with a highly regulated economy to a more decentralized and economically liberal democracy and is working to end a long-running civil war. With these transitions in mind, we used a horizon-scanning approach to assess the 40 emerging issues most affecting Myanmar's forests, including internal conflict, land-tenure insecurity, large-scale agricultural development, demise of state timber enterprises, shortfalls in government revenue and capacity, and opening of new deforestation frontiers with new roads, mines, and hydroelectric dams. Averting these threats will require, for example, overhauling governance models, building capacity, improving infrastructure- and energy-project planning, and reforming land-tenure and environmental-protection laws. Although challenges to conservation in Myanmar are daunting, the political transition offers an opportunity for conservationists and researchers to help shape a future that enhances Myanmar's social, economic, and environmental potential while learning and applying lessons from other countries. Our approach and results are relevant to other countries undergoing similar transitions

Multistate mark-recapture approach to estimating survival of PIT-tagged salamanders following timber harvest

Data associated with a PIT-tag telemetry study of salamanders conducted on the Nantahala National Forest, North Carolina, USA. Full details of this study will be provided in the manuscript.1) Connette_PITdata.csv - File gives the study plot and PIT-tag identification of each salamander, as well as their complete detection histories [coded as 1 (PIT-detection only), 2 (PIT and Visual detection), or 3 (not detected)] -- 2) CapDates.csv – File gives the study plot, PIT-tag identification, and initial capture date of each salamander -- 3) HarvestCovs.csv – File gives the study plot, PIT-tag identification, and survey-specific indicator variables for each individual designating whether they were in an unlogged (0) or logged plot (1) -- 4) DaysSinceRain.csv – File gives the number of days since the last rainfall event for each survey date -- 5) PITmodel.txt – File gives the full R script for the analysis conducted in Connette & Semlitsch, 2015

Distribution of a Stream-breeding Salamander, Desmognathus ocoee, in Terrestrial Habitat Suggests the Ecological Importance of Low-order Streams

Stream location and salamander count data from a study conducted on the Nantahala National Forest, North Carolina, USA. Also provided is an R script for conducting the analyses described in the manuscript. See manuscript for full details of the methods.Files: 1) StreamDist.R - File gives the full R script for conducting the analyses described in Connette et al., 2016. This analysis estimates the relationship between count data for stream salamanders (Desmognathus ocoee) and stream locations in the surrounding landscape. -- 2) StreamData.zip – The zip folder contains the following data files used for analysis: -- a) MRCdata.csv – “Id” column gives unique survey plot names, “Desoco” column gives counts of Desmognathus ocoee at each survey plot, “Eurwil” column gives counts of Eurycea wilderae at each survey plot; -- b. MRCplots.csv - “Id” column gives unique survey plot names, “POINT_X” gives the x-coordinate of each survey plot in UTMs, “POINT_Y” gives the y-coordinate of each survey plot in UTMs (UTM zone 17) -- c) P181.csv,…,P404.csv – “POINTID” is a unique identifier for each 1-m section of stream in the surrounding landscape, “GRID_CODE” gives an indicator for stream width (0.5=seep, 1=small stream, 2=large stream), “POINT_X” gives the x-coordinate for each 1-m section of stream, “POINT_Y” gives the y-coordinate for each 1-m section of stream. “Distance” gives the distance in meters from the center of the survey plot to each 1-m section of stream

Droughts Reduce Growth Rates and Increase Vulnerability to Increasingly Frequent and Severe Drying Events in an Aquatic Ectotherm

Many aquatic organisms are experiencing increasingly severe and frequent droughts and drying events. Simultaneously, drought effects are carrying over to non-drought years as ecosystems remain in incomplete states of recovery. Aquatic organisms are thus faced with fewer sequential years under degraded environmental conditions to prepare for increasingly severe droughts and potential drying events. We assessed the effect of droughts and sex on the growth, mass, and mass-dependent estivation potential of long-lived aquatic salamanders (Greater Sirens, Siren lacertina) that estivate during drying events brought on by severe droughts. We calculated growth rates of S. lacertina based on mark–recapture data spanning 11 yr of a severe drought local minimum (of past 50 yr) in the southeastern United States. Sirens showed a distinct seasonal gain in body length and mass from March through September and little growth for the rest of the year. Gains during the growth season were strongly reduced by drought conditions. Although male and female sirens were predicted to reach a similar maximum body size, females grew much slower. Recruitment into drying event ‘‘size refugia’’ is constrained by drying event severity (determines minimum size required), frequency (determines available time between events to grow), and environmental conditions between drying events (determines the rate of growth). Thus, increases in drying event severity and frequency will require faster growth to a larger body size for successful recruitment into a size class that is resistant to drying events. The slower growth of females and reduction of growth during suboptimal years (mild to moderate droughts) suggest that the life history strategy of Greater Sirens for persisting through drying events potentially increases their demographic susceptibility to the predicted effects of climate change

Droughts Reduce Growth Rates and Increase Vulnerability to Increasingly Frequent and Severe Drying Events in an Aquatic Ectotherm

Many aquatic organisms are experiencing increasingly severe and frequent droughts and drying events. Simultaneously, drought effects are carrying over to nondrought years as ecosystems remain in incomplete states of recovery. Aquatic organisms are thus faced with fewer sequential years under degraded environmental conditions to prepare for increasingly severe droughts and potential drying events. We assessed the effect of droughts and sex on the growth, mass, and mass-dependent estivation potential of long-lived aquatic salamanders (Greater Sirens, Siren lacertina) that estivate during drying events brought on by severe droughts. We calculated growth rates of S. lacertina based on mark–recapture data spanning 11 yr of a severe drought local minimum (of past 50 yr) in the southeastern United States. Sirens showed a distinct seasonal gain in body length and mass from March through September and little growth for the rest of the year. Gains during the growth season were strongly reduced by drought conditions. Although male and female sirens were predicted to reach a similar maximum body size, females grew much slower. Recruitment into drying event ‘‘size refugia’’ is constrained by drying event severity (determines minimum size required), frequency (determines available time between events to grow), and environmental conditions between drying events (determines the rate of growth). Thus, increases in drying event severity and frequency will require faster growth to a larger body size for successful recruitment into a size class that is resistant to drying events. The slower growth of females and reduction of growth during suboptimal years (mild to moderate droughts) suggest that the life history strategy of Greater Sirens for persisting through drying events potentially increases their demographic susceptibility to the predicted effects of climate change

Trap characteristics and species morphology explain size-biased sampling of two salamander species

Demographic studies often depend on sampling techniques providing representative samples from populations. However, the sequence of events leading up to a successful capture or detection is susceptible to biases introduced through individual-level behaviour or physiology. Passive sampling techniques may be especially prone to sampling bias caused by size-related phenomena (e.g., physical limitations on trap entrance). We tested for size-biased sampling among five types of passive traps using a 9-year data set for two species of aquatic salamanders that have a 20 and 61 fold change in length over their ontogeny (<i>Amphiuma means</i>, <i>Siren lacertina</i>). Size-biased trapping was evident for both species, with body size distributions (body length mean and SD) of captured individuals differing among sampling techniques. Because our two species differed in girth at similar lengths, we were able to show that size biases (in length) were most likely caused by girth limitations on trap entry rates, and potentially by differences in retention rates. Accounting for the biases of sampling techniques may be critical when assessing current population status and demographic change