Estimating the global population size and highlighting conservation priority areas for the endangered Titicaca grebe
Data files
Dec 23, 2024 version files 271.82 KB
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Grebe_Surveys_not_Used_in_Analysis.xlsx
9.63 KB
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R._microptera_Occupancy_Model_All_Input_Data.xlsx
38.28 KB
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README.md
4.58 KB
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Rollandia_microptera_points_rounded.csv
219.33 KB
Abstract
The Titicaca grebe (Rollandia microptera) is a poorly studied endangered species, only found in the Lake Titicaca watershed of Peru and Bolivia. Population surveys undertaken in the early twenty-first century suggested that the species had declined in number by >70%. We conducted a population survey of the grebe between March and August 2022 in Peru and Bolivia, using both maximum entropy and Bayesian occupancy models to estimate factors affecting habitat suitability for the grebe. We conducted surveys between March and August 2022 in Peru and Bolivia. Contrary to the International Union for Conservation of Nature (IUCN) population estimates of <1,000 individuals, there are likely tens of thousands of individual grebes. The population estimation was sensitive to the type of model used. Distance from shore and fishing intensity were the most significant factors influencing grebe populations. The Reserva Nacional del Titicaca, the only protected area in the lake, covers some of the most suitable Titicaca grebe habitat across its entire range. The population of the Titicaca grebe is significantly higher than previous estimates, but we do not recommend a change to its conservation status because of the lack of conservation efforts for this species, and the long-term risks associated with global warming and fisheries bycatch.
README: Estimating the Global Population Size and Highlighting Conservation Priority Areas for the Endangered Titicaca Grebe
https://doi.org/10.5061/dryad.tqjq2bw63
Description of the data and file structure
This is supplemental material of the article "Estimating the Global Population Size and Highlighting Conservation Priority Areas for the Endangered Titicaca Grebe"
This includes the R code used in this analysis, the population data, and the rasters which were produced as part of the output. It also includes a word document with a link to the function used to convert continous rasters to binary rasters which is referenced in the text, but not in the bibliography as it was published as part of a blog rather than as part of a published R package.
File Explanations
Rollandia_microptera_points_rounded.csv
- rounded data points of the locations of Titicaca Grebes observed in this study. The locations have been rounded due to the species' endangered status
Data Inputs
On Dryad
R._microptera_Occupancy_Model_All_Input_Data.xlsx
- Data inputs used for the Occupancy Model.
- Column A - names of locations
- Species - Scientific name of the Titicaca Grebe
- V1, V2, V3 - whether the Titicaca Grebe was observed in this survey
- Vegetation - % of pixel covered by totora
- Distance_tiol_Park - Distance to the Reserva Nacional del Titicaca, in metres
- Distance_Shore - distance to the lakeshore, in metres
- Distance_Village - Distance to the nearest habitable place, in metres
- Distance_Cages - Distance from pisciculture, in metres
- Nets - No. of fishing nets observed
- Fish_Cages - No. of fish cages observed
- Cages_Present_Biry - Binary as to whether fish cages are in the pixel
- Fishing_Intensity - Pixel value in the probability of fisheries rasters
- Water_Depth - Depth in metres of the lake
- det.covs.Time_Start. - 3 columns, number of minutes since midnight when survey started*
- det.covs.Duration - 3 columns, duration in minutes of the survey *
- det.covs.Survey_Party - 3 columns, survey party involved*
- det.covs.day - 3 columns, number of days since the start of the year of survey *
- det.covs.Transect_Length - 3 columns, length of transect in km *
- Lat_Start - Latitude of the start of the survey
- Lat_End - Latitude of the end of the survey
- Long_Start - Longitude of the start of the survey
- Long_End - Longitude of the end of the survey
- coords.x & coords.y - midpoint of the survey
*Note that all det.covs, or detection covariates, are in three columns to represent the (up to) three repeated surveys of each site
null indicates no survey occurred
Grebe_Surveys_not_Used_in_Analysis.xlsx
- surveys not included in the analysis outside of Lake Titicaca
On Zenodo (found in Supplementary Information link)
Rollandia_microptera_Totora_1km_only.png & Totora_1km.asc
- Totora raster
Rollandia_microptera_Distance_Shore_1km_only.png
& Distance_Shore_1km.asc
- distance from shore raster
Rollandia_microptera_Distance_Cages_1km_only.png
& Cages_Present_1km.asc
- distance from cages raster
Rollandia_microptera_Distance_Settlement_1km_only.png
& Distance_Settlement_1km.asc
- distance from settlements raster
Rollandia_microptera_Bathymetry_1km_only.png
& Bathymetry_1km.asc
- water depth raster
Rollandia_microptera_Fishing_Intensity_only.png
& Fishing_Intensity.asc
- probability of fisheries raster
Distance_Protected_Area_1km.asc
- Distance to protected area raster
Code and Calculations (found in Supplementary Information and Software links)
PopDensityCalcs.xlsx
- Population density calculations
Morrow_Function_Link.docx
- link to blogpost where function I used in my own code originated from
code-jwd.R
, Grebe_Thresholding.R
, Example_spOccupancy.R
- code used in the analysis, with explanatory notes in the code
Data Outputs (found in Supplementary Information link)
GrebeOccupancyRaster.tif
and Occupany_Map.png
- raster of the occupancy model results
Fifty_Percent_Occupany_Minimum_threshold_Map.tif
- Binary Occupancy Map with 50% cutoff
Fifty_Percent_MaxEnt_Minimum_threshold_Map.tif
- Binary MaxEnt Map with 50% cutoff
BinaryOccupany_Minimum_threshold_Map.tif
- Binary Occupancy Map with minimum presence cutoff
BinaryMaxEnt_Minimum_threshold_Map.tif
- Binary MaxEnt Map with minimum presence cutoff
SD_Occurance_Map.png
- Standard Deviation of Occupancy Map predictions
AbundanceMaps.png & NMixMap.tiff
- N-mixture map results