Amazona obscured occurrences, background points, and environmental data
Data files
Feb 18, 2024 version files 19.67 MB
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amazona_bg_env.csv
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buffer_shapefiles.zip
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obscured_amazona.csv
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README.md
Abstract
Aim: Introduced species offer insight on whether and how organisms can shift their ecological niches during translocation. The genus Amazona offers a clear test case, where sister species Red-crowned (A. viridigenalis) and Lilac-crowned Parrots (A. finschi) have established breeding populations in southern California following introduction via the pet trade from Mexico where they do not coexist. After establishment in the 1980s, introduced population sizes have increased, with mixed species flocks found throughout urban Los Angeles. Here, we investigate the differences between the environmental conditions of the native and introduced ranges of these now co-occurring species.
Location: Southern California and Mexico.
Methods: Using environmental data on climate and habitat from their native and introduced ranges, we tested whether Red-crowned and Lilac-crowned Parrots have divergent realized niches between their native ranges, and whether each species has significantly shifted its realized niche to inhabit urban southern California. We also analyzed data from Texas and Florida introductions of Red-crowned Parrots for comparative analysis.
Results: There are significant differences in the native-range niches of both parrot species, but a convergence into a novel, shared environmental niche into urban southern California, characterized by colder temperatures, less tree cover, and lower rainfall. Texas and Florida Red-crowned Parrots also show evidence for niche shifts with varying levels of niche conservatism through the establishment of somewhat different realized niches.
Main Conclusions: Despite significant niche shifts, introduced parrots are thriving, suggesting a broad fundamental niche and an ability to exploit urban resources. Unique niche shifts in different U.S. introductions indicate that Amazona parrots can adapt to diverse environmental conditions, with cities offering a resource niche and the timing of introduction playing a crucial role. Cities can potentially serve as refugia for threatened parrot species, but the risk of hybridization between species emphasizes the need for ongoing monitoring and genetic investigations.
README: Amazona Obscured Occurrences, Background Points, and Environmental Data
Brenda Ramirez, ramirezb@oxy.edu, Moore Laboratory of Zoology, Occidental College
The main file for our Amazona analysis is "obscured_amazona.csv" which contains obscured coordinates of the Red-crowned (Amazona viridigenalis) and Lilac-crowned (Amazona finschi) Parrots from both their native and introduced ranges. These coordinates were obscured to protect the endangered parrots from the risk of poaching. To obscure the coordinates, we followed best practices by generalizing the spatial information to a metric grid where all records are referenced to the centroid and then rounding the coordinates to 0.1 degrees. We generated background points within buffers of each population (California, Texas, Florida, and both coasts of Mexico) and extracted environmental values from them as well as the true occurrence points at 1km^2 resolution to assess niche characteristics and evaluate how they differed.
Description of the data and file structure
- "obscured_amazona.csv" contains obscured Amazona presences for each state which is our base dataset.
- "amazona_bg_env.csv" contains the environmental conditions of all predictors at the 1km2 resolution for both presences and absences in each region.
Environmental data included: Bioclimatic variables from Bioclim, Elevation, Vegetation greenness (Normalized Difference Vegetation Index: NDVI), Greenness seasonality (standard deviation of NDVI: NDVI_std), Urbanization measure (Quik Scatterometer: QSCAT), and Percentage of tree cover from MODIS (Tree_Cover). These environmental layers can be used to assess a species niche based on locality data.
The buffer shapefiles for each population are also included.
Sharing/Access information
Links to publicly accessible locations of the data:
Code/Software
All data were processed using R 4.2.1 with the packages 'ade4', 'auk', 'dismo', 'dplyr', 'ecospat', 'ENMeval', 'ENMTools', 'factoextra ,'ggplot2', 'latticeExtra', 'maptools', 'raster', 'rasterVis', 'RColorBrewer', 'rmaxent', 'sf', and 'tidyverse'
Scripts include:
- "FLAPP_analysis.R" used to compare environmental conditions between the presences of each population.
- "create_pseudoabsences.R" used to create pseudoabsences for each population using a buffer around the occurrence points.
- "ecospat.R" used to create the PCAs and to assess the niche differentiations between the native and introduced populations (adapted from the Ecospat package vignette: https://cran.r-project.org/web/packages/ecospat/vignettes/vignette_ecospat_package.pdf). Note, variable correlations should be taken into account when conducting this analysis.
- "recip_sdms.R" used to create the reciprocal species distribution models for each species. The habitat suitability was predicted for the native range and that suitability was then projected onto the introduced range to test for niche conservatism (adapted from the ENMeval 2.0 Vignette: https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html). Note, variable correlations should be taken into account when conducting this analysis.
Methods
Observations for the Amazona parrots in southern California were collected on iNaturalist through the Free-Flying Los Angeles Parrot Project (FLAPP). Individual parrots were scored based on morphological features to confirm species identification. Only research-grade observations were included in our analysis, which was determined by two agreeing independent scorings of species identification. Observations for Amazona parrots in their separate native ranges of Mexico were downloaded from the eBird database, with filtering done to remove any observations found in introduced areas surrounding their native ranges. Red-crowned Parrot data for Texas and Florida was downloaded from eBird as well and filtered to only include observations with media for species identification. Buffers were created for each population to create randomly generated background points. Environmental data was downloaded from various online databases including Bioclim, MODIS data, and global scatterometer data. The environmental data was then pulled for each parrot (and randomly generated background points) for environmental comparison.
Usage notes
All data were processed using R 4.2.1