DOI: 10.5061/dryad.280gb5mvg
title: Amazona obscured occurrences, background points, and environmental data

description: 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.
description: Observations for the <em>Amazona</em> 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 <em>Amazona</em> 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.
description: All data were processed using R 4.2.1
description: # Amazona Obscured Occurrences, Background Points, and Environmental Data
 ## Brenda Ramirez, , 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: * Bioclim:
 ## 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:
 ). 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: ). Note, variable correlations should be taken into account when conducting this analysis.