DOI: 10.5061/dryad.jdfn2z3kx
title: New England and eastern cottontail data for Maxent and niche overlap modeling

description: When introduced species invade new environments, they often overlap with
 native species currently occupying those spaces, either spatially through
 suitable habitat or environmentally through their realized niches. The
 goal of this research is to determine the overlap between native New
 England cottontail (Sylvilagus transitionalis) and introduced eastern
 cottontail (Sylvilagus floridanus) to identify potential areas of invasion
 by the eastern cottontail and potential areas of refuge for the New
 England cottontail from the eastern cottontail (Connecticut, USA). Using
 presence data from a regional, standardized monitoring protocol, we
 developed habitat suitability models using Maxent and conducted niche
 overlap analyses using environmental principal component analysis. We used
 several covariates that reflected proximity to habitat characteristics,
 such as young forest, shrubland, and understory, as well as proximity to
 threats, such as development. We also included topographic and climatic
 covariates. We used the Guidos software to categorize the spatial
 arrangement of young forest, shrubland, and understory vegetation. We
 found that the overlap in both niches and suitable habitat was high for
 two species. Only areas of low precipitation and high elevation shifted
 niches in favor of the New England cottontail. We also found that habitat
 suitability for the New England cottontail was higher when patches of
 mature forest without understory were within complexes of young forest,
 shrubland, and mature forest with understory. Increasing habitat
 heterogeneity could improve the habitat suitability of existing patches or
 create new patches for New England cottontail. However, habitat management
 alone is likely not enough to discourage eastern cottontail; thus, direct
 species management, such as removal of eastern cottontail and augmentation
 of New England cottontail populations, should be explored.
description: # New England and eastern cottontail data for Maxent and niche overlap
 modeling
 [https://doi.org/10.5061/dryad.jdfn2z3kx](https://doi.org/10.5061/dryad.jdfn2z3kx) ## Description of the data and file structure The data provided was used in the paper "High Overlap in Niches and Suitable Habitat Between an Imperiled and Introduced Cottontail." The location data was derived from the New England Cottontail Regional Monitoring Program, where biologists from each state in the current New England cottontail  (*Sylvilagus transitionalis*; NEC) range (Connecticut, Maine, Massachusetts, New Hampshire, New York, and Rhode Island) collected cottontail fecal pellets at designated sites. Pellets for the introduced eastern cottontail (*Sylvilagus flroidanus*; EC) were also collected for this effort. The species location data included was only for pellets collected in Connecticut and at a coarser resolution (1 km) to prevent harm to the New England cottontail. The environmental covariates for both the Maxent and niche overlap models were collected from existing geospatial products and are at a 10 m spatial resolution.  ### Files and variables #### File: EC\_Maxent\_2016\_2022\_1km\_buff.csv **Description:** Thinned eastern cottontail (EC) species location data collected within Connecticut from 2016-2022 at a 1 km resolution.  ##### Variables * Species: Species abbreviation * X: X coordinates (North American Datum 1983 State Plane Connecticut FIPS 0600 (Meters)) * Y: Y coordinates (North American Datum 1983 State Plane Connecticut FIPS 0600 (Meters)) #### File: NEC\_maxent\_2016\_2022\_1km\_buff.csv **Description:** Thinned New England cottontail (NEC) species location data collected within Connecticut from 2016-2022 at a 1 km resolution.  ##### Variables * Species: Species abbreviation * X: X coordinates (North American Datum 1983 State Plane Connecticut FIPS 0600 (Meters)) * Y: Y coordinates (North American Datum 1983 State Plane Connecticut FIPS 0600 (Meters)) #### File: Run\_niche\_overlap\_HPC\_final\_DD.R **Description:** R code to prepare data and run a niche overlap analysis for New England and eastern cottontail. The code contains the descriptions for each of the raster files in the Niche_covariates.zip.   #### File: Niche\_covariates.zip **Description:** Covariates for the niche overlap analysis for New England and eastern cottontail. Most covariates used within the niche overlap models are ESRI grid files, which are groups of several subfiles, so the covariates are organized into folders. The folder for each covariate must be read into R using the raster package to run the niche overlap analysis. Alternatively, files can be opened and viewed in GIS software, such as ArcPro. The covariate files include distance to Japanese barberry (*Berberis thunbergii*) understory vegetation ("ba_d_hyd_1"), distance to buildings ("distb_hyd_1"),  eastern aspect ("east_hyd"), elevation ("elev_hydro"), distance to forested/shrub wetlands ("fw_d_hyd_1"), distance to greenbrier (*Smilax rotundifolia*) understory vegetation ("gb_d_hyd_1"), distance to mixed forest ("mf_d_hyd_1"), distance to mixed invasive understory vegetation ("mi_d_hyd_1"), northern aspect ("north_hyd"), distance to regenerating forests and clearcuts ("reg_d_hyd_1"), distance to shrublands ("sh_d_hyd_1"), slope ("slope_hyd_10"), distance to transitional to forest ("tr_d_hyd_1"), and annual precipitation totals ("weight_prec"). The categorical predictor ("gd_cat_mask.tif") is an output of a Morphological Spatial Pattern Analysis conducted in the Guidos software. We used the young forest and shrubland vegetation map and the understory vegetation map as habitat in the analysis. The software categorizes habitat into 6 spatial classes, core or interior habitat (category 5), edge or the perimeter of core (category 2), core openings or background classes found within core (category 6), perforations or the perimeter of core openings (category 3), fragments or disjointed habitat areas that are too small to contain core (category 4), margin or habitat that did not fit into any other category (category 1), and background is classified as the absence of habitat (category 0). Distance and elevation covariates are measured in meters and precipitation is measured in millimeters. #### File: Maxent\_covariates.zip **Description:** Covariates used within the Maxent models for New England and eastern cottontail. The ASCII files can be used directly within the Maxent software. Alternatively, files can be opened and viewed in GIS software, such as ArcPro. Covariate files include distance to Japanese barberry (*Berberis thunbergii*) understory vegetation ("ba_d_hyd_1.asc"), distance to buildings ("distb_hyd_1.asc"), eastern aspect ("east_hyd_1019.asc"), elevation ("elev_hydro.asc"), distance to forested/shrub wetlands ("fw_d_hyd_1.asc"), distance to greenbrier (*Smilax rotundifolia*) understory vegetation ("gb_d_hyd_1.asc"), distance to mixed forest ("mf_d_hyd_1.asc"), distance to mixed invasive understory vegetation ("mi_d_hyd_1.asc"), northern aspect ("north_hyd_1019.asc"), annual precipitation totals ("prec_hydro_avg.asc"), distance to regenerating forests and clearcuts ("reg_d_hyd_1.asc"), distance to shrublands ("sh_d_hyd_1.asc"), slope ("slope_hyd_1019.asc"), and distance to transitional to forest ("tr_d_hyd_1.asc"). The categorical predictor ("gd_cat_mask.asc") is an output of a Morphological Spatial Pattern Analysis conducted in the Guidos software. We used the young forest and shrubland vegetation map and the understory vegetation map as habitat in the analysis. The software categorizes habitat into 6 spatial classes, core or interior habitat (category 5), edge or the perimeter of core (category 2), core openings or background classes found within core (category 6), perforations or the perimeter of core openings (category 3), fragments or disjointed habitat areas that are too small to contain core (category 4), margin or habitat that did not fit into any other category (category 1), and background is classified as the absence of habitat (category 0). Distance and elevation covariates are measured in meters and precipitation is measured in millimeters. ## Code/software Code for the niche overlap analysis (Run_niche_overlap_HPC_final_DD.R) that was run using R 4.3.1 through the Storrs High Performing Computer (HPC) at the University of Connecticut. The Maxent model was run directly in the Maxent software version 3.4.4.