Phenotypic differences between urban and rural populations are well-documented, but the evolutionary processes driving trait variation along urbanization gradients are often unclear. We combined spatial data on abundance, trait variation, and measurements of fitness to understand cline structure and test for natural selection on heritable coat color morphs (melanic, gray) of eastern gray squirrels (Sciurus carolinensis) along an urbanization gradient. Population surveys using remote cameras and visual counts at 76 sites along the urbanization gradient revealed a significant cline in melanism, decreasing from 48% in the city center to <5% in rural woodlands. Among 76 squirrels translocated to test for phenotypic selection, survival was lower for the melanic than gray morph in rural woodlands, whereas there was no difference in survival between color morphs in the city. These results suggest the urban-rural cline in melanism is explained by natural selection favoring the gray morph in rural woodlands combined with relaxed selection in the city. Our study illustrates how trait variation between urban and rural populations can emerge from selection primarily in rural populations rather than adaptation to novel features of the urban environment. This reposotory contains a) occupancy data, point count data, and R code used to estimate the urban-rural cline in melanism, and b) radiotelemetry data and R code used to estimate differential survival between color morphs in urban and rural environments.
Data from: Rural selection drives the evolution of an urban-rural cline in coat color in gray squirrels
Data files
Sep 19, 2023 version files 71.59 KB
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cline_subsetModel.R
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cline_subsetModel.Rdata
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cline.R
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cline.Rdata
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README.md
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survival.R
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survival.Rdata
Abstract
README: Data for "Rural selection drives the evolution of an urban-rural cline in coat color in gray squirrels"
https://doi.org/10.5061/dryad.9w0vt4bn5
Description of the data and file structure
This repository contains data and code for the following manuscript:
Cosentino, B.J., Vanek, J.P., and J.P. Gibbs. Rural selection drives the evolution of an urban-rural cline in coat color in gray squirrels. Ecology and Evolution.
The following files are included:
cline.Rdata
Data used to fit the cline in melanism using all data. NA values represent days when trail cameras were not active and point counts were not conducted at a given site.
cline.R
R code used to fit the cline in melanism using all data. The script was run with R version 4.0.2, and it uses the jagsUI package (version 1.5.2).
cline_subsetModel.Rdata
Data used to fit the cline in melanism with a subset of data. Variable definitions are as follows:
- y.occ.g = gray detections
- y.occ.m = melanic detections
- y.ct.g = gray counts
- y.ct.m = melanic counts
- nsites = number of sites
- nsurveys.occ = total number of survey days for occupancy data
- nsurveys.ct = total number of surveys for count data
- distance = distance from city center in km
- dist.city.s = standardized distance from city center
- temp.avg = mean daily temp (Celcius) for survey period inclusive of camera & count surveys (9/16/21-10/18/22)
- temp.avg.occ = standardized mean daily temperature covariate for occupancy surveys
- temp.avg.ct = standardized mean daily temperature covariate for count surveys
- Xdist = sequence of distances for prediction
- Xtemp = sequence of mean daily temps for prediction
cline_subsetModel.R
R code used to fit the cline in melanism with a subset of data.
survival.Rdata
Radiotelemetry data used for survival analysis. NA values represent missing data. Variable definitions are as follows:
- id = unique squirrel id
- CAPTURE_DATE = date of capture and translocation
- END_DATE = date of final status
- MORPH = color morph
- SEX = sex
- MASS = mass in grams
- CSIZE = collar size (14 or 21 g)
- LANDSCAPE = urban or rural environment
- DAYS.ACTIVE = number of days between translocation and final status recorded
- STATUS = final status (confirmed mortality, probable mortality, possible mortality, missing, active)
- tmp.start = daily mean temperature averaged for the first week post.translocation (Celcius)
survival.R
R code used for survival analysis. The script was run with R version 4.0.2, and it uses the tidyverse (version 2.0.0), survival (3.5.3) and survminer (0.4.9) packages.