DOI: 10.5061/dryad.p2ngf1vz3
title: Density dependence maintains long-term stability despite increased isolation and inbreeding in the Florida Scrub-Jay

description: Isolation caused by anthropogenic habitat fragmentation can destabilize
 populations. Populations relying on the inflow of immigrants can face
 reduced fitness due to inbreeding depression as fewer new individuals
 arrive. Empirical studies of the demographic consequences of isolation are
 critical to understanding how populations persist through changing
 conditions. We used a 34-year demographic and environmental dataset from a
 population of cooperatively-breeding Florida Scrub-Jays (Aphelocoma
 coerulescens) to create mechanistic models linking environmental and
 demographic factors to population growth rates. We found that the
 population has not declined despite both declining immigration and
 increasing inbreeding, owing to a coinciding response in breeder survival.
 We find evidence of density-dependent immigration, breeder survival, and
 fecundity, indicating that interactions between vital rates and local
 density play a role in buffering the population against change. Our study
 elucidates the impacts of isolation on demography and how long-term
 stability is maintained via demographic responses.
description: All work was approved by the Cornell University Institutional
 Animal Care and Use Committee (IACUC 2010-0015) and authorized by permits
 from the US Fish and Wildlife Service (TE824723-8), the US Geological
 Survey (banding permit 07732), and the Florida Fish and Wildlife
 Conservation Commission (LSSC-10-00205).
description: # Density dependence maintains long-term stability despite increased
 isolation and inbreeding in the Florida Scrub-Jay
 [https://doi.org/10.5061/dryad.p2ngf1vz3](https://doi.org/10.5061/dryad.p2ngf1vz3) This dataset contains raw census data (**FullLOI.txt**), derived vital rates (**vr_clean_F_4stageDemo.rdata**, **vr_clean_M_4stageDemo.rdata**), ecological metrics (**reqsoi_update.txt**, **acorns_update.txt**, **TerrYrBurnArea.txt**, **TerrMap.txt**, **TerrsToKeep.txt**, **densityCalcDemo.rdata**, **env_var_updateDemo.txt**, **envFac_annual.txt**), pedigree information (**pedInbr.txt**, **kinship_coef_Demo.rdata**), and demographic models created using these data (**vr_modelsDemo_revision_20240518.rdata**, **vr_modelsDemo.rdata**, **Demo_LTRE_results_20240518.rdata**), including model validation results (**vr_modelsDemo_validation_revisions_20240518.rdata**). ## Description of the data and file structure #### **FullLOI.txt** * USFWS: Individual ID * Year: Year of census * TerrYr: Territory ID-Year combination code * Terr: Territory ID * Sex: Assigned sex (M = male, F = female, NA = unassigned) * mate_USFWS: Individual ID of mate, none if individual is unpaired * social.class: Classification of individual as juvenile, helper, or breeder * fecundity: Number of offspring produced by individual in census year * pair.status: Classification of breeding pair as newly formed this census year (new), continuous from the previous census year (old), or unpaired (none). * survival: Identification of whether individual survives (1) to next census year, or does not (0) * transition: Identification of whether individual forms a new pair next census year (1), does not (0), or could not due to death or already being a breeder (NA) * divorce: Identification of whether individual does not remained paired with current mate (1) contingent on both mates surviving (NA if either mate dies or if individual is unpaired) * back_transition: Identification of whether individual re-forms a pair (1) after either divorce or death of a mate (NA if unpaired or if pair persists) * category: Categorization of individual based on first observation before the census period (founder), at nest on the study tact (resident), or after dispersing into the study tract (immigrant) #### **reqsoi\_update.txt** Raw EQSOI measurements by month (columns) and year (rows) from 1949-2022 #### **acorns\_update.txt** * YEAR: Year of measurement * acorns: Total number of acorns collected * posts: Total number of posts samples * acorns.mean: Mean number of acorns per sampled post #### **TerrYrBurnArea.txt** * TerrYr: Territory ID-Year combination code * Year: Year of census * TSF: Time since fire in days * TSF_yr: Time since fire in years * CellCount: Number of grid cells burned * area: Total number of grid cells * area_ha: Total area in hectares * Terr: Territory ID #### **TerrMap.txt** * Tract: Study tract area as either main study tract (Demo) or additional southern tract not included in this study (South) * TerrYr: Territory ID-Year combination code * Year: Year of census * easting: easting measurement of TerrYr centroid * northing: northing measurement of TerrYr centroid * ha: TerrYr area in hectares * Terr: Territory ID #### **TerrsToKeep.txt** * Year: Year of census * TerrYr: Territory ID-Year combination code * Terr: Territory ID * n: Number of census years territory is within the study tract area * Tract: Study tract area as either main study tract (Demo) or additional southern tract not included in this study (South) * Include: Whether TerrYr should be included within the study * ContinuityNum: ID for the continuity of Territory ID. Territory continuity advances beyond 1 if there are any discontinuities in its occupation (e.g. Territory ID is not used for a year and completely new individuals are censused in the Territory ID once it is used again) #### **pedInbr.txt** * Fam: Family ID assigned to branches of the population pedigree * USFWS: Individual ID * Dad: Individual ID of father (0 if father unknown) * Mom: Individual ID of mother (0 if mother unknown) * Sex: Sex of individual (1 = male, 2 = female) * pedF: Pedigree based inbreeding coefficient #### **env\_var\_updateDemo.txt** * Year: Year of census * acorns: Mean number of acorns per sampled post * burn: Total area in hectares * EQSOI: Mean EQSOI measurement over the census year * density: Number of individuals per hectare #### **envFac\_annual.txt** * social.class: Grouping social class * Sex: Grouping Sex * acorns: Mean number of acorns per sampled post (scaled) * burn: Total area in hectares (scaled) * Year: Year of census * EQSOI: Mean EQSOI measurement over the census year (scaled) * density: Number of individuals per hectare (scaled * pedF.bF: Mean inbreeding coefficient of breeding females * pedF.bM: Mean inbreeding coefficient of breeding males * pedF.hF: Mean inbreeding coefficient of helper females * pedF.hM: Mean inbreeding coefficient of helper males * pedF.j: Mean inbreeding coefficient of juveniles * pair.Fped.new: Mean relatedness of breeders in new pairs * pair.Fped.est: Mean relatedness of breeders in established pairs #### **vr\_clean\_F\_4stageDemo.rdata** Data frame of annual vital rates and population stage census vector calculated for female individuals, with repeated measures for iterations of sampling unsexed individuals #### **vr\_clean\_M\_4stageDemo.rdata** Data frame of annual vital rates population stage census vector calculated for male individuals, with repeated measures for iterations of sampling unsexed individual #### **densityCalcDemo.rdata** Data frame of the number of individuals and territory areas over time across study period, with columns for individuals subdivided by social classes #### **kinship\_coef\_Demo.rdata** Data frame of kinship coefficients calculated between each individual within the study #### **vr\_modelsDemo\_revision\_20240518.rdata** Annual models that link vital rates to environmental factors from enfFac_annual.txt #### **vr\_modelsDemo.rdata** Individual-based models that link vital rates to environmental factors from enfFac_annual.txt and individual inbreeding coefficients #### **vr\_modelsDemo\_validation\_revisions\_20240518.rdata** Residual simulations and validation test results for models from vr_modelsDemo_revision_20240518.rdata #### **Demo\_LTRE\_results\_20240518.rdata** Transient life table response models and resulting data frames include the contribution of individual vital rates, covariation between vital rates, and variation in modeled covariates on variation in the population growth rate, and population growth rate values (lambda) ## Sharing/Access information Links to other publicly accessible locations of the data: * [https://github.com/jtsummers53/LTRE_project](https://github.com/jtsummers53/LTRE_project) ## Code/Software To run analyses of Summers et al. 2024, run scripts in the following order (these are found on Zenodo): 1. pop_densityDemo_20231216.R - genrate popualtion density data and list of territories to include 2. vr_calculate_script_20240508.R - calculate mean annual vital rates 3. env_vr_finalDemo_20231216.R - generate environmental factor data frame 4. env_model_vrDemo_pop_20240422.R - generate annual generalized linear models of vital rates 5. lag_transient_LTRE_popEnv_20240518.Rmd - run transient life table response experiments 6. lag_transient_LTRE_popEnv_detrendPb_20240517.Rmd - run simulations with breeder survival de-trended 7. supp_plots_20240510.R - generate supplementary tables and figures