Virginia Tech
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Dataset and code for "Common-garden experiment reveals outbreeding depression and region-of-origin effects on reproductive success in a frequently translocated tortoise"

posted on 2024-06-14, 19:02 authored by Kevin LoopeKevin Loope

Data include nest site, hatching success and genetically-determined parentage data for clutches of gopher tortoises (Gopherus polyphemus) translocated to Nokuse, a private reserve in the panhandle of Florida. Human-mediated animal movement can expose wildlife populations to novel environments. Phenotypic plasticity can buffer against the challenges presented by novel environments, while adaptation to local ecosystems may limit resilience in novel ecosystems. Outbreeding depression during the mixing of disparate gene pools can also reduce reproductive success after long-distance movement. Here, we use a “common garden” population of gopher tortoises (Gopherus polyphemus), translocated from numerous sites across the state of Florida, USA, to a mitigation site in the northwest (panhandle) region to assess whether geographic origin, outbreeding effects, and behavioral plasticity influence reproductive success in this threatened keystone species. We found that females from northeast Florida produced clutches with lower hatching success than females from other regions. We detected regional differentiation in nest site selection behavior in the common environment of the translocation site, though these differences did not mediate the regional effect on hatching success. We also found evidence for outbreeding depression: hatching success declined with increasing parental geographic and genetic distances, dropping from 93% to 67% across the range of observed parental genetic distances. Together, these results suggest that newly admixed populations may suffer reproductive costs due to historic population differentiation, and that undetected outbreeding depression could significantly hamper conservation efforts for this species and others undergoing a variety of human-mediated movements.


Department of Defense Strategic Environmental Research and Development Program (RC18-C1-1103)

Florida Fish and Wildlife Commission (PGNOHPWK)



University Libraries, Virginia Tech


Bruce, FL

Corresponding Author Name

Kevin J. Loope

Corresponding Author E-mail Address

Files/Folders in Dataset and Description

NokuseHatchingSuccess.R This file contains all code used to analyze data and produce figures. It imports data files from the "Data" folder and outputs files to the "Figures" and "Tables" folders. Data/ ibutton_data.csv This file contains raw temperature data recorded from within each nest. Columns are: serial: iButton serial number year: year the the datapoint was collected time: the time the datapoint was collected value: the nest temperature, measured at the center of the nest, in degrees C. NestID: the nest's name site: the site the nest was located in duration: the number of days of the ibutton dataset for the given nest GT_nests_data.csv This file contains all relevant data about nest characteristics and hatching success Columns are: NestID: the nest's name NestBottom_cm: the depth from the surface to bottom of the nest cavity, in cm NestDistBurrow: the distance from the center of the nest to the mouth of the associated burrow BurrowOrient: the compass orientation of the burrow (facing out) Densiometer: the number of shaded cells (out of 90) for a hemispherical densiometer facing south immediately above the nest ClutchSize: the number of eggs recorded at time of excavation iBCenterTemp: the ibutton serial number for the nest BrokenSearching: the number of eggs in the nest that were broken by researchers while finding the nest BrokenExcavation: the number of eggs in the nest that were broken by researchers while excavating the nest DeadAnts: the number of dead hatchlings found upon nest excavation (killed by fire ants) Hatchlings: the number of eggs that hatched in the lab obs_genotypes.csv the observed multilocus genotypes for all adults genotyped in the study (used to calculate genetic distance) Columns are: ID: tortoise ID remaining columns: two for each locus source_locations.csv the source locations for each tortoise genotyped Columns are: ID: tortoise ID latitude: latitude (decimal degrees) longitude: longitude (decimal degrees) level: whether the location reflects the source site or the source county center parentage.csv MotherID and associated info for each nest Columns are: Site: which translocation site was the nest at (Magnolia or Wolf) Nest: the NestID MotherID: the mother's ID County: the mother's source county counties_regions.csv A dataframe connecting each source county to it's associated region (panhandle, north, central, south Florida) County: the county name Zone: the region for the county Nok_PRISM_site_800m_monthly_normals.csv the 30-year climate normals, downloaded from for the period 1981 to 2010 for each mother's source site. Columns are: Name: NestID Longitude: longitude (decimal degrees) Latitude: latitude (decimal degrees) Elevation (m): elevation in meters Date: month (including annual) ppt_mm: precipitation for the Date, in mm tmin_c: minimum tmeperature for the Date, in degrees C tmean_c mean tmeperature for the Date, in degrees C tmax_c: maximum tmeperature for the Date, in degrees C allele_length_adjust.csv the file that translates allele names to allele sizes compatible with repeat motifs for use in calculating genetic dsitance using the stepwise mutation model of Kosman and Jokela 2019. Columns are: old: allele name new: allele length adjusted to fit the motif identified in "repeat" locus: the locus rep: the repeat length of the motif nokuse_mag_2022v3.BestConfig.txt nokuse_mag_2022v3.DadGenotype nokuse_mag_2022v3.MumGenotype nokuse_wolf_2022v5.BestConfig.txt nokuse_wolf_2022v5.DadGenotype nokuse_wolf_2022v5.MumGenotype These are output files directly from program Colony containing parentage assignments and adult estimated genotypes. See Colony documentation for details. SMMv [directory] Contains the results of running the output genotypes manually through the Locus program described in Kosman & Jokela 2019 for the stepwise mutation model calculation of genetic distance nokuse_magnolia_2022v3.dat nokuse_wolf_2022v5.dat These are input files for Colony containing all genotypes and settings for parentage analysis. See Colony documentation for details.

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