Dataset and code for "Common-garden experiment reveals outbreeding depression and region-of-origin effects on reproductive success in a frequently translocated tortoise"
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.
Funding
Department of Defense Strategic Environmental Research and Development Program (RC18-C1-1103)
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 https://prism.oregonstate.edu/ 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.