Data from: Population viability of the orchid Gymnadenia conopsea increases with population size but is not related to genetic diversity
Data files
Dec 31, 2024 version files 1.37 MB
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Data_long_surv_with_2021_no_prev_dormancy_LA_clean_v4.xlsx
1.36 MB
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README.md
4.13 KB
Abstract
Population size is a main indicator of conservation potential, thought to predict both current and long-term population viability. However, few studies have directly examined the links between the size and the genetic and demographic properties of populations, using metrics that integrate effects across the whole life cycle. In this study, we combined six years of demographic data with SNP-based estimates of genetic diversity from 18 Swedish populations of the orchid Gymnadenia conopsea. We assessed whether stochastic growth rate increases with population size and genetic diversity, and used stochastic LTRE analysis to evaluate how underlying vital rates contribute to among-population variation in growth rate. For each population, we also estimated the probability of quasi-extinction (shrinking below a threshold size) and of a severe (90%) decline in population size, within the next 30 years. Estimates of stochastic growth rate indicated that ten populations are declining, seven increasing, and one population is approximately stable. SLTRE decomposition showed that low mean adult survival and growth characterized strongly declining populations, whereas high mean fecundity characterized strongly increasing populations. Stochastic growth rate increased with population size, mainly due to higher survival in larger populations, but was not related to genetic diversity. One third of the populations were predicted to go extinct and eight populations to undergo a 90% decrease in population size in the coming 30 years. Low survival in small populations most likely reflects a positive association between local environmental conditions and population size.
Synthesis: The association between G. conopsea population size and viability was driven by variation in survival, and there was no sign that ongoing declines are due to genetic erosion. This suggests that large populations occur in favourable habitats that buffer effects of climatic variation. The results also illustrate that demographic metrics can be more informative than genetic metrics, regarding conservation priority.
README: Population viability of the orchid Gymnadenia conopsea increases with population size but is not related to genetic diversity
https://doi.org/10.5061/dryad.j6q573nqn
Description of the data and file structure
Demographic data was collected during six years in 18 populations of the perennial orchid Gymnadenia conopsea. Populations are located in Öland, Sweden, and vary in census size from 11 to >30000 flowering individuals.
Files and variables
File: Data_long_surv_with_2021_no_prev_dormancy_LA_clean v4.xlsx
Description: Demographic data collected during six years in 18 populations of Gymnadenia conopsea. Each row in the dataset corresponds to one individual in one year. Empty cells in the dataset indicate missing values in a given year, such as leaf length and width, or number of flowers in vegetative individuals.
Variables:
ID | Individual identity |
---|---|
Pop | Population |
Year | Year |
survthis | Survival year t (binomial) |
survnext | Survival year t+1 (binomial) |
flowthis | Flowering year t (binomial) |
flownext | Flowering year t+1 (binomial) |
Statethis | Status year t (F = flowering, M = missing, V = vegetative) |
Fl.nthis | Number of flowers year t |
L.nthis | Number of leaves year t |
L1Wthis | Leaf width leaf 1 year t (cm) |
L1Lthis | Leaf length leaf 1 year t (cm) |
L2Wthis | Leaf width leaf 2 year t (cm) |
L2Lthis | Leaf length leaf 2 year t (cm) |
Statenext | Status year t+1 (F = flowering, M = missing, V = vegetative) |
Fl.nnext | Number of flowers year t+1 |
L.nnext | Number of leaves year t+1 |
L1Wnext | Leaf width leaf 1 year t+1 (cm) |
L1Lnext | Leaf length leaf 1 year t+1 (cm) |
L2Wnext | Leaf width leaf 2 year t+1 (cm) |
L2Lnext | Leaf length leaf 2 year t+1 (cm) |
LA_totthis | Total leaf area year t (cm^2) |
LA_totnext | Total leaf area year t+1 (cm^2) |
ID_YEAR | Individual identity with year |
LA | Total leaf area year t including imputed values (cm^2) |
method | Method used to impute (see supplementary material) |
dormant | Dormant year t (binomial) |
LA_next | Total leaf area year t+1 including imputed values (cm^2) |
fec.seeds | Number of seeds |
plot | Plot identity |
plot_num | Plot number within population |
new_plot | Plot created in year t (binomial) |
stage | Stage year t (continuous=alive, dead, dormant) |
stageNext | Stage year t+1 (continuous=alive, dead, dormant) |
dormantNext | Dormant year t+1 (binomial) |
Code/software
The integral population model (IPM) used to estimate vital rates and quantify population growth rate was built in R, and can be followed in the R-script "IPM.Rmd".
The model used to impute missing values was built in R, and can be followed in the R-script "Imputation of values.Rmd".
Both scripts run with empty cells in the data sheet.
Methods
The dataset contains six years of demographic data (2017-2022) from each of 18 populations of Gymnadenia conopsea on the island of Öland in Sweden, and the code to run integral projection models in R.