DOI: 10.5061/dryad.j6q573nqn
title: Data from: Population viability of the orchid Gymnadenia conopsea increases with population size but is not related to genetic diversity

description: 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.
description: The dataset contains six years of demographic data (2017-2022)
 from each of 18 populations of <em>Gymnadenia conopsea </em>on
 the island of Öland in Sweden, and the code to run integral projection
 models in R.
description: # 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](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 &gt;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.