Data from: Growth and longevity of the endangered freshwater pearl mussel (Margaritifera margaritifera): Implications for conservation and management
Data files
May 20, 2024 version files 2.51 MB

A_cor.xlsx

Amax.xlsx

H_at_age.rds

H_cor.xlsx

Iw.xlsx

mean_ci_gompertz.csv

mean_ci_lester.csv

mean_ci_logistic.csv

mean_ci_power.csv

mean_ci_vb.csv

meas_and_rec_H.rds

pars_gompertz.rds

pars_lester.rds

pars_logistic.rds

pars_power.rds

pars_vb.rds

preds_ALL.rds

preds_gompertz.rds

preds_lester.rds

preds_logistic.rds

preds_power.rds

preds_vb.rds

R2.rds

README.md

RSE.rds

RSS.rds

shell_size.xlsx

Size_and_age_variables.xlsx
Abstract
Key lifehistory data, such as growth and age, are necessary to effectively manage and conserve threatened freshwater mussel species. Traditionally growth and age studies require large yet destructive sample sizes covering all age classes. Such methods pose a risk to populations of conservation concern, and therefore alternative methods that need only limited sample sizes are necessitated to prevent further threats to such populations. We applied retrospective shell growth at age reconstructions to 98 critically endangered freshwater pearl mussel (FPM) individuals from 34 populations across Finland and Sweden, enabling the use of extremely small sample sizes (n = 1–6 per population). We compared the performance of six different growth models with the reconstructed sizeatage data across FPM juvenile (<20 years old) and adult life stages. The growth reconstruction model showed reasonable skill in reconstructing FPM growth patterns. The von Bertalanffy model was shown to be a good general descriptor of growth for FPM, but it systematically underestimated the asymptotic size. The power law model was the most accurate in estimating juvenile growth (lowest deviances from the sizeatage data). FPM showed great variability in longevity (A_{max} = 54–254 years) and growth constant k (0.018– 0.057 year^{1}). Our results show that reasonable estimates of growth can be attained even when sample sizes are extremely limited. The results can be further applied to gain knowledge on the population’s age structure, size at maturation, and recovery potential. The methodology is applicable to other freshwater mussel species of conservation concern.
README: Data from: Growth and longevity of the endangered freshwater pearl mussel (Margaritifera margaritifera): Implications for conservation and management
Authors and correspondence:
Sabrina Nykänen, sabrina.s.nykanen@jyu.fi, https://orcid.org/0000000168088457
Jouni Taskinen, jouni.k.taskinen@jyu.fi, https://orcid.org/0000000300989560
Mahsa Hajisafarali, mahsa.m.hajisafarali@jyu.fi
Anna Kuparinen, anna.k.kuparinen@jyu.fi, https://orcid.org/0000000278078946
Description of the data and file structure
This section consists of the following files:
"A_cor.xlsx"  Table containing the age of the corroded shell area (i.e. the number of missing increments)
"ID" = identifier of the mussel individuals
"A_cor" = age of the corroded shell area (years)
"Amax.xlsx"  Table containing the maximum observed age (i.e. age at time of death)
"river" = sampled river
"ID" = identifier of the mussel individuals
"Amax" = maximum observed age for the mussel individual (years)
"H_at_age.rds"  RDS file contaning sizeatage data
columns represent the individuals, row number indicates the age, values are heights in mm
"H_cor.xlsx"  Table containing the height of the corroded shell portion along the commissural plane
"ID" = identifier of the mussel individuals
"H_cor" = age of the corroded shell area (mm)
"Iw.xlsx"  Table containing external shell increment
columns represent the individuals, first row is the first measured growth increment, values are increments in mm
"mean_ci_gompertz.csv"  Table containing mean and confidence interval for Gompertz model parameters
"river" = sampled river
"Asym_mean" = mean for asymptotic height (mm)
"Asym_lwr" = lower limit for asymptotic height (mm)
"Asym_upr" = upper limit for asymptotic height (mm)
"b2_mean" = mean for displacement of the curve on the xaxis
"b2_lwr" = lower limit for displacement of the curve on the xaxis
"b2_upr" = upper limit for displacement of the curve on the xaxis
"b3_mean" = mean for growth rate
"b3_lwr" = lower limit for growth rate
"b3_upr" = upper limit for growth rate
"n" = number of converged models
"mean_ci_lester.csv"  Table containing mean and confidence interval for Lester biphasic model parameters
"river" = sampled river
"h_mean" = mean for juvenile growth rate (mm /year)
"h_lwr" = lower limit for juvenile growth rate (mm /year)
"h_upr" = upper limit for juvenile growth rate (mm /year)
"y_int_mean" = mean for yintercept of the model
"y_int_lwr" = lower limit for yintercept of the model
"y_int_upr" = upper limit for yintercept of the model
"t1_mean" = mean for xintercept of the model
"t1_lwr" = lower limit for xintercept of the model
"t1_upr" = upper limit for xintercept of the model
"g_mean" = mean for investment in reproduction (gonad weight/somatic weight)
"g_lwr" = lower limit for investment in reproduction (gonad weight/somatic weight)
"g_upr" = upper limit for investment in reproduction (gonad weight/somatic weight)
"K_mean" = mean for growth constant that describes the rate at which Hinf is reached
"K_lwr" = lower limit for growth constant that describes the rate at which Hinf is reached
"K_upr" = upper limit for growth constant that describes the rate at which Hinf is reached
"Hinf_mean" = mean for asymptotic height (mm)
"Hinf_lwr" = lower limit for asymptotic height (mm)
"Hinf_upr" = upper limit for asymptotic height (mm)
"t0_mean" = mean for theoretical age at which the height of the organism is zero
"t0_lwr" = lower limit for theoretical age at which the height of the organism is zero
"t0_upr" = upper limit for theoretical age at which the height of the organism is zero
"n" = number of converged models
"mean_ci_logistic.csv"  Table containing mean and confidence interval for logistic model parameters
"river" = sampled river
"Asym_mean" = mean for asymptotic height (mm)
"Asym_lwr" = lower limit for asymptotic height (mm)
"Asym_upr" = upper limit for asymptotic height (mm)
"xmid_mean" = mean for age when mussels have reached half of the asymptotic height
"xmid_lwr" = lower limit for age when mussels have reached half of the asymptotic height
"xmid_upr" = upper limit for age when mussels have reached half of the asymptotic height
"1/scal_mean" = mean for growth rate
"1/scal_lwr" = lower limit for growth rate
"1/scal_upr" = upper limit for growth rate
"n" = number of converged models
"mean_ci_power.csv"  Table containing mean and confidence interval for power law model parameters
"river" = sampled river
"Hinf_mean" = mean for asymptotic height (mm)
"Hinf_lwr" = lower limit for asymptotic height (mm)
"Hinf_upr" = upper limit for asymptotic height (mm)
"a_mean" = mean for absolute rate of growth
"a_lwr" = lower limit for absolute rate of growth
"a_upr" = upper limit for absolute rate of growth
"b_mean" = mean for rate at which the asymptotic size is approached
"b_lwr" = lower limit for rate at which the asymptotic size is approached
"b_upr" = upper limit for rate at which the asymptotic size is approached
"n" = number of converged models
"mean_ci_vb.csv"  Table containing mean and confidence interval for von Bertalanffy model parameters
"river" = sampled river
"Hinf_mean" = mean for asymptotic height (mm)
"Hinf_lwr" = lower limit for asymptotic height (mm)
"Hinf_upr" = upper limit for asymptotic height (mm)
"K_mean" = mean for growth constant that describes the rate at which Hinf is reached
"K_lwr" = lower limit for growth constant that describes the rate at which Hinf is reached
"K_upr" = upper limit for growth constant that describes the rate at which Hinf is reached
"t0_mean" = mean for theoretical age at which the height of the organism is zero
"t0_lwr" = lower limit for theoretical age at which the height of the organism is zero
"t0_upr" = upper limit for theoretical age at which the height of the organism is zero
"n" = number of converged models
"meas_and_rec_H.rds"  RDS file contaning measured nd reconstructed terminal heights
"Country" = country where the river is situated
"river" = sampled river
"ID" = identifier of the mussel individuals
"L_m" = measured length of the mussel
"H_mm" = measured height of the mussel
"H_rec" = reconstructed terminal height
"pars_gompertz.rds"  RDS file contaning the Gompertz growth model parameters
"River" = sampled river
"ID" = identifier of the mussel individuals
"Asym" = asymptotic height (mm)
"b2" = displacement of the curve on the xaxis
"b3" = growth rate
"pars_lester.rds"  RDS file contaning the Lester biphasic growth model parameters
"river" = sampled river
"id" = identifier of the mussel individuals
"h" = juvenile growth rate (mm /year)
"y_int" = yintercept of the model
"t1" = xintercept of the model
"g" = investment in reproduction (gonad weight/somatic weight)
"K" = growth constant that describes the rate at which Hinf is reached
"H_inf" = asymptotic height (mm)
"t0" = theoretical age at which the height of the organism is zero
"T" = age at maturity
"pars_logistic.rds"  RDS file contaning the logistic growth model parameters
"river" = sampled river
"id" = identifier of the mussel individuals
"Asym" = asymptotic height (mm)
"xmid" = age when mussels have reached half of the asymptotic height
"scal" = caling parameter for the xaxis with which the growth rate can be calculated as 1/scal
"pars_power.rds"  RDS file contaning the power law growth model parameters
"river" = sampled river
"id" = identifier of the mussel individuals
"a" = absolute rate of growth
"b" = rate at which the asymptotic size is approached
"A_s" = age (years) of the first observed increment
"H(A_s)" = height (mm) at A_s
"Hinf" = asymptotic height (mm)
"pars_vb.rds"  RDS file contaning the von Bertalanffy growth model parameters
"river" = sampled river
"id" = identifier of the mussel individuals
"Hinf" = asymptotic height (mm)
"K" = growth constant that describes the rate at which Hinf is reached
"t0" = theoretical age at which the height of the organism is zero
"preds_ALL.rds"  RDS file contaning all the height predictions for all the fitted models
"river" = sampled river
"id" = identifier of the mussel individuals
"age" = age (years)
"obs_mm" = reconstructed height at age (mm)
"vb_fit" = fitted height (mm) with von Bertalanffy
"gompertz_fit" = fitted height (mm) with Gompertz
"logistic_fit" = fitted height (mm) with logistic
"lester_fit" = fitted height (mm) with Lester biphasic
"power_fit" = fitted height (mm) with power law
"exp_fit" = fitted height (mm) with exponential
"preds_gompertz.rds"  RDS file contaning the height predictions for Gompertz growth model
"age" = age (years)
"river" = sampled river
"id" = identifier of the mussel individuals
"gompertz_fit" = fitted height (mm) with Gompertz
"obs_mm" = reconstructed height at age (mm)
"preds_lester.rds"  RDS file contaning the height predictions for Lester biphasic growth model
"age" = age (years)
"river" = sampled river
"id" = identifier of the mussel individuals
"lester_fit" = fitted height (mm) with Lester biphasic
"preds_logistic.rds"  RDS file contaning the height predictions for logistic growth model
"age" = age (years)
"river" = sampled river
"id" = identifier of the mussel individuals
"logistic_fit" = fitted height (mm) with logistic
"obs_mm" = reconstructed height at age (mm)
"preds_power.rds"  RDS file contaning the height predictions for power law and exponential growth model
"age" = age (years)
"river" = sampled river
"id" = identifier of the mussel individuals
"pwr_fit" = fitted height (mm) with power law
"inc" = growth increment (mm)
"obs_mm" = reconstructed height at age (mm)
"exp_fit" = fitted height (mm) with exponential
"preds_vb.rds"  RDS file contaning the height predictions for von Bertalanffy growth model
"age" = age (years)
"river" = sampled river
"id" = identifier of the mussel individuals
"vb_fit" = fitted height (mm) with von Bertalanffy
"obs_mm" = reconstructed height at age (mm)
"R2.rds"  RDS file contaning regression coefficients
"river" = sampled river
"id" = identifier of the mussel individuals
colums indicate the models, values indicate the regression coefficients
"RSE.rds"  RDS file contaning residual standard errors
"river" = sampled river
"id" = identifier of the mussel individuals
colums indicate the models, values indicate the residual standard errors
"RSS.rds"  RDS file contaning sums of squared residuals
"river" = sampled river
"id" = identifier of the mussel individuals
colums indicate the models, values indicate the sums of squared residuals
"shell size.xlsx"  Table containing the measured size of the mussels
"Country" = country where the river is situated
"river" = sampled river
"ID" = identifier of the mussel individuals
"L_m" = measured length of the mussel
"H_mm" = measured height of the mussel
"Size and age variables.xlsx"  Table containing observed shell size and age variables for all the freshwater pearl mussel individuals
"Country" = country where the river is situated
"River" = sampled river
"ID" = identifier of the mussel individuals
"L(mm)" = shell length
"H(mm)" = shell height
"Hcor (mm)" = height of the corroded shell portion along the commissural plane
"Aobs (years)" = number of observed winter lines
"Acor (years)" = estimated age of the corroded shell portion
"A (years)" = estimated age at death (= Aobs + Acor)
"H measured in lab"= 1: Height was measured in laboratory from the shell crosssection attached to the glass slides for age determination
"Empty shell" = 1: Individual was dead at the time of collection, i.e. an empty shell in good condition
Missing data code : NA
Code/Software
This section consists of the following codes/software.
Codes/Software for running the data analysis and producing the figures in the manuscript.
"Figures.R"  Generates the all the figures of the manuscript in R, except Figures 1b and S2.
"Growth_models.R"  Fits the growth models (von Bertalanffy, Gompertz, logistic, Lester biphasic, power law, exponential) to the sizeatage data produced with "Shell_growth_reconstruction.R" in R.
"LM_and_Figs1b_and_S2.R"  Fits the linear regression model where the reconstructed heights were evaluated against the measured shell heights and generates Figures 1b and S2 in R.
"Mean_and_CI.R"  Calculates the mean and confidence intervals for the model parameters in R.
"Shell_growth_reconstruction.R"  Script for calculating the reconstructed heights of the mussel individuals.