Data from: Is phenotypic plasticity use-it-or-lose-it? Exploring genetic assimilation of salinity-plastic traits across threespine stickleback (Gasterosteus aculeatus) populations
Data files
Oct 15, 2025 version files 18.97 GB
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Clutch_DailySurvivalCoefVar.csv
133.24 KB
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Clutch_HatchingSurvival.csv
25.25 KB
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Individ_FreshwaterLength.csv
23.79 KB
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Individ_FreshwaterMetrics.csv
16.25 KB
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Individ_LandmarkSamples.csv
60.13 KB
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Individ_LRLandmarks.csv
952.30 KB
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Individ_MorphologyMetrics.csv
79.22 KB
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MeasuringPhotos.zip
18.97 GB
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PopSal_ProcrustesVariances.csv
897 B
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Population_FreshwaterMetrics.csv
4.26 KB
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Population_PlasticityIndices.csv
1.96 KB
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README.md
24.72 KB
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Tank_11MonthSurvival.csv
7.80 KB
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Tank_MonthlySurvivalCoefVar.csv
4.45 KB
Abstract
Understanding the response of phenotypically plastic traits to novel environments is critical to predicting evolutionary dynamics. We lab-reared multiple wild-caught threespine stickleback (Gasterosteus aculeatus) populations under a range of salinities and recorded the plasticity of morphological, physiological, and fitness-related traits. Following freshwater colonisation, populations showed a short-term increase or maintenance of salinity tolerance breadth (i.e., consistency of survival across salinities) – while a subsequent loss of salinity tolerance occurred in most, but not all, populations over the longer term. Despite variability amongst physiological and morphological responses to increased salinity across populations, we found that resolution of generalist-specialist trade-offs may drive plasticity loss: less plastic populations grew faster in freshwater. Our findings establish that predicted Simpson-Baldwin dynamics (plasticity gain and then subsequent loss under relaxed selection) can apply to plastic traits in natural populations, although the underlying mechanisms may be variable, even within species.
Dataset DOI: 10.5061/dryad.h70rxwdxp
Description of the data and file structure
These datasets provide raw and processed data used for analyses of threespine stickleback (Gasterosteus aculeatus) population salinity tolerance, using split-clutch experiments raising individuals from embryo to 11 months in 5 salinity treatments at 0ppt, 10ppt, 20ppt, 30ppt, and 40ppt. Clutches were generated from wild-caught individuals from 9 populations in Alaska and Scotland, including a variety of anadromous and freshwater populations of ages between 30 and 16,000 years. Data include metrics of growth and survival to 11 months, as well as morphometric landmark data (and corresponding photographs) of 11-month-old fish, and gill ionocyte characteristics derived from histological analysis of 11-month-old fish. Also included are analyses of trait plasticity across salinity treatments for each population, and analyses of patterns in trait variation across salinity treatments.
Files and variables
Populations in these datasheets are referred to with two-letter abbreviations which refer to their place of origin and are different to their classifications in the paper: "KB"="A_S", "RS"="A_A", "FK"="YF1_S", "LB"="YF_A", "CR"="YF2_S", "HW"="YF3_S", "BB"="OF1_A", "CL"="OF2_A", "DM"="OF_S".
File: Individ_FreshwaterLength.csv
Description: The 11-month standard lengths (in mm) of individual fish raised in the freshwater (0ppt) treatment within this experiment, as well as the average number of fish in each tank over this time period, and the calculated residual length from a linear model of length against average number of fish in the tank. Note that tanks containing fewer than 5 fish on average are not included in this dataset.
Variables
- Tank: The rearing tank of the individual
- Population: The two-letter code for the population of origin of the individual
- Type: The evolutionary history of the population of origin of the individual: anadromous, young freshwater (<200 years since isolation from anadromous), or old freshwater (>12,000 years since isolation from anadromous)
- PhotoID: The ID code of the photograph used to measure the standard length of the fish
- Length: The standard length of the fish, in mm, measured using ImageJ of a calibrated photograph
- AvgFishInTank: The average number of fish in the tank over the 11 months of the experiment
- DensityCorrectedLength: The residual of a linear model of all freshwater standard lengths against the average number of fish in the tank, i.e., the difference between the expected standard length of the fish and its actual standard length, in mm
File: Individ_MorphologyMetrics.csv
Description: Morphological metrics for each individual in the experiment at 11 months of age: the standard length (to 2dp), left-right fluctuating asymmetry, and the average Procrustes Distance between the individual's landmarks and the consensus mean shape of fish in that salinity/population treatment combination.
Variables
- Individual: The unique ID code of the fish, containing its population, rearing salinity, tank code, and number
- tank: The rearing tank of the individual
- population: The two-letter code for the population of origin of the individual
- salinity: The rearing salinity in ppt of the fish, divided by 10 (e.g. '1'='10ppt')
- ProcDist: The average Procrustes Distance between landmark locations between the fish's landmarks (see Individ_LRLandmarks.csv) and the consensus mean landmark locations for that population/salinity treatment
- fluctasymm: The left-right fluctuating asymmetry score for landmark location across left- and right-facing photographs of the individual fish
- length: The standard length of the fish, in mm, measured using ImageJ of a calibrated photograph
File: Population_FreshwaterMetrics.csv
Description: The population average metrics of various morphological, growth, survival, and physiological metrics of 11-month-old fish reared in freshwater (0ppt) conditions in the experiment, as well as the population salinity tolerance breadth for each population across 0-30ppt salinity treatments, average standard length of wild-caught adults from that population, and plasticity index of ionocyte area across 0-30ppt salinity treatments for that population.
Variables
- Population: The two-letter code for the population of origin of the fish
- PopulationType: The evolutionary history of the population of origin of the fish: anadromous, young freshwater (<200 years since isolation from anadromous), or old freshwater (>12,000 years since isolation from anadromous)
- SalinityToleranceBreadth: The calculated salinity tolerance breadth of percentage survival across 0-30ppt salinity treatments for each population, calculated as 100*(1-((maximum value-minimum value)/(maximum value))), i.e,. '100' implies equal survival across all salinity treatments
- FreshwaterSurvival: The average percentage survival to 11 months in the freshwater treatment (0ppt) for that population
- FreshwaterDensityCorrectedLength: The population average residual of a linear model of all freshwater standard lengths against the average number of fish in the ta,nk i,.e, the average difference between the expected standard lengths of the fish and their actual standard length, in mm
- StErrCorrectedLength: The population standard error of residuals of a linear model of all freshwater standard lengths against the average number of fish in the tank, i.e., the standard error of the difference between the expected standard lengths of the fish and their actual standard length, in mm
- WildAdultLength: The standard length of wild-caught adults from the population used for clutch generation, in mm, measured using ImageJ of a calibrated photograph
- WithinIndivCoeffVarFilamentWidth: The average within-individual coefficient of variation of gill filament width at 11 months for freshwater-raised individuals in that population
- WithinIndivCoeffVarLamellarWidth: The average within-individual coefficient of variation of gill lamellar width at 11 months for freshwater-raised individuals in that population
- WithinIndivCoeffVarInterLamellarWidth: The average within-individual coefficient of variation of gill inter-lamellar width at 11 months for freshwater-raised individuals in that population
- WithinIndivCoeffVarIonocyteRoundness: The average within-individual coefficient of variation of gill ionocyte roundness at 11 months for freshwater-raised individuals in that population
- WithinIndivCoeffVarIonocyteArea: The average within-individual coefficient of variation of gill ionocyte area at 11 months for freshwater-raised individuals in that population
- StErrWithinIndivCoeffVarIonocyteArea: The standard error of the within-individual coefficient of variation of gill ionocyte area at 11 months for freshwater-raised individuals in that population
- WithinIndivCoeffVarIonocyteCoverage: The average within-individual coefficient of variation of gill ionocyte coverage (area of ionocytes per gill filament area) at 11 months for freshwater-raised individuals in that population
- WithinIndivCoeffVarIonocyteRatio: The average within-individual coefficient of variation of gill ionocyte distribution (percentage of ionocytes that were located on the gill lamellae rather than the filament) at 11 months for freshwater-raised individuals in that population
- IonocyteAreaPI: The population plasticity index of average ionocyte area across salinities from 0-30ppt, i.e,. (maximum value-minimum value)/maximum value
- BetweenIndivCoefVarFilamentWidth: The between-individual coefficient of variation of average gill filament width at 11 months for freshwater-raised individuals in that population
- BetweenIndivCoefVarLamellarWidth: The between-individual coefficient of variation of average gill lamellar width at 11 months for freshwater-raised individuals in that population
- BetweenIndivCoefVarInterLamellarWidth: The between-individual coefficient of variation of average gill inter-lamellar width at 11 months for freshwater-raised individuals in that population
- BetweenIndivCoefVarIonocyteArea: The between-individual coefficient of variation of average gill ionocyte area at 11 months for freshwater-raised individuals in that population
- BetweenIndivCoefVarIonocyteCoverage: The between-individual coefficient of variation of average gill ionocyte coverage (area of ionocytes per gill filament area) at 11 months for freshwater-raised individuals in that population
- BetweenIndivCoefVarIonocyteDistribution: The between-individual coefficient of variation of average gill ionocyte distribution (percentage of ionocytes that were located on the gill lamellae rather than the filament) at 11 months for freshwater-raised individuals in that population
- BetweenIndivCoefVarIonocyteRoundness: The between-individual coefficient of variation of average gill ionocyte roundness at 11 months for freshwater-raised individuals in that population
- AvgOfAsymmetry: The population average left-right fluctuating asymmetry score for 11-month-old individuals reared in freshwater, based on landmarks of left- and right-facing photos of each individual
- MorphologicalDisparity: The population average morphological disparity between individuals reared in freshwater, based on landmarks averaged between left- and right-facing photos of each individual
File: Population_PlasticityIndices.csv
Description: Population plasticity indices of various survival, physiologic, and morphological metrics of 11-month-old individuals across salinity rearing treatments of 0-30ppt (i,.e. calculated using population average values at 0ppt, 10ppt, 20ppt, and 30ppt) in this experiment
Variables
- Population: The two-letter code for the population of origin of the fish
- Type: The evolutionary history of the population of origin of the fish: anadromous, young freshwater (<200 years since isolation from anadromous), or old freshwater (>12,000 years since isolation from anadromous)
- SalinityToleranceBreadth: The calculated salinity tolerance breadth of survival across 0-30ppt salinity treatments for each population, calculated as 100*(1-((maximum value-minimum value)/(maximum value,e))), i.e., '100' implies equal survival across all salinity treatments
- FilamentWidthPI: The population plasticity index of average gill filament width across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value))
- LamellarWidthPI: The population plasticity index of average gill lamellae width across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value))
- InterLamellarWidthPI: The population plasticity index of average gill inter-lamellae width across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value))
- IonocyteAreaPI: The population plasticity index of average gill ionocyte area across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value))
- IonocyteCoveragePI: The population plasticity index of average gill ionocyte coverage (area of ionocytes per gill filament area) across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value))
- PercentLamellarPI: The population plasticity index of average gill ionocyte distribution (percentage of ionocytes that were located on the gill lamellae rather than the filament) across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value))
- IonocyteRoundnessPI: The population plasticity index of average gill ionocyte roundness across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value))
- MorphInterIndivVarPI: The population plasticity index of average morphological disparity value across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value)); see 'PopSal_ProcrustesVariances.csv'
- MorphWithinIndivVarPI: The population plasticity index of average morphological left-right fluctuating asymmetry value across 0-30ppt rearing conditions ((maximum value-minimum value)/(maximum value)); see 'Indiv_MorphologyMetrics.csv'
File: PopSal_ProcrustesVariances.csv
Description: The average morphological disparity values between individuals reared in each population/salinity treatment combination
Variables
- Population: The two-letter code for the population of origin of the fish
- Salinity: The rearing salinity in ppt of the fish
- MorphologicalDisparity: The morphological disparity between individuals of that population reared in that salinity, based on landmarks averaged between left- and right-facing photos of each individual
File: Individ_LandmarkSamples.csv
Description: A metadata file of all fish photographs used in morphometric analysis, detailing for each photograph the fish, population, rearing salinity, rearing tank, side photographed, and standard length of the fish in mm
Variables
- PhotoID: The ID code of the photograph used to measure the landmark locations of the fish
- FishID: The unique ID code of the fish, containing its population, rearing salinity, tank code, and number
- Population: The two-letter code for the population of origin of the individual
- Salinity: The rearing salinity in ppt of the fish, divided by 10 (e.g. '1'='10ppt')
- TankID: The rearing tank of the individual
- Side: The orientation of fish shown in the photograph (L=left-facing, R=right-facing)
- Length: The standard length of the fish, in mm, measured using ImageJ of a calibrated photograph
File: Individ_FreshwaterMetrics.csv
Description: The growth and physiological metrics at 11 months of each fish reared in freshwater, including information on their ID, rearing tank, population of origin, rearing salinity, standard length in mm, density-corrected length in mm (by the average number of fish in the tank), and within-individual coefficient of variance in various gill physiological metrics
Variables
- Individual: The unique ID code of the fish, containing its population, rearing salinity, tank code, and number
- Tank: The rearing tank of the individual
- Population: The two-letter code for the population of origin of the individual
- Salinity: The rearing salinity in ppt of the fish, divided by 10 (e.g. '1'='10ppt')
- PopulationPlasticity: The calculated salinity tolerance breadth of survival across 0-30ppt salinity treatments for each population, calculated as 100*(1-((maximum value-minimum value)/(maximum value))), i.e,. '100' implies equal survival across all salinity treatments.
- FishLength: The standard length of the fish, in mm, measured using ImageJ of a calibrated photograph
- AvgOfEstimatedLength: The expected standard length of fish in the tank in mm, based on a linear model of all freshwater fish against the average number of fish in the tank
- DensityCorrectedLength: The residual of a linear model of all freshwater standard lengths against the average number of fish in the tank, i.e,. The difference between the expected standard length of the fish and its actual standard length, in mm
- CoeffVarFilamentWidth: The within-individual coefficient of variation of gill filament width at 11 months
- CoeffVarLamellarWidth: The within-individual coefficient of variation of gill lamellar width at 11 months
- CoeffVarInterLamellarWidth: The within-individual coefficient of variation of gill inter-lamellar width at 11 months
- CoeffVarIonocyteRoundness: The within-individual coefficient of variation of gill ionocyte roundness at 11 months
- CoeffVarIonocyteArea: The within-individual coefficient of variation of gill ionocyte area at 11 months
- CoeffVarIonocyteCoverage: The within-individual coefficient of variation of gill ionocyte coverage (area of ionocytes per gill filament area) at 11 months
- CoeffVarIonocyteRatio: The within-individual coefficient of variation of gill ionocyte distribution (percentage of ionocytes that were located on the gill lamellae rather than the filament) at 11 months
File: Tank_11MonthSurvival.csv
Description: The per-tank percentage survival to 11 months for all tanks in the experiment, including calculated survival from fertilisation to 11 months
Variables
- Tank: The rearing tank of the fish
- Population: The two-letter code for the population of origin of the fish
- PopulationType: The evolutionary history of the population of origin of the fish: anadromous, young freshwater (<200 years since isolation from anadromous), or old freshwater (>12,000 years since isolation from anadromous)
- Salinity: The rearing salinity in ppt of the fish
- HatchPercent: The average percent of individuals in each clutch that hatched at that salinity for that population
- SurvivalTo11Months: The percentage of individuals in that tank that survived to 11 months of age from immediately post-hatch
- StandardisedSurvival: The calculated survival percentage of individuals from that population at that salinity for each tank, using the average hatch rate of clutches from that salinity/population combination multiplied by the tank survival to 11 months
File: Clutch_HatchingSurvival.csv
Description: The percentage survival to hatch of each clutch split into each salinity treatment, for each population in the experiment
Variables
- ClutchID: The unique ID of each clutch, containing its population and two-digit ID number
- Salinity: The rearing salinity in ppt of the embryos for that clutch split
- StartEggs: The number of eggs from that clutch that were split into that salinity
- HatchedFry: The number of eggs that successfully hatched into surviving fry for that clutch at that salinity
- PercentSurvivalToHatch: The calculated percentage survival to hatch for that clutch at that salinity, i.,e. (hatched fry/start eggs)*100
- Population: The two-letter code for the population of origin of the embryos
- PopulationType: The evolutionary history of the population of origin of the embryos: anadromous, young freshwater (<200 years since isolation from anadromous), or old freshwater (>12,000 years since isolation from anadromous)
File: Clutch_DailySurvivalCoefVar.csv
Description: The coefficient of variation in percentage survival across the four salinity treatments (0ppt, 10ppt, 20ppt, and 30ppt) for each clutch in the experiment on each day since the clutch was split between salinities (i, day 7 post-fertilisation onwards). The average onset of hatching across populations was Day 21 (at the experimental temperature of 10 degrees Centigrade).
Variables
- Clutch: The unique ID of each clutch, containing its population and two-digit ID number
- Population: The two-letter code for the population of origin of the clutch
- Day: The day post-fertilisation that survival was assessed; clutches were split between salinities on day 7
- AvgOfPercentSurvival: The average survival percentage of embryos for that clutch across salinities on that day
- StDevOfPercentSurvival: The standard deviation of survival percentage of embryos for that clutch across salinity treatments (0-30ppt) on that day
- CoV: The coefficient of variance of survival percentage of embryos for that clutch across salinity treatments (0-30ppt) on that day
File: Tank_MonthlySurvivalCoefVar.csv
Description: The coefficient of variation in percentage survival across the four salinity treatments (0ppt, 10ppt, 20ppt, and 30ppt) for each population in the experiment at the end of each month from 0 (fry hatching and transfer) to 11 months (end of the experiment).
Variables
- Population: The two-letter code for the population of origin of the fish
- MeasureMonth: The month for which survival was assessed (survival was assessed at the end of each month; month '0', representing the start of the experiment, is set at 100% survival)
- AvgOfAvgOfPercentSurvival: The average percentage survival of that population across salinities for that month. Survival in each salinity treatment was first averaged across tanks within that salinity/population treatment combination.
- StDevOfAvgOfPercentSurvival: The standard deviation in percentage survival of that population across salinities for that month. Survival in each salinity treatment was first averaged across tanks within that salinity/population treatment combination.
- CoV: The coefficient of variance in percentage survival across salinities for that population for that month.
File: Individ_LRLandmarks.csv
Description: All morphometric landmarks for each fish in the population were measured at 11 months with photographs on both sides (see Supplementary Materials of the paper for landmark locations). Note that all X coordinates for right-side-facing fish have been multiplied by -1 to allow for specimen alignment. Missing landmarks are recorded as blank cells.
Variables
- PhotoID: The ID code of the photograph used to measure the landmark locations of the fish
- FishID: The unique ID code of the fish, containing its population, rearing salinity, tank code, and number
- Population: The two-letter code for the population of origin of the individual
- Salinity: The rearing salinity in ppt of the fish, divided by 10 (e.g. '1'='10ppt')
- TankID: The rearing tank of the individual
- Side: The orientation of fish shown in the photograph (L=left-facing, R=right-facing)
- Length: The standard length of the fish, in mm, measured using ImageJ of a calibrated photograph
- X1: The X coordinate of landmark 1
- Y1: The Y coordinate of landmark 1
- X2: The X coordinate of landmark 2
- Y2: The Y coordinate of landmark 2
- X3: The X coordinate of landmark 3
- Y3: The Y coordinate of landmark 3
- X4: The X coordinate of landmark 4
- Y4: The Y coordinate of landmark 4
- X5: The X coordinate of landmark 5
- Y5: The Y coordinate of landmark 5
- X6: The X coordinate of landmark 6
- Y6: The Y coordinate of landmark 6
- X7: The X coordinate of landmark 7
- Y7: The Y coordinate of landmark 7
- X8: The X coordinate of landmark 8
- Y8: The Y coordinate of landmark 8
- X9: The X coordinate of landmark 9
- Y9: The Y coordinate of landmark 9
- X10: The X coordinate of landmark 10
- Y10: The Y coordinate of landmark 10
- X11: The X coordinate of landmark 11
- Y11: The Y coordinate of landmark 11
- X12: The X coordinate of landmark 12
- Y12: The Y coordinate of landmark 12
- X13: The X coordinate of landmark 13
- Y13: The Y coordinate of landmark 13
- X14: The X coordinate of landmark 14
- Y14: The Y coordinate of landmark 14
- X15: The X coordinate of landmark 15
- Y15: The Y coordinate of landmark 15
- X16: The X coordinate of landmark 16
- Y16: The Y coordinate of landmark 16
- X17: The X coordinate of landmark 17
- Y17: The Y coordinate of landmark 17
- X18: The X coordinate of landmark 18
- Y18: The Y coordinate of landmark 18
- X19: The X coordinate of landmark 19
- Y19: The Y coordinate of landmark 19
- X20: The X coordinate of landmark 20
- Y20: The Y coordinate of landmark 20
- X21: The X coordinate of landmark 21
- Y21: The Y coordinate of landmark 21
- X23: The X coordinate of landmark 23
- Y23: The Y coordinate of landmark 23
- X25: The X coordinate of landmark 25
- Y25: The Y coordinate of landmark 25
- X27: The X coordinate of landmark 26
- Y27: The Y coordinate of landmark 27
File: MeasuringPhotos.zip
Description: A folder containing all photographs of 11-month-old fish reared as part of this study, facing both left and right, against a calibrated background (small grid squares = 2mm, large grid squares =10mm). File names correspond to PhotoID as referred to in IndividLRLandmarks.csv, and are in the format date(YYMMDD)_tankID_individual/side.jpg. Tank ID is comprised of a two-letter code for the population of origin, a number representing the rearing salinity (0=0ppt, 1=10ppt, 2=20ppt, 3=30ppt, 4=40ppt), and a lower-case letter of the individual tank. 'Side' is either L (left-facing) or R (right-facing). For example, 200626_HW4b_5L.jpg represents a photo taken on 26th June 2020 of the left-facing side of the 5th fish from population HW reared in 40ppt salinity and tank b.
Code/software
All files are in .csv format, other than fish photographs in the .zip folder which are .jpg. R Code used to analyse these datasets can be found at DOI: 10.5281/zenodo.17175842