DOI: 10.5061/dryad.h70rxwdxp
title: Data from: Is phenotypic plasticity use-it-or-lose-it? Exploring genetic assimilation of salinity-plastic traits across threespine stickleback (<em>Gasterosteus aculeatus</em>) populations

description: 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.
description: # Data from: Is phenotypic plasticity use-it-or-lose-it? Exploring genetic
 assimilation of salinity-plastic traits across threespine stickleback
 (*Gasterosteus aculeatus*) populations Dataset DOI:
 [10.5061/dryad.h70rxwdxp](https://doi.org/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
 (&lt;200 years since isolation from anadromous), or old freshwater
 (&gt;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 (&lt;200 years since isolation from
 anadromous), or old freshwater (&gt;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 (&lt;200 years since isolation
 from anadromous), or old freshwater (&gt;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 (&lt;200 years since isolation from anadromous), or old
 freshwater (&gt;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 (&lt;200 years since
 isolation from anadromous), or old freshwater (&gt;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](https://doi.org/10.5281/zenodo.17175842)