Data from: Aquatic vegetation promotes prey diversity but not the diversification of predator phenotypes
Data files
Jul 17, 2026 version files 15.99 MB
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Fish-all.phenotypes.csv
224.31 KB
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Fish-Ecotype.parent.genotypes.with.quality.vcf
4.30 MB
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Fish-F2.genotypes.csv
1.09 MB
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Fish-F2.genotypes.with.quality.vcf
8.98 MB
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Fish-F2.phenotypes.and.linkage.map.csv
940.52 KB
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Fish-QTL.analysis.R
6.67 KB
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Fish-survival.and.performance.R
11.20 KB
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Invertebrates-analysis.R
16.58 KB
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Invertebrates-calculating_community_metrics.R
2.28 KB
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Invertebrates-individuals.with.size.and.mass.csv
399.65 KB
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Invertebrates-taxon.traits.csv
3.59 KB
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Mesocosms-treatments.and.final.census.csv
4.21 KB
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README.md
11.84 KB
Abstract
Freshwater fish have evolved to forage in a range of habitats, from open water in lakes to benthic shorelines and streams. Much research has focused on how prey differences, such as zooplankton vs. benthic macroinvertebrates, might select for divergence in predator traits across this habitat gradient. However, major structural components of this habitat contrast, such as aquatic vegetation, may fundamentally constrain foraging success. Here, we used a mesocosm experiment to test for interactive effects of vegetated habitat and fish density on the survival and growth of phenotypically variable juvenile sticklebacks. We investigated two scales of phenotypic variation: distinct lake and stream ecotypes and F2 lake-stream hybrids. We found that macrophytes strongly increased invertebrate biomass and functional richness, which increased fish condition. Surprisingly, relative performance of ecotypes and genotypes depended only on fish density. Stream ecotypes had higher survival than lake ecotypes, as well as higher condition. In parallel, F2 hybrids had higher growth when homozygous for stream alleles at three QTL loci. Together, these findings suggest that adaptive divergence among habitats depends on the ways that prey type, habitat structure, and genetic variation for feeding and growth traits combine with competition to limit the abundance of accessible prey.
Dataset DOI: 10.5061/dryad.0000000gm
Description of the data and file structure
Experimental mesocosms: treatments and mecocosm-level final data
Data files
File: Mesocosms-treatments.and.final.census.csv
Description: This dataset identifies the treatment and experimental block for each of the 50 mesocosms, and gives final plant cover, fish survival metrics, and invertebrate community metrics. Missing data = NA.
Variables
- Mesocosm: tank identifier
- Block: experimental block
- Macrophytes: yes or no for macrophyte treatment
- FinalMacrophyteCover: visual assessment of final plant cover in % cover
- Fish: yes or no for fish presence
- FishDensity: none, low, or high
- FishStart: number of juveniles introduced to the mesocosm
- FishType: none, wild = equal mix of lake and stream ecotypes, or F2 hybrids
- TotalSurvivors: number of surviving juveniles recovered at the end of the experiment
- LakeSurvivors: if an ecotype tank, number genotyped (identified) as an offspring of lake parents bred in the lab
- StreamSurvivors: if an ecotype tank, number genotyped (identified) as an offspring of stream parents bred in the lab
- PropStream: if an ecotype tank, proportion of surviviors genotyped (identified) as stream
- FishSurvivalRate: final survivors as a fraction of FishStart
- InvertAbundance: total number of macroinvertebrates identified (calculated in the Invertebrates section below)
- InvertBiomass: total biomass of macroinvertebrates identified (estimated and calculated in the Invertebrates section below)
- InvertSpeciesRichness: number of taxa of macroinvertebrates identified (calculated in the Invertebrates section below)
- InvertFunctionalRichness: functional richness of macroinvertebrates identified (calculated in the Invertebrates section below)
Invertebrate communities
We identified and measured the macroinvertebrates recovered from each tank at the end of the experiment. We used the measured lengths and equations from the literature to estimate the biomass for each individual. We also gathered trait values for each taxon from the literature. We then calculated community metrics for each mesocosm.
Data files
File: Invertebrates-individuals.with.size.and.mass.csv
Description: This dataset lists every invertebrate recovered from the mesocosm, with identity and size.
Variables
- Mesocosm: tank identifier
- Order: invertebrate order
- Species: invertebrate species
- BodyLength.mm: length in mm, measured on each individual
- Biomass.mg: dry mass in mg, estimated from equations for each taxon
File: Invertebrates-taxon.traits.csv
Description: This spreadsheed lists traits for each invertebrate species. All but AvgMass are taken from the literature and expert knowledge. A more readable version of this information is provided in the supplementary material for the related paper.
Variables
- Species: invertebrate species
- Order: invertebrate order
- Group: additional taxonomic group for interpretability
- AvgMass.fromMesocosms.mg: the average estimated dry mass in mg of all individuals of this taxon found in the mesocosms. Mass was averaged first within each mesocosm where the species was present, and then averaged across mesocosms.
- LifeDuration: less than or greater than one year
- BodyFlexibility: degrees animal can turn its body
- BodyForm: flattened, cylindrical, or spherical
- Locomotion.diving: for the locomotion traits, a total of 10 points are allocated across the options in proportion to their probability of use
- Locomotion.burrowing: for the locomotion traits, a total of 10 points are allocated across the options in proportion to their probability of use
- Locomotion.sprawling.walking: for the locomotion traits, a total of 10 points are allocated across the options in proportion to their probability of use
- Locomotion.semisessile: for the locomotion traits, a total of 10 points are allocated across the options in proportion to their probability of use
Analysis scripts
File: Invertebrates-calculating_community_metrics.R
Description: This R script combines the Invertebrates-individuals.with.size.and.mass.csv and the Invertebrates-taxon.traits.csv data files to calculate the abundance, biomass, species richness, and functional richness of the macroinvertebrates in each mesocosm. These variables have been added to the Mesocosms-treatments.and.final.census.csv data file.
File: Invertebrates-analysis.R
Description: This R script uses the Mesocosms-treatments.and.final.census.csv data file to test for mesocosm treatment effects on the final invertebrate communities. This file also directly uses the Invertebrates-individuals.with.size.and.mass.csv and the Invertebrates-taxon.traits.csv data files to conduct multivariate analyses of treatment effects on invertebrate community composition and trait distributions.
Fish survival and performance
We evaluated survival, final length, and condition in all surviving juvenile sticklebacks, both the lake vs. stream ecotypes and the F2s. Additionally, we used QTL (Quantitative Trait Locus) analysis to test for effects of F2 genotypes on F2 phenotypes, including performance (final length and weight). Finally, we provide comparable genotype information for the F2s and the wild-caught ecotypes that were the parents of the juvenile ecotypes, to provide some context on the ecotype vs. hybrid genetics.
Data files
File: Fish-all.phenotypes.csv
Description: This dataset gives the identity of all surviving stickleback fish, and the mesocosm where they were recovered. All fish were measured for length and weight, but only the F2 hybrids were photographed for individual mouth morphology traits. Missing data = NA.
Variables
- id: fish identifier, assigned at the time of recovery
- Mesocosm: tank identifier
- FishInTank: fish identifier nested within each mesocosm
- FishType: none, wild = equal mix of lake and stream ecotypes, or F2 hybrids
- Ecotype: if an ecotype mesocosm, lake vs. stream ecotype as identified by microsat genotyping to assign to genotyped parents that were either two lake or two stream fish
- Dad: assigned paternal fish based on microsat genotype
- Mom: assigned maternal fish based on microsat genotype
- ProbabilityParentage: probability of parentage by analysis of microsats
- Type3: lake, stream, or F2 hybrid
- Length_mm: final standard length measured in mm
- Weight_mg: final wet weight measured in mg
- Log_Condition_mg: weight standardized for the average final length, in log10 space
- Gape_sc: size corrected gape
- BuccalLength_sc: size corrected buccal length
- JawProtrusion_sc: size corrected jaw protrusion
- heightEpaxial_sc: size corrected epaxial muscle height
- widthEpaxial_sc: size corrected epaxial muscle width
- EpaxArea: epaxial muscle area
- BuccalArea: buccal area
- SuI_sc: size corrected suction index
File: Fish-F2.genotypes.csv
Description: This dataset gives the RAD-tag genotypes for each of the 642 sequenced F2s at 563 loci where the F0 parents were opposite homozygotes, so that all F1s were heterozygotes. Genotypes were obtained from the vcf files described below. Missing data = NA.
Variables
- Mesocosm: tank identifier
- id: fish identifier
- chrI_102681 and all subsequent columns: the genotype at the RAD locus identified during mapping to the reference genome as falling on (in the first case) chromosome (chr) 1 at position 102681. Genotypes are coded as 0 for homozygous for the alelle found in the stream female F0, 1 for homozygous for the alelle found in the lake male F0, or 0.5 for heterozygous.
File: Fish-F2.phenotypes.and.linkage.map.csv
Description: This dataset combines the mesocosm treatment information, the phenotype, and the genotype for each of the 613 sufficiently sequenced F2s in the format needed for QTL mapping. The file also includes the linkage map determined using the program JoinMap. Only the 454 loci included in the linkage map are given.
Variables
- id: fish identifier
- Library: illumina library where the fish was sequenced
- Order: a fish identifier using during sequencing
- Mesocosm: tank identifier
- Block: experimental block
- Macrophytes: yes (plants) or no for macrophyte treatment
- FishDensity: none, low, or high
- CombinedTreatment: factor combining the Macrophytes and FishDensity treatments into four combinations
- FishStart: number of juveniles introduced to the mesocosm
- TotalSurvivors: number of surviving juveniles recovered at the end of the experiment
- Length_mm: final standard length measured in mm
- Weight_mg: final wet weight measured in mg
- Log_Length_mm: natural log transformed Length_mm
- Log_Weight_mg: natural log transformed Weight_mg
- Sex: sex inferred from a PCA of all RAD-tag genotypes
- Log_Condition_mg: weight standardized for the average final length, in log10 space
- Condition_mg: weight standardized for the average final length, backtransformed from log10
- JawProtrusion: jaw protrusion, measured from photographs at magnification
- BuccalLength: buccal length, measured from photographs at magnification
- Gape: gape, measured from photographs at magnification
- Gape_sc: size corrected gape
- BuccalLength_sc: size corrected buccal length
- JawProtrusion_sc: size corrected jaw protrusion
- chrI_3617637 and all subsequent columns: the genotype at the RAD locus identified during mapping to the reference genome as falling on (in the first case) chromosome (chr) 1 at position 102681. The first two rows give the chromosome and the distance along the chromosome infered from the linkage map. Genotypes are coded as AA for homozygous for the alelle found in the stream female F0, BB for homozygous for the alelle found in the lake male F0, or AB for heterozygous.
File: Fish-F2.genotypes.with.quality.vcf
Description: VCF file with genotype calls for surviving F2s. Generated from the genomic data archived at SRA BioProject PRJNA789317 : RAD-tag sequencing of Gasterosteus aculeatus lake stream cross. https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA789317
File: Fish-Ecotype.parent.genotypes.with.quality.vcf
Description: VCF file with genotype calls for the parents of the ecotype juveniles. Generated from the genomic data archived at SRA BioProject PRJNA789317 : RAD-tag sequencing of Gasterosteus aculeatus lake stream cross. https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA789317
Analysis scripts
File: Fish-survival.and.performance.R
Description: This R script uses the Mesocosms-treatments.and.final.census.csv and the Fish-all.phenotypes.csv files to test for mesocosm treatment effects on total fish survival, growth, and condition, as well as the relative survival and performance of lake vs. stream ecotypes.
File: Fish-QTL.analysis.R
Description: This R script uses the Fish-F2.phenotypes.and.linkage.map.csv to carry out QTL mapping and identify loci in the F2s associated with growth and mouth traits.
Code/software
All analyses were conducted in R, and packages are listed in each script. All data files are csv files except for the two original vcf files for genotypes, which can be viewed in a text editor.
Access information
RAD-tag genotype data was derived from the following sources:
- SRA BioProject PRJNA789317 : RAD-tag sequencing of Gasterosteus aculeatus lake stream cross. https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA789317
