Characterizing contemporary evolutionary change in a recently isolated population of Threespine Stickleback (Gasterosteus aculeatus L.)
Data files
Dec 14, 2023 version files 843.50 KB
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KOZAK_ALLDATA_COMPILED.csv
579.43 KB
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KOZAK_LL_COMPILED.csv
237.50 KB
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KOZAK_LOSTLAGOON_MAIN_CODE.txt
21.22 KB
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KOZAK_LOSTLAGOON_POOLFSTAT_CODE.txt
2.36 KB
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KOZAK_WIREFRAME.csv
502 B
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README.md
2.49 KB
Abstract
Parallel evolution of lateral plates and body shape in threespine stickleback (Gasterosteus aculeatus) is an iconic example of adaptation. We test a case of contemporary evolutionary transition in a recently isolated population of marine G. aculeatus in British Columbia, Canada. We investigate Ectodysplasin (Eda) genotypes, plate counts, neutral genetic divergence and whole-body phenotypes to determine genetic and phenotypic distance between this population and nearby comparative populations. Our focal population is in the process of adapting both genetically and phenotypically to a freshwater environment and we provide an example of the genetic basis for parallel evolutionon a contemporary timescale. The frequency of Eda genotypes and lateral plate phenotypes in our focal population are not consistent with those of marine or fully freshwater populations. Although our focal population is genetically distinct from nearby marine populations, these fish still more closely resemble marine populations in overall body shape while demonstrating an intriguing intermediate phenotype. Eda frequency and lateral plate phenotype change faster than body shape in response to freshwater conditions, suggesting that the pace of adaptation differs across traits in response to the same environmental conditions. Our results further bolster the case for G. aculeatus as a key model of contemporary evolution.
README: Characterizing contemporary evolutionary change in a recently isolated population of Threespine Stickleback (Gasterosteus aculeatus L.)
https://doi.org/10.5061/dryad.g79cnp5wz
The dataset contains R code and raw data files required to analyze 3D body shape and genetic divergence in this population of threespine stickleback along with a set of comparator data.
Description of the data and file structure
DATA-SPECIFIC INFORMATION FOR:KOZAK_LL_COMPILED.csv
File contents: Specimen information and 3D landmark coordinates obtained from CT scans for specimens from Lost Lagoon
Variable List: see accompanying publication for details about each variable
ID: specimen ID
Population: population name
Eda: ectodysplasin genotype
Sex: genetic sex
RawCoord1-402: raw 3D landmark coordinates in XYZXYZ format
DATA-SPECIFIC INFORMATION FOR:KOZAK_ALLDATA_COMPILED.csv
File contents: Specimen information and 3D landmark coordinates obtained from CT scans for comparator specimens
Variable List: see accompanying publication for details about each variable
ID: specimen ID
Population: population name
Eda: ectodysplasin genotype
Sex: genetic sex
RawCoord1-402: raw 3D landmark coordinates in XYZXYZ format
DATA-SPECIFIC INFORMATION FOR:KOZAK_WIREFRAME.csv
File contents: landmark linkages for wireframe generation in KOZAK_LOSTLAGOON_MAIN_CODE.txt
Sharing/Access information
Pooled sequencing pipeline code and information is being used by multiple collaborators and is housed separately. This code can be found here: https://dx.doi.org/10.17504/protocols.io.e6nvwk372vmk/v1
Code/Software
Code included here was written for use with the following platforms, packages and their dependencies:
R v.4.2.2
RStudio v.2023.03.0
geomorph v. 4.0.5 geometric morphometrics
ggplot2 v. 3.4.1 plotting
plyr v. 1.8.8 data manipulation
dplyr v.1.1.0 data manipulation
poolfstat v.2.2.1 genetic divergence
methods v.4.2.2 accessing poolfstat results
CODE-SPECIFIC INFORMATION FOR: KOZAK_LOSTLAGOON_MAIN_CODE.txt: this code is the main analysis code for the paper. Poolfstat code is in a separate file due to size of input data (see Sharing/Access information for details on pooled sequencing pipeline).
CODE-SPECIFIC INFORMATION FOR: KOZAK_LOSTLAGOON_POOLFSTAT_CODE.txt: this code is the genetic divergence analysis code, which builds on the output from the pooled sequencing pipline (see Sharing/Access information for details on pooled sequencing pipeline).