DOI: 10.5061/dryad.g79cnp5wz
title: Characterizing contemporary evolutionary change in a recently isolated population of Threespine Stickleback (Gasterosteus aculeatus L.)

description: 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.
description: # Characterizing contemporary evolutionary change in a recently isolated
 population of Threespine Stickleback (Gasterosteus aculeatus L.)
 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:
 ##
 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).