Data and codes for "Large effect life-history genomic regions are associated with functional morphological traits in Atlantic salmon."

dataset

posted on 2025-05-13, 08:10 authored by T AT A

Tutku Aykanat, Paul V. Debes, Shadi Jansouz, Lison Gueguen, Andrew H. House, Annukka Ruokolainen, Jaakko Erkinaro, Victoria L. Pritchard, Craig R. Primmer, Geir H. Bolstad

29 Nov 2024

Code #1: GMMS_DataPrep_15Nov24.R: R code to prepare data for analysis. In addition to formatting data frames, (i) trait values are calculated and integrated to the dataset, and (ii) Coordinates and centroid sizes after Procrustes shape analysis are produced and integrated to the data frame.

Objects required to run the code:

CS_GMdata4: A dataframe that contains phenotypic and genetic information of individuals, and landmark coordinates for large and small cross sections.

GM3.comb: A dataframe that contains phenotypic and genetic information of individuals, and landmark coordinates for the body sections.

Objects produced by the code:

GM_all_list_filtered_15Nov24: a list object that compiles phenotypic, genetic, landmark and procrustes landmark coordinates of all three body planes (small and large cross sections, an dbody section). This object is used in multivariate Procrustes shape analysis in .

dist_S2, dist_L2, dist_B2, and dist_H2: Four data frames for small and large cross sections, and body and head section that contain phenotypic and genetic information of individuals, which are mostly used in linear mixed effect models. Note that dist_H2 is used only when modelling head centroid as a response variable.

Code #2: GMMS_MainDataAnalysis_16Apr25.R: Main analysis code to perform univariate trait analysis, and multivariate Procrustes shape analysis. The code also plots primary Tables and Figures in the MS.

Objects required to run the code:

Pedigree.txt: Pedigree of individuals and their parents.

dist_S2 , dist_L2 , dist_B2, dist_H2: See Above

GM_all_list_filtered_15Nov24: See Above