DOI: 10.5061/dryad.fqz612k1m
title: Ontogenetic variation in the marine foraging of Atlantic salmon functionally links genomic diversity with a major life history polymorphism

description: The ecological role of heritable phenotypic variation in free-living
 populations remains largely unknown. Knowledge of the genetic basis of
 functional ecological processes can link genomic and phenotypic diversity,
 providing insight into polymorphism evolution and how populations respond
 to environmental change. By quantifying the marine diet, of sub-adult
 Atlantic salmon, we assessed how foraging behavior changes along the
 ontogeny, and in relation to genetic variation in two loci with major
 effect on age-at-maturity (six6 and vgll3). We used a two-component,
 zero-inflated negative binomial model to simultaneously quantify foraging
 frequency (zero-inflation components) and foraging outcome (count
 component), separately for fish and crustaceans in the diet. We found that
 older salmon forage for both prey types more actively (as evidenced by
 increased foraging frequency), but with a decreased efficiency (as
 evidenced by fewer prey items in the diet), suggesting an age-dependent
 shift in foraging dynamics. The vgll3 locus was linked to age-dependent
 changes in foraging behavior: younger salmon with vgll3LL (the genotype
 associated with late maturation) tend to forage crustaceans more often
 than those with vgll3EE (the genotype associated with early maturation),
 while the pattern was reversed in older salmon. Vgll3 LL genotype was also
 linked to marginal increase in fish acquisition especially in younger
 salmon, while six6 was not a factor explaining the diet variation. Our
 results suggest a functional role for variation in marine feeding behavior
 linking genomic diversity at vgll3 with age-at-maturity among salmon, with
 potential age-dependent trade-offs maintaining the genetic variation. A
 shared genetic basis between dietary ecology and age-at-maturity likely
 subjects Atlantic salmon populations to evolution induced by bottom-up
 changes in marine productivity.
description: Data and codes to reproduce the results in the MS titled
 Ontogenetic variation in the marine foraging of Atlantic salmon
 functionally links genomic diversity with a major life history
 polymorphism.
description: # Ontogenetic variation in the marine foraging of Atlantic salmon
 functionally links genomic diversity with a major life history
 polymorphism Data and codes to reproduce the results in the MS titled
 Ontogenetic variation in the marine foraging of Atlantic salmon
 functionally links genomic diversity with a major life history
 polymorphism.
 [https://doi.org/10.5061/dryad.fqz612k1m](https://doi.org/10.5061/dryad.fqz612k1m) R is required to run Codes_Aykanat.et.al_dietMS_25Jun24.R; the script was created using version 4.1.0. ### Data files: **diet.data_JA_21Feb24.txt:** The main data frame (a .txt file) that contains data to run the code and replicate the results The variables (columns) in diet.data_JA_21Feb24.txt that were used in the MS: *RG*: Regional group. *season*: Fishing period *FORKLength*: Fork length (cm) of Atlantic salmon. *SeaAgeN*: Sea Age of Atlantic salmon at the time of sampling. *SexC*: Sex of Atlantic salmon. *Vgll3*: Genotype of Atlantic salmon at the vgll3 locus (1=EE, 2=EL, 3=LL genotype).  *Six6*: Genotype of Atlantic salmon at the six6 locus (1=EE, 2=EL, 3=LL genotype). *Location*: The location randpom term used on teh study. *num_fish*: Number of fish in the stomach's of Atlantic salmon.  *num_crus*: Number of crustaceans in the stomach's of Atlantic salmon.  *w_fish* : Weight of fish in the stomach's of Atlantic salmon. *w_crus* : Weight of crustaceans in the stomach's of Atlantic salmon. *them_num*: Number of Hyperiid amphipods (Themisto spp.) in the stomach's of Atlantic salmon.  *copepod_num*: Number of Euphausiids (Krills) in the stomach's of Atlantic salmon. *weight_est*: Weight estimated from gutted weight of Atlantic salmon.   *fishing_season*: Season of the fishing.  *condition*: Condition factor of Atlantic salmon. *.scl*: When a variable is scaled, ".scl*" is added to the variable name. ### Code: **Codes_Aykanat.et.al_dietMS_25Jun24.R:** The R code for reproducing the results presented in the MS The code allows to replicate all images and statistical models in the MS. The information in the code  (written after the “#” character) directs which specific figure or model that any section is relevant for.