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Ontogenetic variation in the marine foraging of Atlantic salmon functionally links genomic diversity with a major life history polymorphism

Cite this dataset

Aykanat, Tutku; Hindar, Kjetil; Jacobsen, Jan Arge (2024). Ontogenetic variation in the marine foraging of Atlantic salmon functionally links genomic diversity with a major life history polymorphism [Dataset]. Dryad. https://doi.org/10.5061/dryad.fqz612k1m

Abstract

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.

README: 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

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.

Methods

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.

Funding

The Research Council of Norway, Award: 280308

Research Council of Finland, Award: 328860

Research Council of Finland, Award: 353388

Research Council of Finland, Award: 325964