DOI: 10.5061/dryad.w0vt4b8sq
title: Vitamin D status is heritable and under environment-dependent selection in the wild

description: Vitamin D has a well-established role in skeletal health and is
 increasingly linked to chronic disease and mortality in humans and
 companion animals. Despite the clear significance of vitamin D for health
 and obvious implications for fitness under natural conditions, no
 longitudinal study has tested whether the circulating concentration of
 vitamin D is under natural selection in the wild. Here, we show that
 concentrations of dietary-derived vitamin D and endogenously-produced
 vitamin D metabolites are heritable and largely polygenic in a wild
 population of Soay sheep (Ovis aries). Vitamin D status was positively
 associated with female adult survival, and vitamin D status predicted
 female fecundity in particular, good environment years when sheep density
 and competition for resources was low. Our study provides evidence that
 vitamin D status has the potential to respond to selection, as well as new
 insights into how vitamin D metabolism is associated with fitness in the
 wild. 
description: The full methods on how data was collected and processed is
 included in the main manuscript associated with this dataset.
 Scripts for analysis are available at
 https://github.com/sejlab/Soay_Vitamin_D. Further information on all data
 can be found in the main manuscript and in the file
 "README_VitD_MS_Phenotype_Dataframe_Descriptions.xlsx".
description: IMPORTANT INFORMATION ABOUT THE DATA: The
 attached files contain data derived from the long-term field project
 monitoring individual Soay sheep on St Kilda and their environment. If you
 plan to analyse the data for a novel analysis, there are a number of
 reasons why it would be very helpful if you could contact Josephine
 Pemberton (j.pemberton@ed.ac.uk) before doing so: 1) If
 you are interested in analysing the detailed project data in any depth you
 may find it helpful to have our full relational database rather than the
 file(s) available here.  If so, then we have a simple process for bringing
 you onto the project as a collaborator. 2) Occasionally
 we discover and correct errors in the data. Some sheep identifiers have
 been recoded over time and should therefore not be linked with data
 archived from other papers using the Soay sheep data.
 3) The data are complex and workers who do not know the study
 system may benefit from advice when interpreting it. 4)
 At any one time, quite a few people within the existing project
 collaboration are analysing data from this project. Someone else may
 already be conducting the analysis you have in mind and it is desirable to
 prevent duplication of effort. 5) In order to maintain
 funding for the project(s), every few years we have to write proposals for
 original analyses to funding agencies. It is therefore very helpful for
 those running the project to know what data analyses are in
 progress. DATA DESCRIPTION: These
 data are related to the manuscript MEC-21-0375. Scripts for analysis are
 available at https://github.com/sejlab/Soay_Vitamin_D
 <strong> *** DATAFILE
 "VitD_MS_Phenotype_Data_2021.csv" </strong><br>
  <br> This is the phenotypic data used in the analysis. Missing data
 is denoted as NA. Headers are as follows:<br>  <br>
 <strong>ID    </strong>Individual sheep identifier<br>
 <strong>Sex    </strong>Sex of the individual where 1 is
 female and 2 is male<br> <strong>Age    </strong>Age of
 the individual in years at time of sampling<br>
 <strong>AgeGroup</strong>    Age grouped (0: lambs, 1:
 yearlings, 2: 2-6 years, 3: 7+ years)<br> <strong>CoatBin  
  </strong>Coat colour where 1 is dark and 2 is light<br>
 <strong>Year    </strong>Year of
 sampling/measurement<br> <strong>Total.25D</strong>  
  Plasma concentrations of total 25(OH)D in nmol/l<br>
 <strong>X25OHD2</strong>    Plasma concentrations of 25(OH)D2
 in nmol/l<br> <strong>X25OHD3</strong>    Plasma
 concentrations of 25(OH)D3 in nmol/l<br> <strong>Weight  
  </strong>August body mass (kg)<br> <strong>MumID  
  </strong>Mother's individual identifier<br>
 <strong>BirthYear    </strong>Year of birth<br>
 <strong>Survival    </strong>0 = individual died over the
 subsequent winter following measurement OR 1 = individual survived over
 winter<br> <strong>EweFecundity</strong>    Female
 breeding success in the spring following sampling<br>
 <strong>MaleABS    </strong>Male breeding success in the
 spring following sampling<br>
 <strong>MaleABSBin</strong>    Male breeding success in the
 spring following sampling as a binary variable (0 - did not sire
 offspring, 1 - did sire offspring)<br>
 <strong>EweLambingThisSpring    </strong>Female lambing status
 in the spring of the same year (prior to sampling in August) where N = no
 lamb(s), L0 = had a lamb(s) of which none survived to 3 months, L1 = had a
 lamb(s) of which at least one survived to 3 months
 <strong>*** DATAFILE
 "soayimp_genotype_data.RData"</strong>
 This is an .RData file for loading into the software R. It
 contains a GenABEL object that contains all SNP genotype information
 corresponding to each individual. <strong>***
 DATAFILE "Vit_Reg_h2.RData"</strong>
 This is an .RData file for loading in the software R and contains
 the following objects necessary to conduct the analysis:
 <strong>makeGRM</strong> - This is a function to
 create the genomic relatedness matrix from GCTA output.<br>
 <strong>ASReml.EstEffects</strong> - This is a function to
 extract the heritability and other random effects from ASReml-R
 models.<br> <strong>VITD </strong>- This is the dataset
 in "VitD_MS_Phenotype_Data_2021.csv" formatted for analysis in
 R<br> <strong>grminv</strong> - This is the genomic
 relatedness matrix created using GCTA.
 <strong>*** DATAFILE
 "4_Updated_Pedigree_Feb2017.txt"</strong>
 This file contains the pedigree with ID, MOTHER and FATHER.
 Missing data is NA. <strong>*** DATAFILE
 "Soay_Vitamin_D-master.zip"</strong>
 This is a saved version of the Github repository
 https://github.com/sejlab/Soay_Vitamin_D 
 <strong>*** SUPPLEMENTARY FILE
 "TableS9_GWAS_Results.zip"</strong>
 Table S9. Full genome-wide association results for total 25(OH)D,
 25(OH)D2, 25(OH)D3 plasma concentrations in Soay sheep. A1 and A2 are the
 reference and alternate allele at each SNP. effB is the slope of the
 effect of allele A2, with the standard error se_effB. Chi2.1df and P1df
  is the association chi-squared statistic and associated P-value,
 respectively, before correction with genomic control λ. Pc1df is the
 corrected P-value after genomic control. Exp is the corresponding P-value
 for that SNP locus assuming a null distribution of P-values (see Figure
 2). Q.2 is the minor allele frequency.