DOI: 10.5061/dryad.k3311
title: Data from: Genetic drift outweighs natural selection at toll-like receptor (TLR) immunity loci in a reintroduced population of a threatened species

description: During population establishment, genetic drift can be the key driver of
 changes in genetic diversity, particularly while the population is small.
 However, natural selection can also play a role in shaping diversity at
 functionally important loci. We used a well-studied, re-introduced
 population of the threatened Stewart Island robin (N = 722 pedigreed
 individuals) to determine whether selection shaped genetic diversity at
 innate immunity toll-like receptor (TLR) genes, over a 9-year period of
 population growth following establishment with 12 genetic founders. We
 found no evidence for selection operating with respect to TLR diversity on
 first-year overwinter survival for the majority of loci, genotypes and
 alleles studied. However, survival of individuals with TLR4BE genotype was
 significantly improved: these birds were less than half as likely to die
 prior to maturity compared with all other TLR4 genotypes. Furthermore, the
 population frequency of this genotype, at a two-fold excess over
 Hardy–Weinberg expectation, was increased by nonrandom mating.
 Near-complete sampling and full pedigree and reproductive data enabled us
 to eliminate other potential causes of these patterns including
 inbreeding, year effects, density dependence, selection on animals at
 earlier life history stages or genome-level association of the TLR4E
 allele with ‘good genes’. However, comparison of observed levels of gene
 diversity to predictions under simulated genetic drift revealed results
 consistent with neutral expectations for all loci, including TLR4.
 Although selection favoured TLR4BE heterozygotes in this population, these
 effects were insufficient to outweigh genetic drift. This is the first
 empirical study to show that genetic drift can overwhelm natural selection
 in a wild population immediately following establishment.
description: Individual
 dataThis .csv file contains
 a list of all known individuals (“Band”). For each individual, other
 variables are – “Cohort”: breeding season (cohort) in which individuals
 were hatched. “Surv1yr”: whether or not they survived their first winter.
 “F”: individual inbreeding coefficient. “H”: standardised multilocus
 heterozygosity, calculated using R package ‘Rhh’ (“NA” indicates values
 that cannot be calculated due to insufficient genotyping data). “Rbm” and
 “Rwm”: relatedness coefficient to “blue-metal” and “white-metal”.
 Genotypes for each of the seven TLR loci (missing data are blanks) are
 also provided.Individual.csvPairwise dataThis .csv file contains genotypes for breeding pairs, i.e. data used for simulation of Mendelian inheritance and random mating. Variables are – “Cohort”: breeding season (year). “Sire” and “Sire TLR4”: identity of the male and his TLR4 genotype ("0" if ungenotyped). “Dam” and “Dam TLR4”: identity of the female and her TLR4 genotype ("0" if ungenotyped). “Total offspring”: total number of known offspring (2-week-olds) produced by this pair. “Geno’d offspring”: number of offspring that were genotyped. “Pair bred before?”: whether the pair had bred before (0 = no, 1 = yes).Pairwise.csvPedigree and survival tableThis .csv file contains the pedigree data used for the genedropping analysis (founder genotypes can be found in “Individual” worksheet. The first nine columns comprise a key for indicating which adults were alive on the island in each year, which can be used as a reference for splitting up molecular data by year. Other columns – “ID”: animal ID. “Sire”: male parent (“NA” if it’s a founder). “Dam”: female parent (“NA” if it’s a founder). "UNK" used for unknown parents.Juveniles per pairThis .csv file is for generating Supplementary Figure 5: numbers of juveniles produced by each pair in each year. Variables are – “NestID”: unique identifier for each pair in each year (i.e. total number of labels = number of pair-years in the analysis). “Cohort”: breeding season (year). “JuvSurv”: number of juveniles produced by this nest that survived their first winter.Juv per pair.csv