DOI: 10.5061/dryad.r7sqv9sct
title: Stronger population differentiation at infection-sensing than infection-clearing innate immune loci in songbirds: different selective regimes for different defenses

description: Parasite-mediated selection is widespread at loci involved in immune
 defence, but different defences may experience different selective
 regimes. For defences involved in clearing infections, purifying selection
 favouring a single most efficacious allele likely predominates. However,
 for defences involved in sensing and recognizing infections, evolutionary
 arms races may make positive selection particularly important. This could
 manifest primarily within populations (e.g., balancing selection
 maintaining variation) or among them (e.g., spatially varying selection
 enhancing population differences in allele frequencies). We genotyped
 three toll-like receptors (TLR; involved in sensing infections) and three
 avian beta-defensins (involved in clearing infections) in 96 song sparrows
 (Melospiza melodia) from three breeding populations that differ in disease
 resistance. Variation-based indicators of selection (proportion of
 variable sites, proportion of nonsynonymous SNPs, proportion of sites
 bearing signatures of positive or purifying selection, rare allele
 frequencies) did not differ appreciably between the two locus types.
 However, differentiation was generally higher at infection-sensing than
 infection-clearing loci. Allele frequencies differed markedly at TLR3,
 driven by a variant predicted to alter protein function. Geographically
 structured variants at infection-sensing loci may reflect local adaptation
 to spatially heterogeneous parasite communities. Selective
 regimes experienced by infection-sensing versus infection-clearing loci
 may differ primarily due to parasite-mediated population differentiation.
description: Methods are described in Boyd RJ, MR Denommé, LA Grieves, and EA
 MacDougall-Shackleton. Stronger population differentiation at
 infection-sensing than infection-clearing innate immune loci in songbirds:
 different selective regimes for different defences. Evolution (in
 press).
description: References in datafiles to populations QUBS, RARE and AFAR
 correspond respectively to eastern, central and western locations
 described in the paper. Dataset includes:
 Summary file with sample ID, population, and whether or not
 sequence was obtained from each of six loci. Each row represents an
 individual song sparrow (n=96) and columns correspond to the six loci
 sequenced. This file is named
 <em>Boyd2Post_PopulationsAndLocusCoverage</em>.
 5 DNA sequence files (one for each variable locus) presented in
 FASTA format. For each file, the first sequence is a reference sequence
 from GenBank, and the rest are song sparrow sequences used in this
 study. File names are as follows, <em>Boyd2Post_AvBD2sequences.txt</em> (61 sequences),  <em>Boyd2Post_AvBD7sequences.txt</em> (75 sequences),  <em>Boyd2Post_TLR1LBsequences.txt</em> (73 sequences),  <em>Boyd2Post_TLR3sequences.txt</em> (72 sequences),  <em>Boyd2Post_TLR4sequences.txt</em> (71 sequences). Datafile of single-nucleotide polymorphisms (SNPs) detected. The file is named <em>Boyd2Post_SNPs_Fst. </em>Each row represents a SNP. Columns are as follows, Locus: the locus where the SNP occurs AA site: amino acid position, relative to the start of the sequence Mutation type: synonymous or nonsynonymous Fst: observed population structuring across the 3 populations, as calculated in Genepop Phased haplotype datafile. The file is named <em>Boyd2Post_PhasedHaplotypes</em>. Each row represents an individual song sparrow (n=85) and columns correspond to the five variable loci sequenced.