DOI: 10.5061/dryad.3vb7h
title: Data from: Immunogenetic heterogeneity in a widespread ungulate: the European roe deer (Capreolus capreolus)

description: Understanding how immune genetic variation is shaped by selective and
 neutral processes in wild populations is of prime importance in both
 evolutionary biology and epidemiology. The European roe deer (Capreolus
 capreolus) has considerably expanded its distribution range these last
 decades, notably by colonizing agricultural landscapes. This range shift
 is likely to have led to bottlenecks and increased roe deer exposure to a
 new range of pathogens that until recently predominantly infected humans
 and domestic fauna. We therefore investigated the historical and
 contemporary forces that have shaped variability in a panel of genes
 involved in innate and acquired immunity in roe deer, including Mhc-Drb
 and genes encoding cytokines or toll-like receptors (TLRs). Together, our
 results suggest that genetic drift is the main contemporary evolutionary
 force shaping immunogenetic variation within populations. However, in
 contrast to the classical view, we found that some innate immune genes
 involved in micropathogen recognition (e.g. Tlrs) continue to evolve
 dynamically in roe deer in response to pathogen-mediated positive
 selection. Most studied Tlrs (Tlr2, Tlr4 and Tlr5) had similarly high
 levels of amino acid diversity in the three studied populations including
 one recently established in southwestern France that showed a clear
 signature of genetic bottleneck. Tlr2 implicated in the recognition of
 Gram-positive bacteria in domestic ungulates, showed strong evidence of
 balancing selection. The high immunogenetic variation revealed here
 implies that roe deer are able to cope with a wide spectrum of pathogens
 and to respond rapidly to emerging infectious diseases.
description: Microsatellite
 dataMicrosatellite genotypes
 of the three roe deer study populations (12 loci)Roedeer_microsatellite_Genotypes_Quemereetal.txt454 sequencing of the MHC-Drb exon 2Raw sequence 454 data + primers with MID barcodes. We used a modified version of the primers LA31 (5’- GATCCTCTCTCTGCAGCACATTTCCT-3’) and LA32 (5’-TTCGCGTCACCTCGCCGCTG-3’) initially designed for cattle (Sigurdardottir et al. 1991), with the addition of individual-specific MIDS (Multiplex Identifiers) and adaptors required for emPCR and 454 sequencing.MHC-DRB_CaCapreolus_454_rawdata.zipPAML4_CodeML_infileswe estimated the non-synonymous/synonymous rate ratio (dN/dS) at each codon site using the Bayesian approach implemented in the CodeML program of the PAML4 package (Yang 2007) .Input files for DNAsp (Phased Haplotypes)This files contains the DNA sequences alignments (phased haplotypes) of each immunity-related genes (fasta format).DNAsp_phased_input_fasta.zipAlignment of (unique) haplotypes for each immunity-related genesThis files contains the fasta alignment of (unique) haplotypes for each immunity-related gene.unique_haplotypes_fasta_alignement.zipGenotypic data for all individuals and immune lociThis file includes the genotypic data off all individuals for the 8 innate immune loci (21 SNPs genotyped using the KASPar technology) and the Mhc-Drb (sequences are available in genbank, accession numbers are in the supplementary material of the paper- Table S2)Roedeer_Immunogenetics_Genotypicdata_Quemereetal_final.txt