DOI: 10.5061/dryad.d2547d810
title: Adult survival in migratory caribou is negatively associated with MHC functional diversity

description: The genes of the major histocompatibility complex (MHC) are involved in
 acquired, specific immunity in vertebrates. Yet, only a few studies have
 investigated the fitness consequences of MHC gene diversity in wild
 populations. Here, we looked at the association between annual survival
 and body mass and MHC-DRB exon 2 (MHC-DRB) genetic diversity, obtained
 from high-throughput sequencing, in two declining migratory caribou
 (Rangifer tarandus) herds. To disentangle the potential direct and general
 effects of MHC-DRB genetic diversity, we compared different indices of
 diversity that were either based on DNA-sequence variation or on
 physicochemical divergence of the translated peptides, covering a gradient
 of allelic to functional diversity. We found that i) body mass was not
 related to MHC-DRB diversity or genotype and that ii) adult survival
 probability was negatively associated with PAM distance, a corrected
 distance that considers the likelihood of each amino acid substitution to
 be accepted by the processes of natural selection. In addition, we found
 no evidence of fluctuating selection in time on MHC-DRB. We concluded that
 direct effects were involved in the negative relationship between MHC
 functional diversity and survival, although the mechanism underlying this
 result remains unclear. A possible explanation could be that individuals
 with higher MHC diversity suffer higher costs of immunity
 (immunopathology). Further studies are needed to investigate this
 hypothesis. Our results suggest that genetic diversity is not always
 beneficial even in genes that are supposed to be strongly shaped by
 balancing selection.
description: We sampled individuals from the two herds of migratory caribou in
 Northern Québec and Labrador (Canada): Rivière-George herd (RG) and
 Rivière-aux-Feuilles herd (RAF) between 1996 and 2016. Tissue samples were
 collected (biopsies, hair or blood) and DNA was isolated. We used Illumina
 MiSeq technology to sequence a 250 bp fragment of the exon 2 of MHC-DRB
 gene (complete exon has 267 bp in caribou; Kennedy <i>et
 al.</i>, 2010). We amplified this locus with the LA31 and LA32
 primer pair designed by Sigurdardóttir <i>et al. </i>(1991).
 Complete methods of MHC genotyping and assessing MHC diversity are
 presented in the associated manuscript or on demande to the authors.
 Genome-wide diversity was also assessed using a ddRadSeq protocol.
 Complete methods of SNPs genotyping and genome-wide diversity computing
 are presented in Gagnon et al. (2019) or on demand to the
 authors. References : 
 Gagnon M, Yannic G, Perrier C, Côté SD (2019). No
 evidence of inbreeding depression in fast declining herds of migratory
 caribou. <i>J Evol Biol</i> <b>32</b>:
 1368–1381. Kennedy LJ, Modrell
 A, Groves P, Wei Z, Single RM, Happ GM (2010). Genetic diversity of the
 major histocompatibility complex class II in Alaskan caribou herds.
 <i>Int J Immunogenet</i> <b>38</b>:
 109–119. Sigurdardóttir S,
 Borsch C, Gustafsson K, Andersson L (1991). Cloning and sequence analysis
 of 14 DRB alleles of the bovine major histocompatibility complex by using
 the polymerase chain reaction. <i>Anim Genet</i>
 <b>22</b>: 199–209.
  
description: Body mass and survival data could be provided on demand . Please
 read the "READ_ME.txt" file.