10.5061/DRYAD.7M0CFXPTH
Quéméré, Erwan
0000-0002-3880-1933
National Research Institute for Agriculture, Food and Environment
Hessenauer, Pauline
Université Laval
Galan, Maxime
National Research Institute for Agriculture, Food and Environment
Fernandez, Marie
University of Toulouse II - Le Mirail
Merlet, Joël
University of Toulouse II - Le Mirail
Chaval, Yannick
0000-0002-7603-4691
University of Toulouse II - Le Mirail
Morellet, Nicolas
University of Toulouse II - Le Mirail
Verheyden, Hélène
University of Toulouse II - Le Mirail
Gilot-Fromont, Emmanuelle
University of Lyon System
Charbonnel, Nathalie
0000-0002-3880-1933
National Research Institute for Agriculture, Food and Environment
Pathogen-mediated selection favours the maintenance of innate immunity
gene polymorphism in a widespread wild ungulate
Dryad
dataset
2021
FOS: Biological sciences
2021-05-31T00:00:00Z
2021-05-31T00:00:00Z
en
https://doi.org/10.1101/458216
57015 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Toll-like Receptors (TLR) play a central role in recognition and host
frontline defence against a wide range of pathogens. A number of recent
studies have shown that TLR genes (Tlrs) often exhibit large polymorphism
in natural populations. Yet, there is little knowledge on how this
polymorphism is maintained and how it influences disease susceptibility in
the wild. In previous work, we showed that some Tlrs exhibit similarly
high levels of genetic diversity as genes of the Major Histocompatibility
Complex (MHC), and signatures of contemporary balancing selection in roe
deer (Capreolus capreolus), the most abundant cervid species in Europe.
Here, we investigated the evolutionary mechanisms by which
pathogen-mediated selection could shape this innate immunity genetic
diversity by examining the relationships between Tlr (Tlr2, Tlr4 and Tlr5)
genotypes (heterozygosity status and presence of specific alleles) and
infections with Toxoplasma and Chlamydia, two widespread intracellular
pathogens known to cause reproductive failure in ungulates. We showed that
Toxoplasma and Chlamydia exposures vary significantly across year and
landscape structure with few co-infection events detected, and that the
two pathogens exert antagonistic selection on Tlr2 polymorphism. By
contrast, we found limited support for Tlr heterozygote advantage. Our
study confirmed the importance of looking beyond Mhc genes in wildlife
immunogenetic studies. It also emphasized the necessity to consider
multiple pathogen challenges and their spatiotemporal variation to improve
our understanding of vertebrate defence evolution against pathogens.
- 433 annual captures corresponding to 328 different individuals (190
females and 138 males, 164 juveniles and 164 adults, 1 to 5 captures per
individual) - The Tlr (Tlr2, Tlr4 and Tlr5) genes of 157 roe deer from the
area (VCG) had been genotyped in a previous immunogenetic study (Quéméré
et al., 2015 Molecular Ecology). We completed this dataset by genotyping
171 new individuals using exactly the same procedure. DNA was extracted
from alcohol-preserved tissues using the DNeasy Blood and Tissue kit
(QIAGEN). Tlr genes were genotyped using a two-step approach: a pilot
study on 32 individuals was first performed to identify polymorphic sites
(SNPs) by screening almost the entire coding region of the three Tlr genes
(82% in average) including the leucine-rich extracellular region of
receptors involved in antigen-binding (between 2081 and 2436 bps sequenced
per gene). A total of 38 SNPs (6-16 SNPs per locus) were uncovered at this
step. Details about primer sequences, SNP positions and codon changes are
provided in Quéméré et al. (2015). Then we applied the exact test of
linkage disequilibrium (LD) implemented in ARLEQUIN 3.5 (Excoffier
& Lischer, 2010). Based on LD scores and P‐values (after
Bonferonni correction), we identified linkage disequilibrium (LD) groups.
For each group, we selected one SNP (primarily targeting non-synonymous
sites) that was genotyped for all individuals using the KASPar
allele-specific genotyping system provided by KBiosciences (Hoddesdon,
UK). A total of 13 SNPs (out of 38) were typed including 5, 3 and 5 SNPs
for Tlr2, Tlr4 and Tlr5 respectively. Lastly, haplotypes were
reconstructed from the phased SNPs using the procedure implemented in
DNASP v5 (Librado & Rozas, 2009). All sequences have been
submitted to NCBI Genbank (Accession nos. are in Table S2 fot the ms,
Supporting information). - The serological status of roe deer for
Toxoplasma gondii and/or Chlamydia abortus was analysed using classical
enzyme-linked immunosorbent assays (ELISA) with specific commercial kits
(Sevila et al., 2014). The specificity and sensitivity of these kits were
respectively 97.4 and 99.4 % for T. gondii and 92.2 and 89 % for C.
abortus. Although the kits were developed for domestic ruminants, they
were shown to be reliable and efficient in wild ungulates with a high
concordance (0.8) between ELISA and the Modified Agglutination Test, a
reference test for Toxoplasma in roe deer (Gotteland et al., 2014).
According to the manufacturer’s instructions, blood samples with antibody
recognition level (ARL) > 30% and >40% were considered
positive for T. gondii and C. abortus respectively (see Sevila et al.,
2014 for further details). In total, we obtained the Toxoplasma and
Chlamydia serological status of 277 (with 74 repeated measures) and 196
(36 repeated measures) roe deer respectively (caught between 2008 and
2016).