DOI: 10.5061/dryad.mq7n0
title: Data from: Host-parasite network structure is associated with community-level immunogenetic diversity

description: Genes of the major histocompatibility complex (MHC) encode proteins that
 recognize foreign antigens and are thus crucial for immune response. In a
 population of a single host species, parasite-mediated selection drives
 MHC allelic diversity. However, in a community-wide context, species
 interactions may modulate selection regimes because the prevalence of a
 given parasite in a given host may depend on its prevalence in other
 hosts. By combining network analysis with immunogenetics, we show that
 host species infected by similar parasites harbour similar alleles with
 similar frequencies. We further show, using a Bayesian approach, that the
 probability of mutual occurrence of a functional allele and a parasite in
 a given host individual is nonrandom and depends on other host–parasite
 interactions, driving co-evolution within subgroups of parasite species
 and functional alleles. Therefore, indirect effects among hosts and
 parasites can shape host MHC diversity, scaling it from the population to
 the community level.
description: Rodent DRB Alleles from
 AsiaDataset of MHC class II
 DRB exon 2 allele sequences from rodents sampling in Thailand, Laos and
 Cambodia. The name of alleles include the species ID: Bain for Bandicota
 indica ; Basa for Bandicota savilei ; Bebe for Berylmys berdmorei ; Bebo
 for Berylmys bowersi ; Leed for Leopoldamys edwardsi ; Muca for Mus caroli
 ; Muce for Mus cervicolor ; Muco for Mus cookii ; Raex for Rattus exulans
 ; Rasa for Rattus sakaratensis ; Rata for Rattus tanezumi ; RaR3 for
 Rattus tanezumi mitochondrial lineage R3454 raw sequences of the
 MHC class II DRB exon 2 gene from rodents - Run 1This FASTA file contains
 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run).
 The 864 multiplexed amplicons were tagged using both forward and reverse
 primers. The list of the 864 multiplexed samples and associated tags are
 provided in the following file:
 454_Reads_DRB_Asia_Run1.csv.454_Reads_DRB_Asia_Run1.fasta454 quality scores of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 1This file contains the quality scores for the 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run1.csv.454_Reads_DRB_Asia_Run1.qual.txt454 reads of the MHC class II DRB exon 2 gene from rodents including a correction for the reverse tags - Run 1This FASTA file contains 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The reverse tags forming a homopolymer GG with the "454-Adaptor" sequence were truncated. This file contains the raw sequences corrected (addition of a G at the end of the reads) for the concerned tags. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run1.csv.454_Reads_DRB_Asia_Run1_G_add_in_Rev_Tags.fastaInformation concerning the samples multiplexed in the 454 Run 1This SESAME software formatted file contains the sample names, the forward and reverse tag sequences, the forward and reverse primer sequences, the gene name, the species name, the population name and the ploidy level for each of the 864 samples multiplexed in the 454 pyrosequencing run 1.454_Reads_DRB_Asia_Run1.csv454 raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2This FASTA file contains 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run2.csv.454_Reads_DRB_Asia_Run2.fasta454 quality scores of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2This file contains the quality scores for the 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run2.csv.454_Reads_DRB_Asia_Run2.qualInformation concerning the samples multiplexed in the 454 Run 2This SESAME software formatted file contains the sample names, the forward and reverse tag sequences, the forward and reverse primer sequences, the gene name, the species name, the population name and the ploidy level for each of the 864 samples multiplexed in the 454 pyrosequencing run 2.454_Reads_DRB_Asia_Run2.csv454 standard flowgram format (SFF) file of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2This SFF file contains the encoded results of each flowgram for the 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. Note: The SFF file for the run 1 is not available (not provide by the sequencing company).454_Reads_DRB_Asia_Run2.sff