Data from: Host-parasite network structure is associated with community-level immunogenetic diversity

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.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.sf