DOI: 10.5061/dryad.603hs
title: Data from: Contrasting patterns of selection and drift between two categories of immune genes in prairie-chickens

description: Immune-receptor genes of the adaptive immune system, such as the major
 histocompatibility complex (MHC), are involved in recognizing specific
 pathogens and are known to have high rates of adaptive evolution,
 presumably as a consequence of rapid coevolution between hosts and
 pathogens. In contrast, many ‘mediating’ genes of the immune system do not
 interact directly with specific pathogens and are involved in signaling
 (e.g., cytokines) or controlling immune cell growth. As a consequence, we
 might expect stronger selection at immune-receptor than mediating genes,
 but these two types of genes have not been compared directly in wild
 populations. Here, we tested the hypothesis that selection differs between
 MHC (class I and II) and mediating genes by comparing levels of population
 differentiation across the range of greater prairie-chickens (Tympanuchus
 cupido). As predicted, there was stronger population differentiation and
 isolation-by-distance at immune-receptor (MHC) than at either mediating
 genes or neutral microsatellites, suggesting a stronger role of local
 adaptation at the MHC. In contrast, mediating genes displayed weaker
 differentiation between populations than neutral microsatellites,
 consistent with selection favoring similar alleles across populations for
 mediating genes. In addition to selection, drift also had a stronger
 effect on immune-receptor (MHC) than mediating genes as indicated by the
 stronger decline of MHC variation in relation to population size. This is
 the first study in the wild to show that the effects of selection and
 drift on immune genes vary across populations depending on their
 functional role.
description: GPS coordinates for
 study populationstab delimited file with
 GPS coordinates of the six study populations. US State, County, GPS
 (Lat/Long) coordinates for each population.GPS coordinates for
 populations.txtMHC class IA exon 3
 sequencesTympanuchus cupido MHC
 class IA sequences. Aligned fasta file.T. cupido MHC class IA
 sequences alignment.fastaMHC class II (BLB) exon
 2 sequencesTympanuchus cupido MHC
 class II sequences. Aligned fasta file.T. cupido MHC class II
 sequences alignment.fastaData for Fig. 3. genetic
 and geographic distances between populationsData used in Fig. 3.
 Pairwise population Jost’s D values for each genetic marker (MHC,
 mediating and microsatellites) as well as geographic distances and
 differences in population size between population pairs. Tab-delimited
 file.T.
 cupido pairwise population
 comparisons.txtData for Fig1. Genetic
 variation and population sizetab delimited file with
 data used in Figure 1. Contains Population (state code), genetic marker,
 alleles per locus (mean-centered), population size, log of population
 size, squared log of population size, alleles per locus, mean alleles per
 locus (for each marker) and sample size for each
 population.Data for
 Fig1.txtMHC class I
 genotypesNumber of MHC class I
 reads from 454 pyrosequencing by individual and sequence. See MHC class IA
 exon 3 sequences.fasta for aligned sequences. Tab-delimited
 file.MHC class II
 genotypesNumber of MHC class II
 reads from 454 pyrosequencing by individual and sequence. See T. cupido
 MHC class II (BLB) exon 2 sequences.fasta for sequences. Tab-delimited
 file.Sequences from 454
 pyrosequencingFive zipped files
 containing the original sequences from 454 pyrosequencing (5 runs) of MHC
 class I and II in prairie-chickens. The ReadMe.csv file contains the
 unique 8 bp barcodes and individual identifiers used in each of the 5
 files. Each individual is indicated by its two-letter state code and
 number. Additional birds that were sequenced in the files, but not used in
 this study are indicated by "not used".