DOI: 10.5061/dryad.2q8c2
title: Data from: The evolution of highly variable immunity genes across a passerine bird radiation.

description: To survive, individuals must be able to recognize and eliminate pathogens.
 The genes of the major histocompatibility complex (MHC) play an essential
 role in this process in vertebrates as their diversity affects the
 repertoire of pathogens that can be recognized by the immune system.
 Emerging evidence suggests that birds within the parvorder Passerida
 possess an exceptionally high number of MHC genes. However, this has yet
 to be directly investigated using a consistent framework, and the question
 of how this MHC diversity has evolved has not been addressed. We used
 next-generation sequencing to investigate how MHC class I gene copy number
 and sequence diversity varies across the Passerida radiation using twelve
 species chosen to represent the phylogenetic range of this group.
 Additionally, we performed phylogenetic analyses on this data to identify,
 for the first time, the evolutionary model that best describes how MHC
 class I gene diversity has evolved within Passerida. We found evidence of
 multiple MHC class I genes in every family tested, with an extremely broad
 range in gene copy number across Passerida. There was a strong
 phylogenetic signal in MHC gene copy number and diversity, and these
 traits appear to have evolved through a process of Brownian motion in the
 species studied, that is following the pattern of genetic drift or
 fluctuating selection, as opposed to towards a single optimal value or
 through evolutionary ‘bursts’. By characterizing MHC class I gene
 diversity across Passerida in a systematic framework, this study provides
 a first step towards understanding this huge variation.
description: Evolutionary Models
 ScriptR script containing the
 code used to run the evolutionary models and test for phylogentic
 signalHNalla_RV_454_Raw_20120507_1525_1_2Raw (unfiltered) 454 sequence data for Primer Pair 1. Demultiplexed using the software jMHC (2011).Short_RV_454_Raw_20120507_1115_1_2Raw (unfiltered) 454 sequence data for Primer Pair 3. Demultiplexed using the software jMHC (2011).HNalla46_Raw_Data_20151119_1740_1Raw (unfiltered) 454 sequence data for Primer Pair 2. Demultiplexed using the software jMHC (2011).Phylogenetic tree of speciesMaximum clade credibility tree summarising the phylogenetic relationships between the bird species studied (rooted using Gallus gallus).Phylogenetic Tree of SppSamples InfoDetails of of the samples included in the study. The column "Sample Name" specifies the unique name of each sample. The column "Species" indicates which species each sample is from. The column "Location" provides information on the location the sample was collected at.All Spp Final Aligned VariantsAlignment of all 536 alleles identified. Alignment performed manually using BioEdit V.7.2.5 Sequence Alignment Editor (Hall 1999). In FASTA format.All Spp Aligned Variants.fasKey to final allele namesThis file provides a key to the allele names that links the names they have been allocated in the manuscript to the original names of the raw sequences (these numbers match the sequence numbers in the raw sequence files provided). "Species" denotes the species in which the allele was found. "Old Seq Name" refers to the names in the raw sequence files (sequence number). "New Name" refers to the allele name used in the manuscript. "Seq" is the aligned sequence. The alleles which were detected by more than one primer pair are identifiable as their "Old Seq Name" is comprised of more than one sequence number adjoined by a colon.Key to allele names.txtAll Final VariantsAll variants found (unaligned) in FASTA format.All Variants.txt