The evolution of highly variable immunity genes across a passerine bird radiation

Abstract

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.

Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer)

“…Four different primer combinations were used to amplify MHC-I exon 3 alleles in each species to minimize the effects of amplification bias and allelic dropouts which is often a problem when using only one primer pair (Additional file 1: Table S1, Figure S1). Primer combinations 1 and 2 amplify both putatively classical and non-classical alleles whereas primer combination 3 and 4 exclusively amplifies putatively classical and non-classical alleles, respectively [8, 35, 42]. Each individual was represented by one gDNA and one cDNA sample and samples were technically duplicated (two PCRs from 40% of the samples).…”

“…The use of multiple primer combinations enabled a detailed characterization of the total number of classical and non-classical MHC-I alleles per individual since the possibility of amplifying all alleles in an individual increases when different primer combinations are used [8, 42]. The number of alleles per individual was determined by combining the result from all four primer combinations.…”

“…Typically, animals have a handful of functional MHC-I genes, as exemplified by humans (six genes), swine ( Sus scrofa domesticus ; six genes) and domestic chicken ( Gallus gallus ; four genes) [3–5]. On the contrary, songbirds of the order Passeriformes have a larger number of MHC-I genes than most other species investigated to date [6–8]. O’Connor et al (2015) reported between four and 20 MHC-I genes per individual across Passerida (i.e.…”

“…genomic MHC-I exon 3 sequences in open reading frame), and Biedrzycka et al (2017) found 65 alleles per individual, i.e. at least 33 MHC-I genes, in the sedge warbler Acrocephalus schoenobaenus [8, 9]. The functional significance of all these MHC-I gene copies in songbirds is not known.…”

“…The large number of MHC-I genes in the genomes of songbirds indicates either a higher rate of gene duplications in songbirds compared to other animals, or that several copies of their MHC genes have been duplicated simultaneously [6–8]. Very little is known about neo-functionalization among the multiple gene copies in songbirds, though it seems likely that some gene copies have evolved different functions, like the classical and non-classical genes found in other species [27–30].…”