New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines

BACKGROUND: The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune system and has been extensively studied across vertebrate taxa. Although the function of MHC genes appears to be conserved across taxa, there is great variation in the number and organisation of these genes. Among avian species, for instance, there are notable differences in MHC structure between passerine and non-passerine lineages: passerines typically have a high number of highly polymorphic MHC paralogs whereas non-passerines have fewer loci and lower levels of polymorphism. Although the occurrence of highly polymorphic MHC paralogs in passerines is well documented, their evolutionary origins are relatively unexplored. The majority of studies have focussed on the more derived passerine lineages and there is very little empirical information on the diversity of the MHC in basal passerine lineages. We undertook a study of MHC diversity and evolutionary relationships across seven species from four families (Climacteridae, Maluridae, Pardalotidae, Meliphagidae) that comprise a prominent component of the basal passerine lineages. We aimed to determine if highly polymorphic MHC paralogs have an early evolutionary origin within passerines or are a more derived feature of the infraorder Passerida. RESULTS: We identified 177 alleles of the MHC class II β exon 2 in seven basal passerine species, with variation in numbers of alleles across individuals and species. Overall, we found evidence of multiple gene loci, pseudoalleles, trans-species polymorphism and high allelic diversity in these basal lineages. Phylogenetic reconstruction of avian lineages based on MHC class II β exon 2 sequences strongly supported the monophyletic grouping of basal and derived passerine species. CONCLUSIONS: Our study provides evidence of a large number of highly polymorphic MHC paralogs in seven basal passerine species, with strong similarities to the MHC described in more derived passerine lineages rather than the simpler MHC in non-passerine lineages. These findings indicate an early evolutionary origin of highly polymorphic MHC paralogs in passerines and shed light on the evolutionary forces shaping the avian MHC. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-016-0681-5) contains supplementary material, which is available to authorized users

Evolution and ecology of major histocompatibility complex (MHC) genes in south-eastern Australian passerines

© 2015 Dr. Shandiya BalasubramaniamUnderstanding how variation in adaptive genes arises and is maintained is a central focus of evolutionary genetics. A growing number of studies are focussing on the structure, evolution and ecology of major histocompatibility complex (MHC) genes in a range of vertebrate taxa, including fish, amphibians, reptiles, birds and mammals. Comprising the most polymorphic genes in the vertebrate genome, the MHC presents an ideal system for understanding the mechanisms maintaining genetic variation in natural populations. The passerine MHC is typified by a large structure with complex organisation, yet little is known about the origin of this complexity. Most studies have focussed on species within the infraorder Passerida, which represents the bulk of passerine diversity, whereas there is very little information on the MHC in basal passerine lineages. In this study, I focussed on seven Australian passerine species (Brown Treecreeper Climacteris picumnus, Superb Fairy-wren Malurus cyaneus¸ Spotted Pardalote Pardalotus punctatus, Striated Pardalote P. striatus, White-plumed Honeyeater Lichenostomus penicillatus, Fuscous Honeyeater L. fuscus, Yellow-tufted Honeyeater L. melanops) from four families (Climacteridae, Maluridae, Pardalotidae, Meliphagidae) forming a prominent component of the basal passerine lineages. I estimated levels of MHC class II polymorphism and allelic diversity in these species and reconstructed phylogenetic relationships among basal and derived passerine species. I found high levels of allelic diversity and polymorphism in the seven species and evidence of a monophyletic grouping of basal and derived passerine species, suggesting an early evolutionary origin of a complex MHC structure in passerines. The high levels of polymorphism and allelic diversity characteristic of MHC genes are thought to be generated and maintained by a combination of different evolutionary processes. I characterised the MHC class II β exon 2 genes in two congeneric study species, the spotted and striated pardalote, and tested for signatures of recombination, gene conversion and balancing selection at the species level. I found evidence of multiple gene loci and putative pseudogenes, as well as evidence of MHC variation having been shaped by historical balancing selection, recombination and gene conversion in both species. MHC variation at the population level may be affected by both selective and neutral processes. I examined how habitat configuration and dispersal behaviour influence MHC class II β exon 2 variation in the brown treecreeper. Dispersal behaviour in the brown treecreeper is sex-biased and dispersal ability is strongly linked to the availability of connecting habitat. I performed pairwise comparisons of population genetic differentiation at MHC and microsatellite markers to determine if the relative influence of selective and neutral processes varied between a) the dispersive (female) and philopatric (male) sexes, and b) habitats with dispersed and aggregated configurations of tree cover. MHC alleles were also clustered into functional supertypes to test for signatures of balancing selection across populations. I found differences in extent of genetic differentiation based on sex and habitat type, reflecting males’ philopatric behaviour and females’ reliance on suitable habitat for dispersal. Most MHC supertypes were maintained across populations, indicating the effects of balancing selection. The MHC plays a crucial role in the vertebrate immune response to pathogens and parasites. Understanding the evolutionary implications of host-parasite interactions first requires an understanding of the key pathogens and parasites affecting passerine species. Avian haematozoa are ideal models for studying host-parasite interactions because they infect a large number of host species and are widely distributed. I assessed the prevalence and diversity of avian haematozoa in three host species, the brown treecreeper, spotted pardalote and striated pardalote using microscopy and molecular techniques. I identified four lineages of Haemoproteus infection in total, of which three are previously unreported, as well as present the first record of haematozoan infection in these species of passerine. This study highlights the complexity of the MHC in basal passerine species and demonstrates the influence of multiple evolutionary processes in shaping MHC variation at the species and population level. The research presented in this thesis adds to a growing body of knowledge on the MHC in non-model vertebrate species and provides a number of avenues for further research into the evolution of the passerine MHC

MHCIIB exon 2 sequence data (Corvida) supporting the following publication: New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines

MHCIIB exon 2 sequence data from seven passerine species, obtained through 454 and Sanger sequencing<br

MHCIIB exon 2 sequence data (Pardalotidae) supporting the following publication: MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion

159bp fragments of the MHC class II β exon 2 region in two pardalote species, the spotted (<i>Pardalotus punctatus</i>) and striated pardalote (<i>P. striatus</i>

MHCIIB exon 2 sequences supporting the publication: Associations among habitat configuration, sex-biased dispersal and MHC class II β genetic variation in the brown treecreeper (Climacteris picumnus)

198 MHCIIB exon 2 sequences from the brown treecreeper, Climacteris picumnus, sequenced using 454 sequencing technique

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Additional file 1: of New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines

MHC class II β exon 2 alleles identified through cloning and 454 sequencing methods. Sample size, range and total number of alleles per species, and putative number of loci per species are given. (XLSX 8 kb