ArticleBMC evolutionary biology2010
454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher.
Article in BMC evolutionary biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed, 125 citations in OpenAlex.
- Palaeognaths Reveal Evolutionary Ancestry of the Avian Major Histocompatibility Complex Class II.Genome biology and evolution · 2024Article
- A new method for ecologists to estimate heterozygote excess and deficit for multi-locus gene families.Ecology and evolution · 2024Article
- Partial molecular characterization, expression pattern and polymorphism analysis of MHC I genes in Chinese domestic goose (Anser cygnoides).Genetics and molecular biology · 2024Article
- Article
- Extensive MHC class IIβ diversity across multiple loci in the small-spotted catshark (Scyliorhinus canicula).Scientific reports · 2023Article
- MHCtools - an R package for MHC high-throughput sequencing data: Genotyping, haplotype and supertype inference, and downstream genetic analyses in non-model organisms.Molecular ecology resources · 2022Article
- Intra-specific copy number variation of MHC class II genes in the Siamese fighting fish.Immunogenetics · 2022Article
- Diversity of MHC IIB genes and parasitism in hybrids of evolutionarily divergent cyprinoid species indicate heterosis advantage.Scientific reports · 2021Article
- Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad.Ecology and evolution · 2021Article
- MHC Genotyping by SSCP and Amplicon-Based NGS Approach in Chamois.Animals : an open access journal from MDPI · 2020Article
- Allelic diversity and patterns of selection at the major histocompatibility complex class I and II loci in a threatened shorebird, the Snowy Plover (Charadrius nivosus).BMC evolutionary biology · 2020Article
- Not all birds have a single dominantly expressed MHC-I gene: Transcription suggests that siskins have many highly expressed MHC-I genes.Scientific reports · 2019Article
- Review
- Article
- Evolution of Copy Number at the MHC Varies across the Avian Tree of Life.Genome biology and evolution · 2019Article
- Article
- Lack of evidence for selection favouring MHC haplotypes that combine high functional diversity.Heredity · 2018Article
- Genotyping strategy matters when analyzing hypervariable major histocompatibility complex-Experience from a passerine bird.Ecology and evolution · 2018Article
- Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.BMC evolutionary biology · 2017Article
- A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non-model species.BMC research notes · 2017Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBecause of their functional significance, the Major Histocompatibility Complex (MHC) class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping.
resultsHere we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family.
conclusions454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective, genotyping of MHC systems of virtually any complexity.
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