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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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2
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Stervander M, Dierickx EG, Thorley J, Brooke MDL, Westerdahl H. High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice. Mol Ecol 2020; 29:3578-3592. [PMID: 32416000 DOI: 10.1111/mec.15471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/14/2020] [Accepted: 05/04/2020] [Indexed: 12/30/2022]
Abstract
Small population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity and its effects on mate choice and survival in the Critically Endangered Raso lark Alauda razae, a species restricted to the 7 km2 islet of Raso, Cape Verde, since ~1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC-I genotype/diversity on mate choice or survival. However, we demonstrate that MHC-I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by cosegregation of multiple haplotypes comprising 2-8 linked MHC-I loci. Within-locus homozygosity is high, contributing to low population-wide diversity. Conversely, each individual had comparably many alleles, 6-16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within-individual MHC-I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species' adaptive potential.
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Affiliation(s)
- Martin Stervander
- Department of Biology, Lund University, Lund, Sweden.,Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Elisa G Dierickx
- Department of Zoology, University of Cambridge, Cambridge, UK.,Fauna & Flora International, Cambridge, UK
| | - Jack Thorley
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - M de L Brooke
- Department of Zoology, University of Cambridge, Cambridge, UK
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3
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Not all birds have a single dominantly expressed MHC-I gene: Transcription suggests that siskins have many highly expressed MHC-I genes. Sci Rep 2019; 9:19506. [PMID: 31862923 PMCID: PMC6925233 DOI: 10.1038/s41598-019-55800-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/18/2019] [Indexed: 01/03/2023] Open
Abstract
Passerine birds belong to the most species rich bird order and are found in a wide range of habitats. The extremely polymorphic adaptive immune system of passerines, identified through their major histocompatibility complex class I genes (MHC-I), may explain some of this extreme radiation. Recent work has shown that passerines have higher numbers of MHC-I gene copies than other birds, but little is currently known about expression and function of these gene copies. Non-passerine birds have a single highly expressed MHC-I gene copy, a pattern that seems unlikely in passerines. We used high-throughput sequencing to study MHC-I alleles in siskins (Spinus spinus) and determined gene expression, phylogenetic relationships and sequence divergence. We verified between six and 16 MHC-I alleles per individual and 97% of these were expressed. Strikingly, up to five alleles per individual had high expression. Out of 88 alleles 18 were putatively non-classical with low sequence divergence and expression, and found in a single phylogenetic cluster. The remaining 70 alleles were classical, with high sequence divergence and variable degrees of expression. Our results contradict the suggestion that birds only have a single dominantly expressed MHC-I gene by demonstrating several highly expressed MHC-I gene copies in a passerine.
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4
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Razali H, O'Connor E, Drews A, Burke T, Westerdahl H. 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 Res Notes 2017; 10:346. [PMID: 28754172 PMCID: PMC5534077 DOI: 10.1186/s13104-017-2654-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 07/21/2017] [Indexed: 11/24/2022] Open
Abstract
Background High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms. However, illumina MiSeq amplicon sequencing (MiSeq), which offers a much higher read depth, is now superseding 454. The aim of this study was to quantitatively and qualitatively evaluate the performance of MiSeq in relation to 454 for genotyping MHC class I alleles using a house sparrow (Passer domesticus) dataset with pedigree information. House sparrows provide a good study system for this comparison as their MHC class I genes have been studied previously and, consequently, we had prior expectations concerning the number of alleles per individual. Results We found that 454 and MiSeq performed equally well in genotyping amplicons with low diversity, i.e. amplicons from individuals that had fewer than 6 alleles. Although there was a higher rate of failure in the 454 dataset in resolving amplicons with higher diversity (6–9 alleles), the same genotypes were identified by both 454 and MiSeq in 98% of cases. Conclusions We conclude that low diversity amplicons are equally well genotyped using either 454 or MiSeq, but the higher coverage afforded by MiSeq can lead to this approach outperforming 454 in amplicons with higher diversity. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2654-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haslina Razali
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Emily O'Connor
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden.
| | - Anna Drews
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
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5
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Pardal S, Drews A, Alves JA, Ramos JA, Westerdahl H. Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit. Immunogenetics 2017; 69:463-478. [PMID: 28534224 PMCID: PMC5486808 DOI: 10.1007/s00251-017-0993-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/22/2017] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) encodes proteins that are central for antigen presentation and pathogen elimination. MHC class I (MHC-I) genes have attracted a great deal of interest among researchers in ecology and evolution and have been partly characterized in a wide range of bird species. So far, the main focus has been on species within the bird orders Galliformes and Passeriformes, while Charadriiformes remain vastly underrepresented with only two species studied to date. These two Charadriiformes species exhibit striking differences in MHC-I characteristics and MHC-I diversity. We therefore set out to study a third species within Charadriiformes, the Icelandic subspecies of black-tailed godwits (Limosa limosa islandica). This subspecies is normally confined to parasite-poor environments, and we hence expected low MHC diversity. MHC-I was partially characterized first using Sanger sequencing and then using high-throughput sequencing (MiSeq) in 84 individuals. We verified 47 nucleotide alleles in open reading frame with classical MHC-I characteristics, and each individual godwit had two to seven putatively classical MHC alleles. However, in contrast to previous MHC-I data within Charadriiformes, we did not find any evidence of alleles with low sequence diversity, believed to represent non-classical MHC genes. The diversity and divergence of the godwits MHC-I genes to a large extent fell between the previous estimates within Charadriiformes. However, the MHC genes of the migratory godwits had few sites subject to positive selection, and one possible explanation could be a low exposure to pathogens.
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Affiliation(s)
- Sara Pardal
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal.
| | - Anna Drews
- MEEL - Molecular Ecology and Evolution Laboratory, Lund University, Ecology building, SE-223 62, Lund, Sweden.
| | - José A Alves
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,South Iceland Research Centre, University of Iceland, Fjolheimer, IS-800, Selfoss, Iceland
| | - Jaime A Ramos
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Helena Westerdahl
- MEEL - Molecular Ecology and Evolution Laboratory, Lund University, Ecology building, SE-223 62, Lund, Sweden
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6
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Population genetic diversity and geographical differentiation of MHC class II DAB genes in the vulnerable Chinese egret (Egretta eulophotes). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0876-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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7
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O'Connor EA, Strandh M, Hasselquist D, Nilsson JÅ, Westerdahl H. The evolution of highly variable immunity genes across a passerine bird radiation. Mol Ecol 2016; 25:977-89. [DOI: 10.1111/mec.13530] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/24/2015] [Accepted: 12/09/2015] [Indexed: 11/29/2022]
Affiliation(s)
- E. A. O'Connor
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
| | - M. Strandh
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
| | - D. Hasselquist
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
| | - J.-Å. Nilsson
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
| | - H. Westerdahl
- Molecular Ecology and Evolution Lab; Lund University; Ecology building 223 62 Lund Sweden
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8
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Jaratlerdsiri W, Deakin J, Godinez RM, Shan X, Peterson DG, Marthey S, Lyons E, McCarthy FM, Isberg SR, Higgins DP, Chong AY, John JS, Glenn TC, Ray DA, Gongora J. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PLoS One 2014; 9:e114631. [PMID: 25503521 PMCID: PMC4263668 DOI: 10.1371/journal.pone.0114631] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/11/2014] [Indexed: 12/22/2022] Open
Abstract
The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.
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Affiliation(s)
- Weerachai Jaratlerdsiri
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Janine Deakin
- Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2601, Australia
| | - Ricardo M. Godinez
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, United States of America
- Department of Genetics, Harvard Medical School, 77 Louis Pasteur Ave., Boston, Massachusetts 02115, United States of America
| | - Xueyan Shan
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America
| | - Daniel G. Peterson
- Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America
| | - Sylvain Marthey
- Animal Genetics and Integrative Biology, INRA, UMR 1313 Jouy-en-Josas 78352, France
| | - Eric Lyons
- School of Plant Science, University of Arizona, Tucson, Arizona 85721, United States of America
| | - Fiona M. McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States of America
| | - Sally R. Isberg
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
- Center for Crocodile Research, P.O. Box 329, Noonamah, Northern Territory 0837, Australia
| | - Damien P. Higgins
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Amanda Y. Chong
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
| | - John St John
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, United States of America
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602, United States of America
| | - David A. Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America
- Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America
| | - Jaime Gongora
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
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9
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Jones MR, Cheviron ZA, Carling MD. Variation in positively selected major histocompatibility complex class I loci in rufous-collared sparrows (Zonotrichia capensis). Immunogenetics 2014; 66:693-704. [DOI: 10.1007/s00251-014-0800-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/25/2014] [Indexed: 11/25/2022]
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10
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Lillie M, Shine R, Belov K. Characterisation of major histocompatibility complex class I in the Australian cane toad, Rhinella marina. PLoS One 2014; 9:e102824. [PMID: 25093458 PMCID: PMC4122387 DOI: 10.1371/journal.pone.0102824] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/20/2014] [Indexed: 11/19/2022] Open
Abstract
The Major Histocompatibility Complex (MHC) class I is a highly variable gene family that encodes cell-surface receptors vital for recognition of intracellular pathogens and initiation of immune responses. The MHC class I has yet to be characterised in bufonid toads (Order: Anura; Suborder: Neobatrachia; Family: Bufonidae), a large and diverse family of anurans. Here we describe the characterisation of a classical MHC class I gene in the Australian cane toad, Rhinella marina. From 25 individuals sampled from the Australian population, we found only 3 alleles at this classical class I locus. We also found large number of class I alpha 1 alleles, implying an expansion of class I loci in this species. The low classical class I genetic diversity is likely the result of repeated bottleneck events, which arose as a result of the cane toad's complex history of introductions as a biocontrol agent and its subsequent invasion across Australia.
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Affiliation(s)
- Mette Lillie
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Richard Shine
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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11
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Wang Y, Qiu M, Yang J, Zhao X, Wang Y, Zhu Q, Liu Y. Sequence variations of the MHC class I gene exon 2 and exon 3 between infected and uninfected chickens challenged with Marek's disease virus. INFECTION GENETICS AND EVOLUTION 2013; 21:103-9. [PMID: 24200589 DOI: 10.1016/j.meegid.2013.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 11/17/2022]
Abstract
The major histocompatibility complex (MHC) among chickens has been well established as being associated with disease resistance and pathogens infection, but the genetic differences in MHC between chickens susceptible to certain infections and those chickens that remain uninfected have not been sufficiently determined. In this study, we sought the genetic basis that may underlie differences in susceptibility to infection among chickens by challenging four groups of broilers with Marek's disease virus (MDV). Over the course of the experiment, lesions began to appear between 21 and 35 days post challenge (dpc), and commercial broilers were not necessarily better than indigenous chickens in terms of disease resistance. The four groups showed neutral resistance to MDV infection validated by challenge results and evolutionary analysis of exons 2 and 3 of the MHC class I region. Several variable sites in exon 2 and exon 3 were exclusively appeared in infected chickens. Exon 3 was likely more crucial than exon 2 in disease resistance. Our observations offered a support for a potential association between promiscuous pathogens and conspicuous genetic diversity in the MHC class I region.
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Affiliation(s)
- Ye Wang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China
| | - Mohan Qiu
- Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Jiandong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xiaoling Zhao
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China
| | - Yan Wang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China
| | - Qing Zhu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China
| | - Yiping Liu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China.
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12
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Westerdahl H, Stjernman M, Råberg L, Lannefors M, Nilsson JÅ. MHC-I affects infection intensity but not infection status with a frequent avian malaria parasite in blue tits. PLoS One 2013; 8:e72647. [PMID: 24023631 PMCID: PMC3758318 DOI: 10.1371/journal.pone.0072647] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/12/2013] [Indexed: 12/23/2022] Open
Abstract
Host resistance against parasites depends on three aspects: the ability to prevent, control and clear infections. In vertebrates the immune system consists of innate and adaptive immunity. Innate immunity is particularly important for preventing infection and eradicating established infections at an early stage while adaptive immunity is slow, but powerful, and essential for controlling infection intensities and eventually clearing infections. Major Histocompatibility Complex (MHC) molecules are central in adaptive immunity, and studies on parasite resistance and MHC in wild animals have found effects on both infection intensity (parasite load) and infection status (infected or not). It seems MHC can affect both the ability to control infection intensities and the ability to clear infections. However, these two aspects have rarely been considered simultaneously, and their relative importance in natural populations is therefore unclear. Here we investigate if MHC class I genotype affects infection intensity and infection status with a frequent avian malaria infection Haemoproteus majoris in a natural population of blue tits Cyanistes caeruleus. We found a significant negative association between a single MHC allele and infection intensity but no association with infection status. Blue tits that carry a specific MHC allele seem able to suppress H. majoris infection intensity, while we have no evidence that this allele also has an effect on clearance of the H. majoris infection, a result that is in contrast with some previous studies of MHC and avian malaria. A likely explanation could be that the clearance rate of avian malaria parasites differs between avian malaria lineages and/or between avian hosts.
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Affiliation(s)
| | | | - Lars Råberg
- Department of Biology, Lund University, Lund, Sweden
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13
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Characteristics of MHC class I genes in house sparrows Passer domesticus as revealed by long cDNA transcripts and amplicon sequencing. J Mol Evol 2013; 77:8-21. [PMID: 23877344 DOI: 10.1007/s00239-013-9575-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
In birds the major histocompatibility complex (MHC) organization differs both among and within orders; chickens Gallus gallus of the order Galliformes have a simple arrangement, while many songbirds of the order Passeriformes have a more complex arrangement with larger numbers of MHC class I and II genes. Chicken MHC genes are found at two independent loci, classical MHC-B and non-classical MHC-Y, whereas non-classical MHC genes are yet to be verified in passerines. Here we characterize MHC class I transcripts (α1 to α3 domain) and perform amplicon sequencing using a next-generation sequencing technique on exon 3 from house sparrow Passer domesticus (a passerine) families. Then we use phylogenetic, selection, and segregation analyses to gain a better understanding of the MHC class I organization. Trees based on the α1 and α2 domain revealed a distinct cluster with short terminal branches for transcripts with a 6-bp deletion. Interestingly, this cluster was not seen in the tree based on the α3 domain. 21 exon 3 sequences were verified in a single individual and the average numbers within an individual were nine and five for sequences with and without a 6-bp deletion, respectively. All individuals had exon 3 sequences with and without a 6-bp deletion. The sequences with a 6-bp deletion have many characteristics in common with non-classical MHC, e.g., highly conserved amino acid positions were substituted compared with the other alleles, low nucleotide diversity and just a single site was subject to positive selection. However, these alleles also have characteristics that suggest they could be classical, e.g., complete linkage and absence of a distinct cluster in a tree based on the α3 domain. Thus, we cannot determine for certain whether or not the alleles with a 6-bp deletion are non-classical based on our present data. Further analyses on segregation patterns of these alleles in combination with dating the 6-bp deletion through MHC characterization across the genus Passer may solve this matter in the future.
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14
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Aguilar JRD, Schut E, Merino S, Martínez J, Komdeur J, Westerdahl H. MHC class II B diversity in blue tits: a preliminary study. Ecol Evol 2013; 3:1878-89. [PMID: 23919136 PMCID: PMC3728931 DOI: 10.1002/ece3.598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/17/2013] [Indexed: 12/18/2022] Open
Abstract
In this study, we partly characterize major histocompatibility complex (MHC) class II B in the blue tit (Cyanistes caeruleus). A total of 22 individuals from three different European locations: Spain, The Netherlands, and Sweden were screened for MHC allelic diversity. The MHC genes were investigated using both PCR-based methods and unamplified genomic DNA with restriction fragment length polymorphism (RFLP) and southern blots. A total of 13 different exon 2 sequences were obtained independently from DNA and/or RNA, thus confirming gene transcription and likely functionality of the genes. Nine out of 13 alleles were found in more than one country, and two alleles appeared in all countries. Positive selection was detected in the region coding for the peptide binding region (PBR). A maximum of three alleles per individual was detected by sequencing and the RFLP pattern consisted of 4-7 fragments, indicating a minimum number of 2-4 loci per individual. A phylogenetic analysis, demonstrated that the blue tit sequences are divergent compared to sequences from other passerines resembling a different MHC lineage than those possessed by most passerines studied to date.
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Affiliation(s)
- Juan Rivero-de Aguilar
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC)J. Gutiérrez Abascal 2, E-28006, Madrid, Spain
| | - Elske Schut
- Behavioural Ecology and Self-Organization, The University of GroningenPO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Santiago Merino
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC)J. Gutiérrez Abascal 2, E-28006, Madrid, Spain
| | - Javier Martínez
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de AlcaláAlcalá de Henares, E-28871, Madrid, Spain
| | - Jan Komdeur
- Behavioural Ecology and Self-Organization, The University of GroningenPO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Ecology Building, Lund UniversitySölvegatan 37, SE-22362, Lund, Sweden
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15
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Follin E, Karlsson M, Lundegaard C, Nielsen M, Wallin S, Paulsson K, Westerdahl H. In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function. Immunogenetics 2013; 65:299-311. [PMID: 23358931 DOI: 10.1007/s00251-012-0676-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 12/24/2012] [Indexed: 11/26/2022]
Abstract
The major histocompatibility complex (MHC) genes are the most polymorphic genes found in the vertebrate genome, and they encode proteins that play an essential role in the adaptive immune response. Many songbirds (passerines) have been shown to have a large number of transcribed MHC class I genes compared to most mammals. To elucidate the reason for this large number of genes, we compared 14 MHC class I alleles (α1-α3 domains), from great reed warbler, house sparrow and tree sparrow, via phylogenetic analysis, homology modelling and in silico peptide-binding predictions to investigate their functional and genetic relationships. We found more pronounced clustering of the MHC class I allomorphs (allele specific proteins) in regards to their function (peptide-binding specificities) compared to their genetic relationships (amino acid sequences), indicating that the high number of alleles is of functional significance. The MHC class I allomorphs from house sparrow and tree sparrow, species that diverged 10 million years ago (MYA), had overlapping peptide-binding specificities, and these similarities across species were also confirmed in phylogenetic analyses based on amino acid sequences. Notably, there were also overlapping peptide-binding specificities in the allomorphs from house sparrow and great reed warbler, although these species diverged 30 MYA. This overlap was not found in a tree based on amino acid sequences. Our interpretation is that convergent evolution on the level of the protein function, possibly driven by selection from shared pathogens, has resulted in allomorphs with similar peptide-binding repertoires, although trans-species evolution in combination with gene conversion cannot be ruled out.
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Affiliation(s)
- Elna Follin
- Immunology Section, BMC-D14, Department of Experimental Medical Sciences, Lund University, 221 84, Lund, Sweden.
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16
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Buehler DM, Verkuil YI, Tavares ES, Baker AJ. Characterization of MHC class I in a long-distance migrant shorebird suggests multiple transcribed genes and intergenic recombination. Immunogenetics 2012; 65:211-25. [PMID: 23239370 DOI: 10.1007/s00251-012-0669-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/12/2012] [Indexed: 12/18/2022]
Abstract
The major histocompatibility complex (MHC) includes highly polymorphic gene families encoding proteins crucial to the vertebrate acquired immune system. Classical MHC class I (MHCI) genes code for molecules expressed on the surfaces of most nucleated cells and are associated with defense against intracellular pathogens, such as viruses. These genes have been studied in a few wild bird species, but have not been studied in long-distance migrating shorebirds. Red Knots Calidris canutus are medium-sized, monogamous sandpipers with migratory routes that span the globe. Understanding how such long-distance migrants protect themselves from disease has gained new relevance since the emergence of avian-borne diseases, including intracellular pathogens recognized by MHCI molecules, such as avian influenza. In this study, we characterized MHCI genes in knots and found 36 alleles in eight individuals and evidence for six putatively functional and expressed MHCI genes in a single bird. We also found evidence for recombination and for positive selection at putative peptide binding sites in exons 2 and 3. These results suggest surprisingly high MHC diversity in knots, given their demographic history. This may be a result of selection from diverse pathogens encountered by shorebirds throughout their annual migrations.
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MESH Headings
- Amino Acid Sequence
- Animal Migration
- Animals
- Charadriiformes/genetics
- Charadriiformes/immunology
- DNA, Complementary/genetics
- DNA, Intergenic/genetics
- Ecosystem
- Exons/genetics
- Genes, MHC Class I
- Genetic Variation
- Introns/genetics
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Genetic
- RNA, Messenger/blood
- RNA, Messenger/genetics
- Recombination, Genetic
- Selection, Genetic
- Sequence Alignment
- Sequence Homology, Amino Acid
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- Deborah M Buehler
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada.
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17
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Wutzler R, Foerster K, Kempenaers B. MHC class I variation in a natural blue tit population (Cyanistes caeruleus). Genetica 2012; 140:349-64. [PMID: 23073914 DOI: 10.1007/s10709-012-9679-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 09/03/2012] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is central to the vertebrate immune system and its highly polymorphic genes are considered to influence several life-history traits of individuals. To characterize the MHC in a natural population of blue tits (Cyanistes caeruleus) we investigated the class I exon 3 diversity of more than 900 individuals. We designed two pairs of motif-specific primers that reliably amplify independent subsets of MHC alleles. Applying denaturing gradient gel electrophoresis (DGGE) we obtained 48 independently inherited units of unique band patterns (DGGE-haplogroups), which were validated in a segregation analysis within 105 families. In a second approach, we extensively sequenced 6 unrelated individuals to confirm that DGGE-haplogroup composition reflects individual allelic variation. The highest number of different DGGE-haplogroups in a single individual corresponded in 19 MHC exon 3 sequences, suggesting a minimum of 10 amplified MHC class I loci in the blue tit. In total, we identified 50 unique functional and 3 non-functional sequences. Functional sequences showed high levels of recombination and strong positive selection in the antigen binding region, whereas nucleotide diversity was comparatively low in the range of all passerine species. Finally, in a phylogenetic comparison of passerine MHC class I exon 3 sequences we discuss conflicting evolutionary signals possibly due to recent gene duplication, recombination events and concerted evolution. Our results indicate that the described method is suitable to effectively explore the MHC diversity and its ecological impacts in blue tits in future studies.
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Affiliation(s)
- R Wutzler
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82305 Seewiesen, Germany.
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18
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MHC class I of saltwater crocodiles (Crocodylus porosus): polymorphism and balancing selection. Immunogenetics 2012; 64:825-38. [PMID: 22864956 DOI: 10.1007/s00251-012-0637-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
Abstract
Saltwater crocodiles are in high demand for the production of luxury fashion items. However, their susceptibility to disease incurs substantial losses and it is hoped to be able to genetically select these animals for disease resistance. So far, this has only been enabled by phenotypic selection. Investigating the major histocompatibility complex (MHC) could provide insight into the ability of an individual to respond to pathogens acting as a selective pressure on the host. Here, we assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 3 among 42 saltwater crocodiles from nine river basins in the Northern Territory, Australia. We generated 640 sequences using cloning and sequencing methods and identified 43 MHC variants among them. Phylogenetic analyses clustered these variants into two major clades, which may suggest two gene lineages. We found the number of variants within an individual varying between one and seven, indicating that there are at least four gene loci in this species. Selection detection analyses revealed an elevated ratio of nonsynonymous to synonymous substitutions (mean = 1.152 per codon), suggesting balancing selection. Population differentiation analyses revealed that the MHC did not show structuring among the river basins, and there were some shared variants among them. This may be a result of possible gene flow and/or similar selection pressures among populations. These findings provide background knowledge to identify potential MHC markers, which could be used for selecting genetically variable individuals for future disease associations. All MHC class I exon 3 sequences reported in this paper were submitted to the GenBank database with following accession numbers: HQ008785-HQ008789, HQ008791-HQ008798, HQ008808-HQ008815, HQ008824, HQ008826-HQ008830, HQ008835, HQ008839, HQ008842-HQ008850, and JX023536-JX023540.
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Sepil I, Moghadam HK, Huchard E, Sheldon BC. Characterization and 454 pyrosequencing of major histocompatibility complex class I genes in the great tit reveal complexity in a passerine system. BMC Evol Biol 2012; 12:68. [PMID: 22587557 PMCID: PMC3483247 DOI: 10.1186/1471-2148-12-68] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 05/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The critical role of Major Histocompatibility Complex (Mhc) genes in disease resistance and their highly polymorphic nature make them exceptional candidates for studies investigating genetic effects on survival, mate choice and conservation. Species that harbor many Mhc loci and high allelic diversity are particularly intriguing as they are potentially under strong selection and studies of such species provide valuable information as to the mechanisms maintaining Mhc diversity. However comprehensive genotyping of complex multilocus systems has been a major challenge to date with the result that little is known about the consequences of this complexity in terms of fitness effects and disease resistance. RESULTS In this study, we genotyped the Mhc class I exon 3 of the great tit (Parus major) from two nest-box breeding populations near Oxford, UK that have been monitored for decades. Characterization of Mhc class I exon 3 was adopted and bidirectional sequencing was carried using the 454 sequencing platform. Full analysis of sequences through a stepwise variant validation procedure allowed reliable typing of more than 800 great tits based on 214,357 reads; from duplicates we estimated the repeatability of typing as 0.94. A total of 862 alleles were detected, and the presence of at least 16 functional loci was shown - the highest number characterized in a wild bird species. Finally, the functional alleles were grouped into 17 supertypes based on their antigen binding affinities. CONCLUSIONS We found extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. The presence of many functional loci was shown, together with a pseudogene family and putatively non-functional alleles; there was clear evidence that functional alleles were under strong balancing selection. This study is the first step towards an in-depth analysis of this gene complex in this species, which will help understanding how parasite-mediated and sexual selection shape and maintain host genetic variation in nature. We believe that study systems like ours can make important contributions to the field of evolutionary biology and emphasize the necessity of integrating long-term field-based studies with detailed genetic analysis to unravel complex evolutionary processes.
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Affiliation(s)
- Irem Sepil
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, OX1 3PS, UK.
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