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Minias P. Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history. Mol Ecol 2024; 33:e17453. [PMID: 38953291 DOI: 10.1111/mec.17453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 07/03/2024]
Abstract
The major histocompatibility complex (MHC) multigene family encodes key pathogen-recognition molecules of the vertebrate adaptive immune system. Hyper-polymorphism of MHC genes is de novo generated by point mutations, but new haplotypes may also arise by re-shuffling of existing variation through intra- and inter-locus gene conversion. Although the occurrence of gene conversion at the MHC has been known for decades, we still have limited understanding of its functional importance. Here, I took advantage of extensive genetic resources (~9000 sequences) to investigate broad scale macroevolutionary patterns in gene conversion processes at the MHC across nearly 200 avian species. Gene conversion was found to constitute a universal mechanism in birds, as 83% of species showed footprints of gene conversion at either MHC class and 25% of all allelic variants were attributed to gene conversion. Gene conversion processes were stronger at MHC-II than MHC-I, but inter-specific variation at both MHC classes was explained by similar evolutionary scenarios, reflecting fluctuating selection towards different optima and drift. Gene conversion showed uneven phylogenetic distribution across birds and was driven by gene copy number variation, supporting significant role of inter-locus gene conversion processes in the evolution of the avian MHC. Finally, MHC gene conversion was stronger in species with fast life histories (high fecundity) and in long-distance migrants, likely reflecting variation in population sizes and host-pathogen coevolutionary dynamics. The results provide a robust comparative framework for understanding macroevolutionary variation in gene conversion at the avian MHC and reinforce important contribution of this mechanism to functional MHC diversity.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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2
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Wojczulanis-Jakubas K, Hoover B, Jakubas D, Fort J, Grémillet D, Gavrilo M, Zielińska S, Zagalska-Neubauer M. Diversity of major histocompatibility complex of II B gene and mate choice in a monogamous and long-lived seabird, the Little Auk (Alle alle). PLoS One 2024; 19:e0304275. [PMID: 38865310 PMCID: PMC11168636 DOI: 10.1371/journal.pone.0304275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024] Open
Abstract
The major histocompatibility complex (MHC) plays a key role in the adaptive immune system of vertebrates, and is known to influence mate choice in many species. In birds, the MHC has been extensively examined but mainly in galliforms and passerines while other taxa that represent specific ecological and evolutionary life-histories, like seabirds, are underexamined. Here, we characterized diversity of MHC Class II B exon 2 in a colonial pelagic seabird, the Little Auk (or Dovekie Alle alle). We further examined whether MHC variation could be maintained through balancing selection and disassortative mating. We found high polymorphism at the genotyped MHC fragment, characterizing 99 distinct alleles across 140 individuals from three populations. The alleles frequencies exhibited a similar skewed distribution in both sexes, with the four most commonly occurring alleles representing approximately 35% of allelic variation. The results of a Bayesian site-by-site selection analysis suggest evidence of balancing selection and no direct evidence for MHC-dependent disassortative mating preferences in the Little Auk. The latter result might be attributed to the high overall polymorphism of the examined fragment, which itself may be maintained by the large population size of the species.
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Affiliation(s)
| | - Brian Hoover
- Farallon Institute, Petaluma, California, United States of America
| | - Dariusz Jakubas
- Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Jérôme Fort
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS – La Rochelle University, 17000 La Rochelle, France
| | - David Grémillet
- Excellence Chair Nouvelle Aquitaine - CEBC UMR 7372 CNRS, La Rochelle Université, Villiers-en-Bois, France & FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, South Africa
| | | | - Sylwia Zielińska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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Using de novo genome assembly and high-throughput sequencing to characterize the MHC region in a non-model bird, the Eurasian coot. Sci Rep 2022; 12:7031. [PMID: 35488050 PMCID: PMC9054815 DOI: 10.1038/s41598-022-11018-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
Genes of the Major Histocompatibility Complex (MHC) form a key component of vertebrate adaptive immunity, as they code for molecules which bind antigens of intra- and extracellular pathogens (MHC class I and II, respectively) and present them to T cell receptors. In general, MHC genes are hyper-polymorphic and high MHC diversity is often maintained within natural populations (via balancing selection) and within individuals (via gene duplications). Because of its complex architecture with tandems of duplicated genes, characterization of MHC region in non-model vertebrate species still poses a major challenge. Here, we combined de novo genome assembly and high-throughput sequencing to characterize MHC polymorphism in a rallid bird species, the Eurasian coot Fulica atra. An analysis of genome assembly indicated high duplication rate at MHC-I, which was also supported by targeted sequencing of peptide-binding exons (at least five MHC-I loci genotyped). We found high allelic richness at both MHC-I and MHC-II, although signature of diversifying selection and recombination (gene conversion) was much stronger at MHC-II. Our results indicate that Eurasian coot retains extraordinary polymorphism at both MHC classes (when compared to other non-passerine bird species), although they may be subject to different evolutionary mechanism.
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Minias P, Drzewińska-Chańko J, Włodarczyk R. Evolution of innate and adaptive immune genes in a non-model waterbird, the common tern. INFECTION GENETICS AND EVOLUTION 2021; 95:105069. [PMID: 34487864 DOI: 10.1016/j.meegid.2021.105069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Toll-like receptors (TLRs) and the Major Histocompatibility Complex (MHC) are the key pathogen-recognition genes of vertebrate immune system and they have a crucial role in the initiation of innate and adaptive immune response, respectively. Recent advancements in sequencing technology sparked research on highly duplicated MHC genes in non-model species, but TLR variation in natural vertebrate populations has remained little studied and comparisons of polymorphism across both TLRs and MHC are scarce. Here, we aimed to compare variation across innate (four TLR loci) and adaptive (MHC class I and class II) immune genes in a non-model avian species, the common tern Sterna hirundo. We detected relatively high allelic richness at TLR genes (9-48 alleles per locus), which was similar to or even higher than the estimated per locus allelic richness at the MHC (24-30 alleles at class I and 13-16 alleles at class II under uniform sample sizes). Despite this, the total number of MHC alleles across all duplicated loci (four class I and three class II) was much higher and MHC alleles showed greater sequence divergence than TLRs. Positive selection targeted relatively more sites at the MHC than TLRs, but the strength of selection (dN/dS ratios) at TLRs was higher when compared to MHC class I. There were also differences in the signature of positive selection and recombination (gene conversion) between MHC class I and II (stronger signature at class II), suggesting that mechanisms maintaining variation at the MHC may vary between both classes. Our study indicates that allelic richness of both innate and adaptive immune receptors may be maintained at relatively high levels in viable avian populations and we recommend a transition from the traditional gene-specific to multi-gene approach in studying molecular evolution of vertebrate immune system.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland.
| | - Joanna Drzewińska-Chańko
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
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Minias P, Włodarczyk R, Remisiewicz M, Cobzaru I, Janiszewski T. Distinct evolutionary trajectories of MHC class I and class II genes in Old World finches and buntings. Heredity (Edinb) 2021; 126:974-990. [PMID: 33824536 PMCID: PMC8178356 DOI: 10.1038/s41437-021-00427-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/08/2021] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Major histocompatibility complex (MHC) genes code for key proteins of the adaptive immune system, which present antigens from intra-cellular (MHC class I) and extra-cellular (MHC class II) pathogens. Because of their unprecedented diversity, MHC genes have long been an object of scientific interest, but due to methodological difficulties in genotyping of duplicated loci, our knowledge on the evolution of the MHC across different vertebrate lineages is still limited. Here, we compared the evolution of MHC class I and class II genes in three sister clades of common passerine birds, finches (Fringillinae and Carduelinae) and buntings (Emberizidae) using a uniform methodological (genotyping and data processing) approach and uniform sample sizes. Our analyses revealed contrasting evolutionary trajectories of the two MHC classes. We found a stronger signature of pervasive positive selection and higher allele diversity (allele numbers) at the MHC class I than class II. In contrast, MHC class II genes showed greater allele divergence (in terms of nucleotide diversity) and a much stronger recombination (gene conversion) signal. Gene copy numbers at both MHC class I and class II evolved via fluctuating selection and drift (Brownian Motion evolution), but the evolutionary rate was higher at class I. Our study constitutes one of few existing examples, where evolution of MHC class I and class II genes was directly compared using a multi-species approach. We recommend that re-focusing MHC research from single-species and single-class approaches towards multi-species analyses of both MHC classes can substantially increase our understanding MHC evolution in a broad phylogenetic context.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Magdalena Remisiewicz
- Bird Migration Research Station, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Ioana Cobzaru
- Institute of Biology Bucharest, Romanian Academy, Bucharest, Romania
| | - Tomasz Janiszewski
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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Minias P, He K, Dunn PO. The strength of selection is consistent across both domains of the MHC class I peptide-binding groove in birds. BMC Ecol Evol 2021; 21:80. [PMID: 33964878 PMCID: PMC8106206 DOI: 10.1186/s12862-021-01812-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/28/2021] [Indexed: 02/26/2023] Open
Abstract
Background The Major Histocompatibility Complex (MHC) codes for the key vertebrate immune receptors responsible for pathogen recognition. Foreign antigens are recognized via their compatibility to hyper-variable region of the peptide-binding groove (PBR), which consists of two separate protein domains. Specifically, the PBR of the MHC class I receptors, which recognize intra-cellular pathogens, has two α domains encoded by exon 2 (α1) and exon 3 (α2) of the same gene. Most research on avian MHC class I polymorphism has traditionally focused exclusively on exon 3 and comparisons of selection between the two domains have been hampered by the scarcity of molecular data for exon 2. Thus, it is not clear whether the two domains vary in their specificity towards different antigens and whether they are subject to different selective pressure. Results Here, we took advantage of rapidly accumulating genomic resources to test for the differences in selection patterns between both MHC class I domains of the peptide-binding groove in birds. For this purpose, we compiled a dataset of MHC class I exon 2 and 3 sequences for 120 avian species from 46 families. Our phylogenetically-robust approach provided strong evidence for highly consistent levels of selection on the α1 and α2 domains. There were strong correlations in all selection measures (number of positively/negatively selected residues and dN/dS ratios) between both PBR exons. Similar positive associations were found for the level of amino acid polymorphism across the two domains. Conclusions We conclude that the strength of selection and the level of polymorphism are highly consistent between both peptide-binding domains (α1 and α2) of the avian MHC class I. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01812-x.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, USA
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Cruz-López M, Fernández G, Hipperson H, Palacios E, Cavitt J, Galindo-Espinosa D, Gómez Del Angel S, Pruner R, Gonzalez O, Burke T, Küpper C. 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 Evol Biol 2020; 20:114. [PMID: 32912143 PMCID: PMC7488298 DOI: 10.1186/s12862-020-01676-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 08/20/2020] [Indexed: 12/02/2022] Open
Abstract
Background Understanding the structure and variability of adaptive loci such as the major histocompatibility complex (MHC) genes is a primary research goal for evolutionary and conservation genetics. Typically, classical MHC genes show high polymorphism and are under strong balancing selection, as their products trigger the adaptive immune response in vertebrates. Here, we assess the allelic diversity and patterns of selection for MHC class I and class II loci in a threatened shorebird with highly flexible mating and parental care behaviour, the Snowy Plover (Charadrius nivosus) across its broad geographic range. Results We determined the allelic and nucleotide diversity for MHC class I and class II genes using samples of 250 individuals from eight breeding population of Snowy Plovers. We found 40 alleles at MHC class I and six alleles at MHC class II, with individuals carrying two to seven different alleles (mean 3.70) at MHC class I and up to two alleles (mean 1.45) at MHC class II. Diversity was higher in the peptide-binding region, which suggests balancing selection. The MHC class I locus showed stronger signatures of both positive and negative selection than the MHC class II locus. Most alleles were present in more than one population. If present, private alleles generally occurred at very low frequencies in each population, except for the private alleles of MHC class I in one island population (Puerto Rico, lineage tenuirostris). Conclusion Snowy Plovers exhibited an intermediate level of diversity at the MHC, similar to that reported in other Charadriiformes. The differences found in the patterns of selection between the class I and II loci are consistent with the hypothesis that different mechanisms shape the sequence evolution of MHC class I and class II genes. The rarity of private alleles across populations is consistent with high natal and breeding dispersal and the low genetic structure previously observed at neutral genetic markers in this species.
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Affiliation(s)
- Medardo Cruz-López
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Cd. México, Mexico.
| | - Guillermo Fernández
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apartado Postal 811, 82040, Mazatlán, Sinaloa, Mexico
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Eduardo Palacios
- Centro de Investigación Científica y de Educación Superior de Ensenada, Unidad La Paz, Miraflores 334, Col. Bellavista, 23050, La Paz, Baja California Sur, Mexico
| | - John Cavitt
- Avian Ecology Laboratory Department of Zoology, Weber State University, Ogden, UT, 84408, USA
| | - Daniel Galindo-Espinosa
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Carretera al Sur km 5.5, A.P. 19-B, 23080, La Paz, B.C.S., Mexico
| | - Salvador Gómez Del Angel
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Cd. México, Mexico
| | - Raya Pruner
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Panama City, FL, USA
| | - Oscar Gonzalez
- Grupo Aves del Perú, Gómez del Carpio 135, Barrio Medico, 34, Lima, Peru.,Department of Natural Sciences, Emmanuel College, Franklin Springs, GA, 30369, USA
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Clemens Küpper
- Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319, Seewiesen, Germany.
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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: 11] [Impact Index Per Article: 2.2] [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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O'Connor EA, Westerdahl H, Burri R, Edwards SV. Avian MHC Evolution in the Era of Genomics: Phase 1.0. Cells 2019; 8:E1152. [PMID: 31561531 PMCID: PMC6829271 DOI: 10.3390/cells8101152] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.
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Affiliation(s)
| | | | - Reto Burri
- Department of Population Ecology, Institute of Ecology & Evolution, Friedrich Schiller University Jena, 07737 Jena, Germany.
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
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Minias P, Pikus E, Anderwald D. Allelic diversity and selection at the MHC class I and class II in a bottlenecked bird of prey, the White-tailed Eagle. BMC Evol Biol 2019; 19:2. [PMID: 30611206 PMCID: PMC6321662 DOI: 10.1186/s12862-018-1338-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/17/2018] [Indexed: 01/07/2023] Open
Abstract
Background Genes of the Major Histocompatibility Complex (MHC) are essential for adaptive immune response in vertebrates, as they encode receptors that recognize peptides derived from the processing of intracellular (MHC class I) and extracellular (MHC class II) pathogens. High MHC diversity in natural populations is primarily generated and maintained by pathogen-mediated diversifying and balancing selection. It is, however, debated whether selection at the MHC can counterbalance the effects of drift in bottlenecked populations. The aim of this study was to assess allelic diversity of MHC genes in a recently bottlenecked bird of prey, the White-tailed Eagle Haliaeetus albicilla, as well as to compare mechanisms that shaped the evolution of MHC class I and class II in this species. Results We showed that significant levels of MHC diversity were retained in the core Central European (Polish) population of White-tailed Eagles. Ten MHC class I and 17 MHC class II alleles were recovered in total and individual birds showed high average MHC diversity (3.80 and 6.48 MHC class I and class II alleles per individual, respectively). Distribution of alleles within individuals provided evidence for the presence of at least three class I and five class II loci the White-tailed Eagle, which suggests recent duplication events. MHC class II showed greater sequence polymorphism than MHC class I and there was much stronger signature of diversifying selection acting on MHC class II than class I. Phylogenetic analysis provided evidence for trans-species similarity of class II, but not class I, sequences, which is likely consistent with stronger balancing selection at MHC class II. Conclusions Relatively high MHC diversity retained in the White-tailed Eagles from northern Poland reinforces high conservation value of local eagle populations. At the same time, our study is the first to demonstrate contrasting patterns of allelic diversity and selection at MHC class I and class II in an accipitrid species, supporting the hypothesis that different mechanisms can shape evolutionary trajectories of MHC class I and class II genes. Electronic supplementary material The online version of this article (10.1186/s12862-018-1338-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Dariusz Anderwald
- Eagle Conservation Committee, Niepodległości 53/55, 10-044, Olsztyn, Poland
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11
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Minias P, Pikus E, Whittingham LA, Dunn PO. A global analysis of selection at the avian MHC. Evolution 2018; 72:1278-1293. [PMID: 29665025 DOI: 10.1111/evo.13490] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/29/2018] [Accepted: 04/09/2018] [Indexed: 12/29/2022]
Abstract
Recent advancements in sequencing technology have resulted in rapid progress in the study of the major histocompatibility complex (MHC) in non-model avian species. Here, we analyze a global dataset of avian MHC class I and class II sequences (ca. 11,000 sequences from over 250 species) to gain insight into the processes that govern macroevolution of MHC genes in birds. Analysis of substitution rates revealed striking differences in the patterns of diversifying selection between passerine and non-passerine birds. Non-passerines showed stronger selection at MHC class II, which is primarily involved in recognition of extracellular pathogens, while passerines showed stronger selection at MHC class I, which is involved in recognition of intracellular pathogens. Positions of positively selected amino-acid residues showed marked discrepancies with peptide-binding residues (PBRs) of human MHC molecules, suggesting that using a human classification of PBRs to assess selection patterns at the avian MHC may be unjustified. Finally, our analysis provided evidence that indel mutations can make a substantial contribution to adaptive variation at the avian MHC.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland
| | - Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53211
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53211
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12
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Cao Z, He M, Chen X, Wang S, Cai Y, Xie Z, Sun Y, Zhou Y. Identification, polymorphism and expression of MHC class Iα in golden pompano, Trachinotus ovatus. FISH & SHELLFISH IMMUNOLOGY 2017; 67:55-65. [PMID: 28554837 DOI: 10.1016/j.fsi.2017.05.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/18/2017] [Accepted: 05/25/2017] [Indexed: 06/07/2023]
Abstract
The classical major histocompatibility complex class I (MHC I) plays a vital role in the immune system. In this study, we cloned and identified golden pompano (Trachinotus ovatus) MHC Iα (Trov-MHC Iα), which encodes 351 amino acid residues including a leader peptide, α1, α2, α3 domain, a transmembrane region and a cytoplasmic domain. Twenty six different sequences, which encoded various numbers of amino acid residues ranging from 348 to 354, were obtained from 12 individuals. Highly genetic polymorphism was found in the Trov-MHC Iα, especially in the α1 and α2 domains. Meanwhile, in the α1 and α2 domains, 21 positive selected positions were revealed by site models, indicating the diversity of Trov-MHC Iα may be mainly generated by positive selection. Moreover, quantitative real-time reverse transcription PCR and western blotting analyses demonstrated that Trov-MHC Iα was ubiquitously expressed in the nine tested tissues and more highly expressed in intestine, head kidney, gill, and spleen. In the head kidney and spleen, Trov-MHC Iα was significantly upregulated under LPS or poly I:C stimulation. The results of this study provide valuable insight into molecular polymorphism, evolutionary mechanism, expression and function of MHC Iα in the immune system of golden pompano.
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Affiliation(s)
- Zhenjie Cao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan 570228, China
| | - Mingwang He
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou, Hainan 570228, China
| | - Xiaojuan Chen
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, China
| | - Shifeng Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, China
| | - Yan Cai
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan 570228, China
| | - Zhenyu Xie
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, China
| | - Yun Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, China; Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan 570228, China.
| | - Yongcan Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, College of Marine Science, Hainan University, Haikou, Hainan 570228, China.
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Drews A, Strandh M, Råberg L, Westerdahl H. Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer). BMC Evol Biol 2017. [PMID: 28651571 PMCID: PMC5485651 DOI: 10.1186/s12862-017-0970-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) plays a central role in immunity and has been given considerable attention by evolutionary ecologists due to its associations with fitness-related traits. Songbirds have unusually high numbers of MHC class I (MHC-I) genes, but it is not known whether all are expressed and equally important for immune function. Classical MHC-I genes are highly expressed, polymorphic and present peptides to T-cells whereas non-classical MHC-I genes have lower expression, are more monomorphic and do not present peptides to T-cells. To get a better understanding of the highly duplicated MHC genes in songbirds, we studied gene expression in a phylogenetic framework in three species of sparrows (house sparrow, tree sparrow and Spanish sparrow), using high-throughput sequencing. We hypothesize that sparrows could have classical and non-classical genes, as previously indicated though never tested using gene expression. RESULTS The phylogenetic analyses reveal two distinct types of MHC-I alleles among the three sparrow species, one with high and one with low level of polymorphism, thus resembling classical and non-classical genes, respectively. All individuals had both types of alleles, but there was copy number variation both within and among the sparrow species. However, the number of highly polymorphic alleles that were expressed did not vary between species, suggesting that the structural genomic variation is counterbalanced by conserved gene expression. Overall, 50% of the MHC-I alleles were expressed in sparrows. Expression of the highly polymorphic alleles was very variable, whereas the alleles with low polymorphism had uniformly low expression. Interestingly, within an individual only one or two alleles from the polymorphic genes were highly expressed, indicating that only a single copy of these is highly expressed. CONCLUSIONS Taken together, the phylogenetic reconstruction and the analyses of expression suggest that sparrows have both classical and non-classical MHC-I genes, and that the evolutionary origin of these genes predate the split of the three investigated sparrow species 7 million years ago. Because only the classical MHC-I genes are involved in antigen presentation, the function of different MHC-I genes should be considered in future ecological and evolutionary studies of MHC-I in sparrows and other songbirds.
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Affiliation(s)
- Anna Drews
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
| | - Maria Strandh
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Lars Råberg
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Helena Westerdahl
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
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14
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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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15
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Wang Z, Zhou X, Lin Q, Fang W, Chen X. Diversity and selection of MHC class I genes in the vulnerable Chinese egret (Egretta eulophotes). PLoS One 2017; 12:e0176671. [PMID: 28467494 PMCID: PMC5415105 DOI: 10.1371/journal.pone.0176671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/16/2017] [Indexed: 11/19/2022] Open
Abstract
The genes of major histocompatibility complex (MHC) are important to vertebrate immune system. In this study, two new MHC class I genes, designated as Egeu-UAA and Egeu-UBA, were discovered in the vulnerable Chinese egret (Egretta eulophotes). Using a full length DNA and cDNA produced by PCR and RACE methods, these two MHC class I loci were characterized in the genome of the Chinese egret and were also found to be expressed in liver and blood. Both new genes showed the expected eight exons and were similar to two copies of the minimal essential MHC complex of chicken. In genetic diversity, 14 alleles (8 for UAA and 6 for UBA) in the MHC class I gene exon 3 were found in 60 individuals using locus-specific primers and showed little polymorphism. Only three potential amino acid residues were detected under positive selection in potential peptide-binding regions (PBRs) by Bayesian analysis. These new results provide the fundamental basis for further studies to elucidate the molecular mechanisms and significance of MHC molecular adaptation in vulnerable Chinese egret and other ardeids, finding that have not been previously reported.
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Affiliation(s)
- Zeng Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Xiaoping Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Qingxian Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Wenzhen Fang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China
- * E-mail: (WF); (XC)
| | - Xiaolin Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China
- * E-mail: (WF); (XC)
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16
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Fleming-Canepa X, Jensen SM, Mesa CM, Diaz-Satizabal L, Roth AJ, Parks-Dely JA, Moon DA, Wong JP, Evseev D, Gossen DA, Tetrault DG, Magor KE. Extensive Allelic Diversity of MHC Class I in Wild Mallard Ducks. THE JOURNAL OF IMMUNOLOGY 2016; 197:783-94. [PMID: 27342841 DOI: 10.4049/jimmunol.1502450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 05/31/2016] [Indexed: 11/19/2022]
Abstract
MHC class I is critically involved in defense against viruses, and diversity from polygeny and polymorphism contributes to the breadth of the immune response and health of the population. In this article, we examine MHC class I diversity in wild mallard ducks, the natural host and reservoir of influenza A viruses. We previously showed domestic ducks predominantly use UAA, one of five MHC class I genes, but whether biased expression is also true for wild mallards is unknown. Using RT-PCR from blood, we examined expressed MHC class I alleles from 38 wild mallards (Anas platyrhynchos) and identified 61 unique alleles, typically 1 or 2 expressed alleles in each individual. To determine whether expressed alleles correspond to UAA adjacent to TAP2 as in domestic ducks, we cloned and sequenced genomic UAA-TAP2 fragments from all mallards, which matched transcripts recovered and allowed us to assign most alleles as UAA Allelic differences are primarily located in α1 and α2 domains in the residues known to interact with peptide in mammalian MHC class I, suggesting the diversity is functional. Most UAA alleles have unique residues in the cleft predicting distinct specificity; however, six alleles have an unusual conserved cleft with two cysteine residues. Residues that influence peptide-loading properties and tapasin involvement in chicken are fixed in duck alleles and suggest tapasin independence. Biased expression of one MHC class I gene may make viral escape within an individual easy, but high diversity in the population places continual pressure on the virus in the reservoir species.
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Affiliation(s)
- Ximena Fleming-Canepa
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Shawna M Jensen
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Christine M Mesa
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Laura Diaz-Satizabal
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Alexa J Roth
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Julie A Parks-Dely
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Debra A Moon
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Janet P Wong
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Danyel Evseev
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Desolie A Gossen
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - David G Tetrault
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Katharine E Magor
- Department of Biological Sciences and the Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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17
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Zeng QQ, Zhong GH, He K, Sun DD, Wan QH. Molecular characterization of classical and nonclassical MHC class I genes from the golden pheasant (Chrysolophus pictus). Int J Immunogenet 2015; 43:8-17. [PMID: 26700854 DOI: 10.1111/iji.12245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/22/2015] [Indexed: 11/29/2022]
Abstract
Classical major histocompatibility complex (MHC) class I allelic polymorphism is essential for competent antigen presentation. To improve the genotyping efforts in the golden pheasant, it is necessary to differentiate more accurately between classical and nonclassical class I molecules. In our study, all MHC class I genes were isolated from one golden pheasant based on two overlapping PCR amplifications. In total, six full-length class I nucleotide sequences (A-F) were identified, and four were novel. Two (A and C) belonged to the IA1 gene, two (B and D) were alleles derived from the IA2 gene through transgene amplification, and two (E and F) comprised a third novel locus, IA3 that was excluded from the core region of the golden pheasant MHC-B. IA1 and IA2 exhibited the broad expression profiles characteristic of classical loci, while IA3 showed no expression in multiple tissues and was therefore defined as a nonclassical gene. Phylogenetic analysis indicated that the three IA genes in the golden pheasant share a much closer evolutionary relationship than the corresponding sequences in other galliform species. This observation was consistent with high sequence similarity among them, which likely arises from the homogenizing effect of recombination. Our careful distinction between the classical and nonclassical MHC class I genes in the golden pheasant lays the foundation for developing locus-specific genotyping and establishing a good molecular marker system of classical MHC I loci.
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Affiliation(s)
- Q-Q Zeng
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - G-H Zhong
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - K He
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - D-D Sun
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Q-H Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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18
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Gillingham MAF, Courtiol A, Teixeira M, Galan M, Bechet A, Cezilly F. Evidence of gene orthology and trans-species polymorphism, but not of parallel evolution, despite high levels of concerted evolution in the major histocompatibility complex of flamingo species. J Evol Biol 2015; 29:438-54. [DOI: 10.1111/jeb.12798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 11/12/2015] [Accepted: 11/15/2015] [Indexed: 11/30/2022]
Affiliation(s)
- M. A. F. Gillingham
- Equipe Ecologie Evolutive; UMR CNRS 6282 Biogéosciences; Université de Bourgogne; Dijon France
- Centre de Recherche de la Tour du Valat; Arles France
- Department of Evolutionary Genetics; Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
- Institute of Evolutionary Ecology and Conservation Genomics; University of Ulm; Ulm Germany
| | - A. Courtiol
- Department of Evolutionary Genetics; Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - M. Teixeira
- Equipe Ecologie Evolutive; UMR CNRS 6282 Biogéosciences; Université de Bourgogne; Dijon France
| | - M. Galan
- UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); INRA EFPA; Montferrier-sur-Lez Cedex France
| | - A. Bechet
- Centre de Recherche de la Tour du Valat; Arles France
| | - F. Cezilly
- Equipe Ecologie Evolutive; UMR CNRS 6282 Biogéosciences; Université de Bourgogne; Dijon France
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19
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Lyons AC, Hoostal MJ, Bouzat JL. Characterization of major histocompatibility complex class I loci of the lark sparrow (Chondestes grammacus) and insights into avian MHC evolution. Genetica 2015; 143:521-34. [PMID: 26071093 DOI: 10.1007/s10709-015-9850-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 06/06/2015] [Indexed: 11/29/2022]
Abstract
The major histocompatibilty complex (MHC) has become increasingly important in the study of the immunocapabilities of non-model vertebrates due to its direct involvement in the immune response. The characterization of MHC class I loci in the lark sparrow (Chondestes grammacus) revealed multiple MHC class I loci with elevated genetic diversity at exon 3, evidence of differential selection between the peptide binding region (PBR) and non-PBR, and the presence of multiple pseudogenes with limited divergence. The minimum number of functional MHC class I loci was estimated at four. Sequence analysis revealed d N /d S ratios significantly less than one at non-PBR sites, indicative of negative selection, whereas PBR sites associated with antigen recognition showed ratios greater than 1 but non-significant. GenBank surveys and phylogenetic analyses of previously reported avian MHC class I sequences revealed variable signatures of evolutionary processes acting upon this gene family, including gene duplication and potential concerted evolution. An increase in the number of class I loci across species coincided with an increase in pseudogene prevalence, revealing the importance of gene duplication in the expansion of multigene families and the creation of pseudogenes.
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Affiliation(s)
- Amanda C Lyons
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
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20
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Alcaide M, Muñoz J, Martínez-de la Puente J, Soriguer R, Figuerola J. Extraordinary MHC class II B diversity in a non-passerine, wild bird: the Eurasian Coot Fulica atra (Aves: Rallidae). Ecol Evol 2014; 4:688-98. [PMID: 24683452 PMCID: PMC3967895 DOI: 10.1002/ece3.974] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/30/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022] Open
Abstract
The major histocompatibility complex (MHC) hosts the most polymorphic genes ever described in vertebrates. The MHC triggers the adaptive branch of the immune response, and its extraordinary variability is considered an evolutionary consequence of pathogen pressure. The last few years have witnessed the characterization of the MHC multigene family in a large diversity of bird species, unraveling important differences in its polymorphism, complexity, and evolution. Here, we characterize the first MHC class II B sequences isolated from a Rallidae species, the Eurasian Coot Fulica atra. A next-generation sequencing approach revealed up to 265 alleles that translated into 251 different amino acid sequences (β chain, exon 2) in 902 individuals. Bayesian inference identified up to 19 codons within the presumptive peptide-binding region showing pervasive evidence of positive, diversifying selection. Our analyses also detected a significant excess of high-frequency segregating sites (average Tajima's D = 2.36, P < 0.05), indicative of balancing selection. We found one to six different alleles per individual, consistent with the occurrence of at least three MHC class II B gene duplicates. However, the genotypes comprised of three alleles were by far the most abundant in the population investigated (49.4%), followed by those with two (29.6%) and four (17.5%) alleles. We suggest that these proportions are in agreement with the segregation of MHC haplotypes differing in gene copy number. The most widespread segregating haplotypes, according to our findings, would contain one single gene or two genes. The MHC class II of the Eurasian Coot is a valuable system to investigate the evolutionary implications of gene copy variation and extensive variability, the greatest ever found, to the best of our knowledge, in a wild population of a non-passerine bird.
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Affiliation(s)
- Miguel Alcaide
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Joaquin Muñoz
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
- The University of Oklahoma Biological Station15389 Station Road, Kingston, Oklahoma, 73439
| | | | - Ramón Soriguer
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Jordi Figuerola
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
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21
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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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22
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Wang Z, Zhou X, Lin Q, Fang W, Chen X. Characterization, polymorphism and selection of major histocompatibility complex (MHC) DAB genes in vulnerable Chinese egret (Egretta eulophotes). PLoS One 2013; 8:e74185. [PMID: 24019955 PMCID: PMC3760844 DOI: 10.1371/journal.pone.0074185] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/28/2013] [Indexed: 12/15/2022] Open
Abstract
The major histocompatibility complex (MHC) is an excellent molecular marker for the studies of evolutionary ecology and conservation genetics because it is a family of highly polymorphic genes that play a key role in vertebrate immune response. In this study, the functional genes of MHC Class II B (DAB) were isolated for the first time in a vulnerable species, the Chinese egret (Egrettaeulophotes). Using a full length DNA and cDNA produced by PCR and RACE methods, four potential MHC DAB loci were characterized in the genome of this egret and all four were expressed in liver and blood. At least four copies of the MHC gene complex were similar to two copies of the minimal essential MHC complex of chicken, but are less complex than the multiple copies expressed in passerine species. In MHC polymorphism, 19 alleles of exon 2 were isolated from 48 individuals using PCR. No stop codons or frameshift mutations were found in any of the coding regions. The signatures of positive selection detected in potential peptide-binding regions by Bayesian analysis, suggesting that all of these genes were functional. These data will provide the fundamental basis for further studies to elucidate the mechanisms and significance of MHC molecular adaptation in vulnerable Chinese egret and other ardeids.
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Affiliation(s)
- Zeng Wang
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, People’s Republic of China
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, People’s Republic of China
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, People’s Republic of China
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
- * E-mail: (WF); (XC)
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, People’s Republic of China
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
- * E-mail: (WF); (XC)
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23
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Alcaide M, Liu M, Edwards SV. Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3. PeerJ 2013; 1:e86. [PMID: 23781408 PMCID: PMC3685324 DOI: 10.7717/peerj.86] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/23/2013] [Indexed: 01/04/2023] Open
Abstract
Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of exon 3 in non-passerine birds, a pattern that contrasts with among-clade GC patterns found in other avian studies and may suggests different mutational mechanisms. Our primers represent a useful tool for the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds.
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Affiliation(s)
- Miguel Alcaide
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Mark Liu
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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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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Genotyping MHC classIIB in non-model species by reference strand-mediated conformational analysis (RSCA). CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9655-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Alcaide M, Rodríguez A, Negro JJ. Sampling strategies for accurate computational inferences of gametic phase across highly polymorphic major histocompatibility complex loci. BMC Res Notes 2011; 4:151. [PMID: 21615903 PMCID: PMC3126723 DOI: 10.1186/1756-0500-4-151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 05/26/2011] [Indexed: 11/22/2022] Open
Abstract
Background Genes of the Major Histocompatibility Complex (MHC) are very popular genetic markers among evolutionary biologists because of their potential role in pathogen confrontation and sexual selection. However, MHC genotyping still remains challenging and time-consuming in spite of substantial methodological advances. Although computational haplotype inference has brought into focus interesting alternatives, high heterozygosity, extensive genetic variation and population admixture are known to cause inaccuracies. We have investigated the role of sample size, genetic polymorphism and genetic structuring on the performance of the popular Bayesian PHASE algorithm. To cover this aim, we took advantage of a large database of known genotypes (using traditional laboratory-based techniques) at single MHC class I (N = 56 individuals and 50 alleles) and MHC class II B (N = 103 individuals and 62 alleles) loci in the lesser kestrel Falco naumanni. Findings Analyses carried out over real MHC genotypes showed that the accuracy of gametic phase reconstruction improved with sample size as a result of the reduction in the allele to individual ratio. We then simulated different data sets introducing variations in this parameter to define an optimal ratio. Conclusions Our results demonstrate a critical influence of the allele to individual ratio on PHASE performance. We found that a minimum allele to individual ratio (1:2) yielded 100% accuracy for both MHC loci. Sampling effort is therefore a crucial step to obtain reliable MHC haplotype reconstructions and must be accomplished accordingly to the degree of MHC polymorphism. We expect our findings provide a foothold into the design of straightforward and cost-effective genotyping strategies of those MHC loci from which locus-specific primers are available.
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Affiliation(s)
- Miguel Alcaide
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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