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Awadi A, Suchentrunk F, Knauer F, Smith S, Tolesa Z, Ben Slimen H. Spatial diversity of MHC class II DRB exon2 sequences in North African cape hares (Lepus capensis): positive selection and climatic adaptation signals. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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2
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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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He K, Minias P, Dunn PO. Long-Read Genome Assemblies Reveal Extraordinary Variation in the Number and Structure of MHC Loci in Birds. Genome Biol Evol 2021; 13:evaa270. [PMID: 33367721 PMCID: PMC7875000 DOI: 10.1093/gbe/evaa270] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 12/31/2022] Open
Abstract
Our knowledge of the Major Histocompatibility Complex (MHC) in birds is limited because it often consists of numerous duplicated genes within individuals that are difficult to assemble with short read sequencing technology. Long-read sequencing provides an opportunity to overcome this limitation because it allows the assembly of long regions with repetitive elements. In this study, we used genomes based on long-read sequencing to predict the number and location of MHC loci in a broad range of bird taxa. From the long-read-based genomes of 34 species, we found that there was extremely large variation in the number of MHC loci between species. Overall, there were greater numbers of both class I and II loci in passerines than nonpasserines. The highest numbers of loci (up to 193 class II loci) were found in manakins (Pipridae), which had previously not been studied at the MHC. Our results provide the first direct evidence from passerine genomes of this high level of duplication. We also found different duplication patterns between species. In some species, both MHC class I and II genes were duplicated together, whereas in most species they were duplicated independently. Our study shows that the analysis of long-read-based genomes can dramatically improve our knowledge of MHC structure, although further improvements in chromosome level assembly are needed to understand the evolutionary mechanisms producing the extraordinary interspecific variation in the architecture of the MHC region.
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Affiliation(s)
- Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łodz, Poland
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łodz, Poland
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, WI, USA
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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: 37] [Impact Index Per Article: 7.4] [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, Whittingham LA, Dunn PO. Evolution of Copy Number at the MHC Varies across the Avian Tree of Life. Genome Biol Evol 2019; 11:17-28. [PMID: 30476037 PMCID: PMC6319602 DOI: 10.1093/gbe/evy253] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 12/24/2022] Open
Abstract
The evolution of the major histocompatibility complex (MHC) is shaped by frequent gene duplications and deletions, which generate extensive variation in the number of loci (gene copies) between different taxa. Here, we collected estimates of copy number at the MHC for over 250 bird species from 68 families. We found contrasting patterns of copy number evolution between MHC class I and class IIB, which encode receptors for intra- and extracellular pathogens, respectively. Across the avian evolutionary tree, there was evidence of accelerated evolution and stabilizing selection acting on copy number at class I, while copy number at class IIB was primarily influenced by fluctuating selection and drift. Reconstruction of MHC copy number variation showed ancestrally low numbers of MHC loci in nonpasserines and evolution toward larger numbers of loci in passerines. Different passerine lineages had the highest duplication rates for MHC class I (Sylvioidea) and class IIB (Muscicapoidea and Passeroidea). We also found support for the correlated evolution of MHC copy number and life-history traits such as lifespan and migratory behavior. These results suggest that MHC copy number evolution in birds has been driven by life histories and differences in exposure to intra- and extracellular pathogens.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Lódz, Poland
| | - Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Lódz, Poland
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee
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Awadi A, Ben Slimen H, Smith S, Knauer F, Makni M, Suchentrunk F. Positive selection and climatic effects on MHC class II gene diversity in hares (Lepus capensis) from a steep ecological gradient. Sci Rep 2018; 8:11514. [PMID: 30065344 PMCID: PMC6068193 DOI: 10.1038/s41598-018-29657-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/16/2018] [Indexed: 11/24/2022] Open
Abstract
In natural populations, allelic diversity of the major histocompatibility complex (MHC) is commonly interpreted as resulting from positive selection in varying spatiotemporal pathogenic landscapes. Composite pathogenic landscape data are, however, rarely available. We studied the spatial distribution of allelic diversity at two MHC class II loci (DQA, DQB) in hares, Lepus capensis, along a steep ecological gradient in North Africa and tested the role of climatic parameters for the spatial distribution of DQA and DQB proteins. Climatic parameters were considered to reflect to some extent pathogenic landscape variation. We investigated historical and contemporary forces that have shaped the variability at both genes, and tested for differential selective pressure across the ecological gradient by comparing allelic variation at MHC and neutral loci. We found positive selection on both MHC loci and significantly decreasing diversity from North to South Tunisia. Our multinomial linear models revealed significant effects of geographical positions that were correlated with mean annual temperature and precipitation on the occurrence of protein variants, but no effects of co-occurring DQA or DQB proteins, respectively. Diversifying selection, recombination, adaptation to local pathogenic landscapes (supposedly reflected by climate parameters) and neutral demographic processes have shaped the observed MHC diversity and differentiation patterns.
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Affiliation(s)
- Asma Awadi
- Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'Intérêt Agronomique, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.
| | - Hichem Ben Slimen
- Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'Intérêt Agronomique, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,Institut Supérieur de Biotechnologie de Béja, University of Jendouba, Avenue Habib Bourguiba Béja 9000, BP. 382, Béja, Tunisia
| | - Steve Smith
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Felix Knauer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Mohamed Makni
- Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'Intérêt Agronomique, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
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Kaufman J. Unfinished Business: Evolution of the MHC and the Adaptive Immune System of Jawed Vertebrates. Annu Rev Immunol 2018; 36:383-409. [DOI: 10.1146/annurev-immunol-051116-052450] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB2 0ES, United Kingdom
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Krause ET, Bischof HJ, Engel K, Golüke S, Maraci Ö, Mayer U, Sauer J, Caspers BA. Olfaction in the Zebra Finch ( Taeniopygia guttata ): What Is Known and Further Perspectives. ADVANCES IN THE STUDY OF BEHAVIOR 2018. [DOI: 10.1016/bs.asb.2017.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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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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Li D, Sun K, Zhao Y, Lin A, Li S, Jiang Y, Feng J. Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting ( Emberiza jankowskii). PeerJ 2017; 5:e2917. [PMID: 28149689 PMCID: PMC5270597 DOI: 10.7717/peerj.2917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 12/16/2016] [Indexed: 11/23/2022] Open
Abstract
Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size. Many historically significant populations are no longer present in previously populated regions, with only three breeding populations present in Inner Mongolia (i.e., the Aolunhua, Gahaitu and Lubei557 populations). Efforts focused on facilitating the conservation of the Rufous-backed Bunting (Emberiza jankowskii) are becoming increasingly important. However, the genetic diversity of E. jankowskii has not been investigated. In the present study, polymorphism in exon 2 of the MHCIIB of E. jankowskii was investigated. This polymorphism was subsequently compared with a related species, the Meadow Bunting (Emberiza cioides). A total of 1.59 alleles/individual were detected in E. jankowskii and 1.73 alleles/individual were identified in E. cioides. The maximum number of alleles per individual from the three E. jankowskii populations suggest the existence of at least three functional loci, while the maximum number of alleles per individual from the three E. cioides populations suggest the presence of at least four functional loci. Two of the alleles were shared between the E. jankowskii and E. cioides. Among the 12 unique alleles identified in E. jankowskii, 10.17 segregating sites per allele were detected, and the nucleotide diversity was 0.1865. Among the 17 unique alleles identified in E. cioides, eight segregating sites per allele were detected, and the nucleotide diversity was 0.1667. Overall, compared to other passerine birds, a relatively low level of MHC polymorphism was revealed in E. jankowskii, which was similar to that in E. cioides. Positive selection was detected by PAML/SLAC/FEL analyses in the region encoding the peptide-binding region in both species, and no recombination was detected. Phylogenetic analysis showed that the alleles from E. jankowskii and E. cioides belong to the same clade and the two species shared similar alleles, suggesting the occurrence of a trans-species polymorphism between the two Emberiza species.
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Affiliation(s)
- Dan Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
| | - Yunjiao Zhao
- College of Animal Science and Technology, Jilin Agricultural University , Changchun , China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
| | - Shi Li
- College of Animal Science and Technology, Jilin Agricultural University , Changchun , China
| | - Yunlei Jiang
- College of Animal Science and Technology, Jilin Agricultural University , Changchun , China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun , China
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MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion. Immunogenetics 2016; 69:101-111. [PMID: 27717988 DOI: 10.1007/s00251-016-0953-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/26/2016] [Indexed: 12/23/2022]
Abstract
The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influenced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signatures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes.
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Eimes JA, Lee SI, Townsend AK, Jablonski P, Nishiumi I, Satta Y. Early Duplication of a Single MHC IIB Locus Prior to the Passerine Radiations. PLoS One 2016; 11:e0163456. [PMID: 27658204 PMCID: PMC5033386 DOI: 10.1371/journal.pone.0163456] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/08/2016] [Indexed: 01/01/2023] Open
Abstract
A key characteristic of MHC genes is the persistence of allelic lineages over macroevolutionary periods, often through multiple speciation events. This phenomenon, known as trans-species polymorphism (TSP), is well documented in several major taxonomic groups, but has less frequently been observed in birds. The order Passeriformes is arguably the most successful terrestrial vertebrate order in terms of diversity of species and ecological range, but the reasons for this success remain unclear. Passerines exhibit the most highly duplicated MHC genes of any major vertebrate taxonomic group, which may generate increased immune response relative to other avian orders with fewer MHC loci. Here, we describe phylogenetic patterns of the MHC IIB in the passerine family Corvidae. Our results indicate wide-spread TSP within this family, with at least four supported MHC IIB allelic lineages that predate speciation by many millions of years. Markov chain Monte Carlo simulations indicate that divergence of these lineages occurred near the time of the divergence of the Passeriformes and other avian orders. We suggest that the current MHC diversity observed in passerines is due in part to the multiple duplication of a single MHC locus, DAB1, early in passerine evolution and that subsequent duplications of these paralogues have contributed to the enormous success of this order by increasing their ability to recognize and mount immune responses to novel pathogens.
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Affiliation(s)
- John A. Eimes
- Seoul National University, Department of Biological Sciences, Seoul, Korea
| | - Sang-im Lee
- Seoul National University, Institute of Advanced Machines and Design, Seoul, Korea
- * E-mail:
| | - Andrea K. Townsend
- Hamilton College, Department of Biology, Clinton, NY, United States of America
| | - Piotr Jablonski
- Seoul National University, Department of Biological Sciences, Seoul, Korea
| | - Isao Nishiumi
- National Museum of Nature and Science, Department of Zoology, Tsukuba, Japan
| | - Yoko Satta
- The Graduate University for Advanced Studies, Department of Evolutionary Studies of Biosystems, Hayama, Japan
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