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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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2
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Ghani MU, Bo L, Buyang A, Yanchun X, Hussain S, Yasir M. Molecular Characterization of MHC Class I Genes in Four Species of the Turdidae Family to Assess Genetic Diversity and Selection. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5585687. [PMID: 33937397 PMCID: PMC8055405 DOI: 10.1155/2021/5585687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022]
Abstract
In vertebrate animals, the molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immunity. MHC class I deals with intracellular pathogens (virus) in birds. MHC class I diversity depends on the consequence of local and global environment selective pressure and gene flow. Here, we evaluated the MHC class I gene in four species of the Turdidae family from a broad geographical area of northeast China. We isolated 77 MHC class I sequences, including 47 putatively functional sequences and 30 pseudosequences from 80 individuals. Using the method based on analysis of cloned amplicons (n = 25) for each species, we found two and seven MHC I sequences per individual indicating more than one MHC I locus identified in all sampled species. Results revealed an overall elevated genetic diversity at MHC class I, evidence of different selection patterns among the domains of PBR and non-PBR. Alleles are found to be divergent with overall polymorphic sites per species ranging between 58 and 70 (out of 291 sites). Moreover, transspecies alleles were evident due to convergent evolution or recent speciation for the genus. Phylogenetic relationships among MHC I show an intermingling of alleles clustering among the Turdidae family rather than between other passerines. Pronounced MHC I gene diversity is essential for the existence of species. Our study signifies a valuable tool for the characterization of evolutionary relevant difference across a population of birds with high conservational concerns.
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Affiliation(s)
- Muhammad Usman Ghani
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Li Bo
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - An Buyang
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Science, Kyushu University, Fukuoka 810-0000, Japan
| | - Xu Yanchun
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Shakeel Hussain
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Muhammad Yasir
- Department of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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3
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Hibbets EM, Schumacher KI, Scheppler HB, Boersma PD, Bouzat JL. Genetic evidence of hybridization between Magellanic (Sphensicus magellanicus) and Humboldt (Spheniscus humboldti) penguins in the wild. Genetica 2020; 148:215-228. [PMID: 33070222 DOI: 10.1007/s10709-020-00106-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
The process of hybridization between closely related species plays an important role in defining the genetic integrity and overall genetic diversity of species. The distribution range of Magellanic (Spheniscus magellanicus) and Humboldt (Spheniscus humboldti) penguins is predominantly allopatric; however, the species share a region of sympatry where they may hybridize. We analyzed four types of genetic markers (including nuclear and mitochondrial markers) to assess their utility in detecting hybridization events between Magellanic and Humboldt penguins. Genetic assessment of non-introgressed reference samples allowed us to identify three types of informative markers (microsatellites, major histocompatibility complex, and mitochondrial DNA) and detect positive evidence of introgressive hybridization in the wild. Four out of six putative hybrids showed positive evidence of hybridization, revealed by the detection of Humboldt mitochondrial DNA and Magellanic species-specific alleles from nuclear markers. Bayesian Structure analysis, including samples from the sympatric region of the species in the southern Pacific Ocean, confirmed the use of nuclear markers for detecting hybridization and genetic admixture of putative hybrids, but revealed relatively low levels of genetic introgression at the population level. These findings provide insights into the role of hybridization in regions of species sympatry and its potential consequences on the levels of genetic introgression, genetic diversity, and conservation of these penguin species.
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Affiliation(s)
- Eric M Hibbets
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Katelyn I Schumacher
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Hannah B Scheppler
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - P Dee Boersma
- Department of Biology, Center for Ecosystem Sentinels, University of Washington, Seattle, WA, 98195, USA
| | - Juan L Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
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4
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Arauco-Shapiro G, Schumacher KI, Boersma D, Bouzat JL. The role of demographic history and selection in shaping genetic diversity of the Galápagos penguin (Spheniscus mendiculus). PLoS One 2020; 15:e0226439. [PMID: 31910443 PMCID: PMC6946592 DOI: 10.1371/journal.pone.0226439] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/26/2019] [Indexed: 11/25/2022] Open
Abstract
Although many studies have documented the effects of demographic bottlenecks on the genetic diversity of natural populations, there is conflicting evidence of the roles that genetic drift and selection may play in driving changes in genetic variation at adaptive loci. We analyzed genetic variation at microsatellite and mitochondrial loci in conjunction with an adaptive MHC class II locus in the Galápagos penguin (Spheniscus mendiculus), a species that has undergone serial demographic bottlenecks associated with El Niño events through its evolutionary history. We compared levels of variation in the Galápagos penguin to those of its congener, the Magellanic penguin (Spheniscus magellanicus), which has consistently maintained a large population size and thus was used as a non-bottlenecked control. The comparison of neutral and adaptive markers in these two demographically distinct species allowed assessment of the potential role of balancing selection in maintaining levels of MHC variation during bottleneck events. Our analysis suggests that the lack of genetic diversity at both neutral and adaptive loci in the Galápagos penguin likely resulted from its restricted range, relatively low abundance, and history of demographic bottlenecks. The Galápagos penguin revealed two MHC alleles, one mitochondrial haplotype, and six alleles across five microsatellite loci, which represents only a small fraction of the diversity detected in Magellanic penguins. Despite the decreased genetic diversity in the Galápagos penguin, results revealed signals of balancing selection at the MHC, which suggest that selection can mitigate some of the effects of genetic drift during bottleneck events. Although Galápagos penguin populations have persisted for a long time, increased frequency of El Niño events due to global climate change, as well as the low diversity exhibited at immunological loci, may put this species at further risk of extinction.
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Affiliation(s)
- Gabriella Arauco-Shapiro
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Katelyn I. Schumacher
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Dee Boersma
- Center for Ecosystem Sentinels and Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Juan L. Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
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5
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Leclaire S, Strandh M, Dell'Ariccia G, Gabirot M, Westerdahl H, Bonadonna F. Plumage microbiota covaries with the major histocompatibility complex in blue petrels. Mol Ecol 2019; 28:833-846. [PMID: 30582649 DOI: 10.1111/mec.14993] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/05/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023]
Abstract
To increase fitness, a wide range of vertebrates preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC) or that have high MHC diversity. Although MHC often can be assessed through olfactory cues, the mechanism by which MHC genes influence odour remains largely unclear. MHC class IIB molecules, which enable recognition and elimination of extracellular bacteria, have been suggested to influence odour indirectly by shaping odour-producing microbiota, i.e. bacterial communities. However, there is little evidence of the predicted covariation between an animal's MHC genotype and its bacterial communities in scent-producing body surfaces. Here, using high-throughput sequencing, we tested the covariation between MHC class IIB genotypes and feather microbiota in the blue petrel (Halobaena caerulea), a seabird with highly developed olfaction that has been suggested to rely on oduor cues during an MHC-based mate choice. First, we show that individuals with similar MHC class IIB profiles also have similar bacterial assemblages in their feathers. Then, we show that individuals with high MHC diversity have less diverse feather microbiota and also a reduced abundance of a bacterium of the genus Arsenophonus, a genus in which some species are symbionts of avian ectoparasites. Our results, showing that feather microbiota covary with MHC, are consistent with the hypothesis that individual MHC genotype may shape the semiochemical-producing microbiota in birds.
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Affiliation(s)
- Sarah Leclaire
- Laboratoire Evolution & Diversité Biologique, UMR 5174 (CNRS, Université Paul Sabatier, ENFA), Toulouse, France.,Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | - Maria Strandh
- Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Gaia Dell'Ariccia
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | - Marianne Gabirot
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | | | - Francesco Bonadonna
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
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6
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Hofmann MJ, Bracamonte SE, Eizaguirre C, Barluenga M. Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids. BMC Genet 2017; 18:15. [PMID: 28201988 PMCID: PMC5310070 DOI: 10.1186/s12863-017-0474-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes. RESULTS Here, we characterized the genes of MHC class IIB chain of the Midas cichlid species complex (Amphilophus cf. citrinellus) including fish from five lakes in Nicaragua. We designed 19 new specific primers anchored in a stepwise fashion in order to detect all alleles present. We obtained 866 genomic DNA (gDNA) sequences from thirteen individuals and 756 additional sequences from complementary DNA (cDNA) of seven of those individuals. We identified 69 distinct alleles with up to 25 alleles per individual. We also found considerable intron length variation and mismatches of alleles detected in cDNA and gDNA suggesting that some loci have undergone pseudogenization. Lastly, we created a model of protein structure homology for each allele and identified their key structural components. CONCLUSIONS Overall, the Midas cichlid has one of the most diverse repertoires of MHC class IIB genes known, which could serve as a powerful tool to elucidate the process of divergent radiations, colonization and speciation in sympatry.
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Affiliation(s)
- Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Seraina E Bracamonte
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker weg 20, 24105, Kiel, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Christophe Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker weg 20, 24105, Kiel, Germany
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006, Madrid, Spain.
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7
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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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8
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Dalton DL, Vermaak E, Roelofse M, Kotze A. Diversity in the Toll-Like Receptor Genes of the African Penguin (Spheniscus demersus). PLoS One 2016; 11:e0163331. [PMID: 27760133 PMCID: PMC5070850 DOI: 10.1371/journal.pone.0163331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/06/2016] [Indexed: 12/24/2022] Open
Abstract
The African penguin, Spheniscus demersus, is listed as Endangered by the IUCN Red List of Threatened Species due to the drastic reduction in population numbers over the last 20 years. To date, the only studies on immunogenetic variation in penguins have been conducted on the major histocompatibility complex (MHC) genes. It was shown in humans that up to half of the genetic variability in immune responses to pathogens are located in non-MHC genes. Toll-like receptors (TLRs) are now increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune region of African penguins similar to that observed in New Zealand robin that has undergone several severe population bottlenecks. Single nucleotide polymorphism (SNP) diversity across TLRs varied between ex situ and in situ penguins with the number of non-synonymous alterations in ex situ populations (n = 14) being reduced in comparison to in situ populations (n = 16). Maintaining adaptive diversity is of vital importance in the assurance populations as these animals may potentially be used in the future for re-introductions. Therefore, this study provides essential data on immune gene diversity in penguins and will assist in providing an additional monitoring tool for African penguin in the wild, as well as to monitor diversity in ex situ populations and to ensure that diversity found in the in situ populations are captured in the assurance populations.
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Affiliation(s)
- Desiré Lee Dalton
- Centre for Conservation Science, National Zoological Gardens of South Africa, Pretoria, Gauteng, South Africa.,Genetics Department, University of the Free State, Bloemfontein, Free State, South Africa
| | - Elaine Vermaak
- Centre for Conservation Science, National Zoological Gardens of South Africa, Pretoria, Gauteng, South Africa
| | - Marli Roelofse
- Centre for Conservation Science, National Zoological Gardens of South Africa, Pretoria, Gauteng, South Africa
| | - Antoinette Kotze
- Centre for Conservation Science, National Zoological Gardens of South Africa, Pretoria, Gauteng, South Africa.,Genetics Department, University of the Free State, Bloemfontein, Free State, South Africa
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9
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Sallaberry‐Pincheira N, González‐Acuña D, Padilla P, Dantas GPM, Luna‐Jorquera G, Frere E, Valdés‐Velásquez A, Vianna JA. Contrasting patterns of selection between MHC I and II across populations of Humboldt and Magellanic penguins. Ecol Evol 2016; 6:7498-7510. [PMID: 28725416 PMCID: PMC5513272 DOI: 10.1002/ece3.2502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/18/2016] [Accepted: 08/28/2016] [Indexed: 12/21/2022] Open
Abstract
The evolutionary and adaptive potential of populations or species facing an emerging infectious disease depends on their genetic diversity in genes, such as the major histocompatibility complex (MHC). In birds, MHC class I deals predominantly with intracellular infections (e.g., viruses) and MHC class II with extracellular infections (e.g., bacteria). Therefore, patterns of MHC I and II diversity may differ between species and across populations of species depending on the relative effect of local and global environmental selective pressures, genetic drift, and gene flow. We hypothesize that high gene flow among populations of Humboldt and Magellanic penguins limits local adaptation in MHC I and MHC II, and signatures of selection differ between markers, locations, and species. We evaluated the MHC I and II diversity using 454 next-generation sequencing of 100 Humboldt and 75 Magellanic penguins from seven different breeding colonies. Higher genetic diversity was observed in MHC I than MHC II for both species, explained by more than one MHC I loci identified. Large population sizes, high gene flow, and/or similar selection pressures maintain diversity but limit local adaptation in MHC I. A pattern of isolation by distance was observed for MHC II for Humboldt penguin suggesting local adaptation, mainly on the northernmost studied locality. Furthermore, trans-species alleles were found due to a recent speciation for the genus or convergent evolution. High MHC I and MHC II gene diversity described is extremely advantageous for the long-term survival of the species.
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Affiliation(s)
- Nicole Sallaberry‐Pincheira
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
- Escuela de Medicina VeterinariaFacultad Ecología y Recursos NaturalesUniversidad Andrés BelloSantiagoChile
| | | | - Pamela Padilla
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
| | | | - Guillermo Luna‐Jorquera
- Universidad Católica del NorteMillenium Nucleus of Ecology and Sustainable Management of Oceanic Islands ESMOICentro de Estudios Avanzados en Zonas Áridas CEAZACoquimboChile
| | - Esteban Frere
- Centro de Investigaciones de Puerto DeseadoUniversidad Nacional de la Patagonia AustralPuerto DeseadoArgentina
| | - Armando Valdés‐Velásquez
- Laboratorio de Estudios en BiodiversidadFacultad de Ciencias Biológicas y FisiológicasUniversidad Peruana Cayetano HerediaLimaPeru
| | - Juliana A. Vianna
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
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10
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Kikkawa E, Tanaka M, Naruse TK, Tsuda TT, Tsuda M, Murata K, Kimura A. Diversity of MHC class I alleles in Spheniscus humboldti. Immunogenetics 2016; 69:113-124. [PMID: 27654451 DOI: 10.1007/s00251-016-0951-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/10/2016] [Indexed: 10/21/2022]
Abstract
The major histocompatibility complex locus (MHC) is a gene region related to immune response and exhibits a remarkably great diversity. We deduced that polymorphisms in MHC genes would help to solve several issues on penguins, including classification, phylogenetic relationship, and conservation. This study aimed to elucidate the structure and diversity of the so far unknown MHC class I gene in a penguin species. The structure of an MHC class I gene from the Humboldt penguin (Spheniscus humboldti) was determined by using an inverse PCR method. We designed PCR primers to directly determine nucleotide sequences of PCR products from the MHC class I gene and to obtain recombinant clones for investigating the diversity of the MHC class I gene in Humboldt penguins. A total of 24 MHC class I allele sequences were obtained from 40 individuals. Polymorphisms were mainly found in exons 2 and 3, as expected from the nature of MHC class I genes in vertebrate species including birds and mammals. Phylogenetic analyses of MHC class I alleles have revealed that the Humboldt penguin is closely related to the Red Knot (Calidris canutus) belonging to Charadriiformes.
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Affiliation(s)
- Eri Kikkawa
- College of Bioresource Sciences, Nihon University, Tokyo, Japan.,Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masafumi Tanaka
- Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Taeko K Naruse
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
| | - Tomi T Tsuda
- Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan.,Human Life Science, Tokushima Bunri University, Tokushima, Japan
| | - Michio Tsuda
- Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Koichi Murata
- College of Bioresource Sciences, Nihon University, Tokyo, Japan
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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11
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Minias P, Bateson ZW, Whittingham LA, Johnson JA, Oyler-McCance S, Dunn PO. Contrasting evolutionary histories of MHC class I and class II loci in grouse--effects of selection and gene conversion. Heredity (Edinb) 2016; 116:466-76. [PMID: 26860199 DOI: 10.1038/hdy.2016.6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/18/2015] [Indexed: 11/09/2022] Open
Abstract
Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.
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Affiliation(s)
- P Minias
- Department of Teacher Training and Biodiversity Studies, University of Łódź, Łódź, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Z W Bateson
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - L A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - J A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, TX, USA
| | - S Oyler-McCance
- Fort Collins Science Center, US Geological Survey, Fort Collins, CO, USA
| | - P O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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12
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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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13
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Characterization of MHC class II genes in the critically endangered European eel (Anguilla anguilla). CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0501-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Bracamonte SE, Smith S, Hammer M, Pavey SA, Sunnucks P, Beheregaray LB. Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations. FISH & SHELLFISH IMMUNOLOGY 2015; 46:468-476. [PMID: 26093210 DOI: 10.1016/j.fsi.2015.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/04/2015] [Accepted: 06/07/2015] [Indexed: 06/04/2023]
Abstract
Genetic diversity is an essential aspect of species viability, and assessments of neutral genetic diversity are regularly implemented in captive breeding and conservation programs. Despite their importance, information from adaptive markers is rarely included in such programs. A promising marker of significance in fitness and adaptive potential is the major histocompatibility complex (MHC), a key component of the adaptive immune system. Populations of Australian freshwater fishes are generally declining in numbers due to human impacts and the introduction of exotic species, a scenario of particular concern for members of the family Percichthyidae, several of which are listed as nationally vulnerable or endangered, and hence subject to management plans, captive breeding, and restoration plans. We used a next-generation sequencing approach to characterize the MHC IIB locus and provide a conservative description of its levels of diversity in four endangered percichthyids: Gadopsis marmoratus, Macquaria australasica, Nannoperca australis, and Nannoperca obscura. Evidence is presented for a duplicated MHC IIB locus, positively selected sites and recombination of MHC alleles. Relatively moderate levels of diversity were detected in the four species, as well as in different ecotypes within each species. Phylogenetic analyses revealed genus specific clustering of alleles and no allele sharing among species. There were also no shared alleles observed between two ecotypes within G. marmoratus and within M. australasica, which might be indicative of ecologically-driven divergence and/or long divergence times. This represents the first characterization and assessment of MHC diversity for Percichthyidae, and also for Australian freshwater fishes in general, providing key genetic resources for a vertebrate group of increasing conservation concern.
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Affiliation(s)
- Seraina E Bracamonte
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Steve Smith
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Michael Hammer
- Evolutionary Biology Unit, South Australian Museum, North Terrace Adelaide, South Australia 5000 and Curator of Fishes, Museum and Art Gallery of the Northern Territory, PO Box 4646, Darwin, Northern Territory 0801, Australia
| | - Scott A Pavey
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec QC G1V 0A6, Canada
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne 3800, Victoria, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia.
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15
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Kohyama TI, Omote K, Nishida C, Takenaka T, Saito K, Fujimoto S, Masuda R. Spatial and temporal variation at major histocompatibility complex class IIB genes in the endangered Blakiston's fish owl. ZOOLOGICAL LETTERS 2015; 1:13. [PMID: 26605058 PMCID: PMC4657285 DOI: 10.1186/s40851-015-0013-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/25/2015] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Quantifying intraspecific genetic variation in functionally important genes, such as those of the major histocompatibility complex (MHC), is important in the establishment of conservation plans for endangered species. The MHC genes play a crucial role in the vertebrate immune system and generally show high levels of diversity, which is likely due to pathogen-driven balancing selection. The endangered Blakiston's fish owl (Bubo blakistoni) has suffered marked population declines on Hokkaido Island, Japan, during the past several decades due to human-induced habitat loss and fragmentation. We investigated the spatial and temporal patterns of genetic diversity in MHC class IIβ genes in Blakiston's fish owl, using massively parallel pyrosequencing. RESULTS We found that the Blakiston's fish owl genome contains at least eight MHC class IIβ loci, indicating recent gene duplications. An analysis of sequence polymorphism provided evidence that balancing selection acted in the past. The level of MHC variation, however, was low in the current fish owl populations in Hokkaido: only 19 alleles were identified from 174 individuals. We detected considerable spatial differences in MHC diversity among the geographically isolated populations. We also detected a decline of MHC diversity in some local populations during the past decades. CONCLUSIONS Our study demonstrated that the current spatial patterns of MHC variation in Blakiston's fish owl populations have been shaped by loss of variation due to the decline and fragmentation of populations, and that the short-term effects of genetic drift have counteracted the long-term effects of balancing selection.
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Affiliation(s)
- Tetsuo I Kohyama
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Keita Omote
- />Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Chizuko Nishida
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Takeshi Takenaka
- />FILIN, Hachiken 2 Jo Nishi 2, Nishi-ku, Sapporo 063-0842 Japan
| | - Keisuke Saito
- />Institute for Raptor Biomedicine, Kushiro, 084-0922 Japan
| | | | - Ryuichi Masuda
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
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Dearborn DC, Gager AB, Gilmour ME, McArthur AG, Hinerfeld DA, Mauck RA. Non-neutral evolution and reciprocal monophyly of two expressed Mhc class II B genes in Leach’s storm-petrel. Immunogenetics 2014; 67:111-23. [DOI: 10.1007/s00251-014-0813-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/30/2014] [Indexed: 12/21/2022]
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17
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Key FM, Teixeira JC, de Filippo C, Andrés AM. Advantageous diversity maintained by balancing selection in humans. Curr Opin Genet Dev 2014; 29:45-51. [PMID: 25173959 DOI: 10.1016/j.gde.2014.08.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 07/30/2014] [Accepted: 08/02/2014] [Indexed: 11/16/2022]
Abstract
Most human polymorphisms are neutral or slightly deleterious, but some genetic variation is advantageous and maintained in populations by balancing selection. Considered a rarity and overlooked for years, balanced polymorphisms have recently received renewed attention with several lines of evidence showing their relevance in human evolution. From theoretical work on its role in adaptation to empirical studies that identify its targets, recent developments have showed that balancing selection is more prevalent than previously thought. Here we review these developments and discuss their implications in our understanding of the influence of balancing selection in human evolution. We also review existing evidence on the biological functions that benefit most from advantageous diversity, and the functional consequences of these variants. Overall, we argue that balancing selection must be considered an important selective force in human evolution.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - João C Teixeira
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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18
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Liu HY, Xue F, Wan QH, Ge YF. MHC Class II Genes in the Endangered Hainan Eld's Deer (Cervus eldi hainanus). J Hered 2013; 104:874-80. [DOI: 10.1093/jhered/est062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Yao YF, Zhao JJ, Dai QX, Li JY, Zhou L, Wang YT, Ni QY, Zhang MW, Xu HL. Identification and characterization of the major histocompatibility complex class II DQB (MhcMath-DQB1) alleles in Tibetan macaques (Macaca thibetana). ACTA ACUST UNITED AC 2013; 82:113-21. [PMID: 23745600 DOI: 10.1111/tan.12145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/25/2013] [Accepted: 05/19/2013] [Indexed: 11/26/2022]
Abstract
Tibetan macaque (Macaca thibetana), an endangered primate species endemic to China, have been used as experimental animal model for various human diseases. Major histocompatibility complex (MHC) genes play a crucial role in the susceptibility and/or resistance to many human diseases, but little is known about Tibetan macaques. To gain an insight into the MHC background and to facilitate the experimental use of Tibetan macaques, the second exon of Mhc-DQB1 gene was sequenced in a cohort of wild Tibetan macaques living in the Sichuan province of China. A total of 23 MhcMath-DQB1 alleles were identified for the first time, illustrating a marked allelic polymorphism at the DQB1 locus for these macaques. Most of the sequences (74%) observed in this study belong to DQB1*06 (9 alleles) and DQB1*18 (8 alleles) lineages, and the rest (26%) belong to DQB1*15 (3 alleles) and DQB1*17 (3 alleles) lineages. The most frequent alleles detected among these macaques were MhcMath-DQB1*15:02:02 (17.9%), followed by Math-DQB1*06:06, 17:03 and 18:01, which were detected in 9 (16.1%) of the monkeys, respectively. Non-synonymous substitutions occurred at a significantly higher frequency than synonymous substitutions in the peptide-binding region, suggesting balancing selection for maintaining polymorphisms at the MHC class II DQB1 locus. Phylogenetic analyses confirms the trans-species model of evolution of the Mhc-DQB1 genes in non-human primates, and in particular, the extensive allele sharing is observed between Tibetan and other macaque species.
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Affiliation(s)
- Y-F Yao
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
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20
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Gohli J, Anmarkrud JA, Johnsen A, Kleven O, Borge T, Lifjeld JT. FEMALE PROMISCUITY IS POSITIVELY ASSOCIATED WITH NEUTRAL AND SELECTED GENETIC DIVERSITY IN PASSERINE BIRDS. Evolution 2013; 67:1406-19. [DOI: 10.1111/evo.12045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 12/17/2012] [Indexed: 12/16/2022]
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21
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Knafler GJ, Clark JA, Boersma PD, Bouzat JL. MHC diversity and mate choice in the magellanic penguin, Spheniscus magellanicus. ACTA ACUST UNITED AC 2012; 103:759-68. [PMID: 22952272 DOI: 10.1093/jhered/ess054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We estimated levels of diversity at the major histocompatibility complex (MHC) class II DRß1 gene in 50 breeding pairs of the Magellanic penguin and compared those to estimates from Humboldt and Galapagos penguins. We tested for positive selection and 2 conditions required for the evolution of MHC-based disassortative mating: 1) greater MHC diversity between breeding pairs compared to random mating, and 2) associations between MHC genotype and fitness. Cloning and sequencing of the DRß1 gene showed that Magellanic penguins had higher levels of genetic variation than Galapagos and Humboldt penguins. Sequence analysis revealed 45 alleles with 3.6% average proportion of nucleotide differences, nucleotide diversity of 0.030, and observed heterozygosity of 0.770. A gene phylogeny showed 9 allelic lineages with interspersed DRß1 sequences from Humboldt and Galapagos penguins, indicating ancestral polymorphisms. d (N)/d (S) ratios revealed evidence for positive selection. Analysis of breeding pairs showed no disassortative mating preferences. Significant MHC genotype/fitness associations in females suggest, however, that selection for pathogen resistance plays a more important role than mate choice in maintaining diversity at the MHC in the Magellanic penguin. The differential effect of MHC heterozygosity on fitness between the sexes is likely associated with the relative role of hatching and fledging rates as reliable indicators of overall fitness in males and females.
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22
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Independent evolution of functional MHC class II DRB genes in New World bat species. Immunogenetics 2012; 64:535-47. [PMID: 22426641 DOI: 10.1007/s00251-012-0609-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 02/23/2012] [Indexed: 12/21/2022]
Abstract
Genes of the major histocompatibility complex (MHC) play a pivotal role in the vertebrate immune system and are attractive markers for functional, fitness-related, genetic variation. Although bats (Chiroptera) represent the second largest mammalian order and are prone to various emerging infectious diseases, little is known about MHC evolution in bats. In the present study, we examined expressed MHC class II DRB sequences (exons 1 to 4) of New World bat species, Saccopteryx bilineata, Carollia perspicillata, Noctilio albiventris and Noctilio leporinus (only exon 2). We found a wide range of copy number variation of DRB loci with one locus detected in the genus Noctilio and up to ten functional loci observed in S. bilineata. Sequence variation between alleles of the same taxa was high with evidence for positive selection. We found statistical support for recombination or gene conversion events among sequences within the same but not between bat species. Phylogenetic relationships among DRB alleles provided strong evidence for independent evolution of the functional MHC class II DRB genes in the three investigated species, either by recent gene duplication, or homogenization of duplicated loci by frequent gene conversion events. Phylogenetic analysis of all available chiropteran DRB exon 2 sequences confirmed their monophyletic origin within families, but revealed a possible trans-species mode of evolution pattern in congeneric bat species, e.g. within the genera Noctilio and Myotis. This is the first study investigating phylogenetic relationships of MHC genes within bats and therefore contributes to a better understanding of MHC evolution in one of the most dominant mammalian order.
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23
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Evidence for evolutionary convergence at MHC in two broadly distributed mesocarnivores. Immunogenetics 2011; 64:289-301. [DOI: 10.1007/s00251-011-0588-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/31/2011] [Indexed: 12/21/2022]
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Bollmer JL, Hull JM, Ernest HB, Sarasola JH, Parker PG. Reduced MHC and neutral variation in the Galápagos hawk, an island endemic. BMC Evol Biol 2011; 11:143. [PMID: 21612651 PMCID: PMC3118149 DOI: 10.1186/1471-2148-11-143] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 05/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genes at the major histocompatibility complex (MHC) are known for high levels of polymorphism maintained by balancing selection. In small or bottlenecked populations, however, genetic drift may be strong enough to overwhelm the effect of balancing selection, resulting in reduced MHC variability. In this study we investigated MHC evolution in two recently diverged bird species: the endemic Galápagos hawk (Buteo galapagoensis), which occurs in small, isolated island populations, and its widespread mainland relative, the Swainson's hawk (B. swainsoni). RESULTS We amplified at least two MHC class II B gene copies in each species. We recovered only three different sequences from 32 Galápagos hawks, while we amplified 20 unique sequences in 20 Swainson's hawks. Most of the sequences clustered into two groups in a phylogenetic network, with one group likely representing pseudogenes or nonclassical loci. Neutral genetic diversity at 17 microsatellite loci was also reduced in the Galápagos hawk compared to the Swainson's hawk. CONCLUSIONS The corresponding loss in neutral diversity suggests that the reduced variability present at Galápagos hawk MHC class II B genes compared to the Swainson's hawk is primarily due to a founder event followed by ongoing genetic drift in small populations. However, purifying selection could also explain the low number of MHC alleles present. This lack of variation at genes involved in the adaptive immune response could be cause for concern should novel diseases reach the archipelago.
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Affiliation(s)
- Jennifer L Bollmer
- Department of Biology, University of Missouri-St. Louis, One University Boulevard, St. Louis, MO 63121, USA
- Department of Biological Sciences, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, WI 53201, USA
| | - Joshua M Hull
- Wildlife and Ecology Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA
- Department of Animal Science, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Holly B Ernest
- Wildlife and Ecology Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - José H Sarasola
- Department of Evolutionary Ecology, Estación Biológica de Doñana, Avda. Américo Vespucio, 41092 Sevilla, Spain
| | - Patricia G Parker
- Department of Biology, University of Missouri-St. Louis, One University Boulevard, St. Louis, MO 63121, USA
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25
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Strandh M, Lannefors M, Bonadonna F, Westerdahl H. Characterization of MHC class I and II genes in a subantarctic seabird, the blue petrel, Halobaena caerulea (Procellariiformes). Immunogenetics 2011; 63:653-66. [PMID: 21607694 DOI: 10.1007/s00251-011-0534-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Accepted: 05/09/2011] [Indexed: 12/24/2022]
Abstract
The great polymorphism observed in the major histocompatibility complex (MHC) genes is thought to be maintained by pathogen-mediated selection possibly combined with MHC-disassortative mating, guided by MHC-determined olfactory cues. Here, we partly characterize the MHC class I and II B of the blue petrel, Halobaena caerulea (Procellariiformes), a bird with significant olfactory abilities that lives under presumably low pathogen burdens in Subantarctica. Blue petrels are long-lived, monogamous birds which suggest the necessity of an accurate mate choice process. The species is ancestral to songbirds (Passeriformes; many MHC loci), although not to gamefowls (Galliformes; few MHC loci). Considering the phylogenetic relationships and the low subantarctic pathogen burden, we expected few rather than many MHC loci in the blue petrel. However, when we analysed partial MHC class I and class II B cDNA and gDNA sequences we found evidence for as many as at least eight MHC class I loci and at least two class II B loci. These class I and II B sequences showed classical MHC characteristics, e.g. high nucleotide diversity, especially in putative peptide-binding regions where signatures of positive selection was detected. Trans-species polymorphism was found between MHC class II B sequences of the blue petrel and those of thin-billed prion, Pachyptila belcheri, two species that diverged ∼25 MYA. The observed MHC allele richness in the blue petrel may well serve as a basis for mate choice, especially since olfactory discrimination of MHC types may be possible in this species.
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Affiliation(s)
- Maria Strandh
- Behavioral Ecology Group, CEFE-CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France.
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26
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Characterisation of class II B MHC genes from a ratite bird, the little spotted kiwi (Apteryx owenii). Immunogenetics 2011; 63:223-33. [PMID: 21221966 DOI: 10.1007/s00251-010-0503-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Accepted: 12/11/2010] [Indexed: 12/15/2022]
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27
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Miller HC, Allendorf F, Daugherty CH. Genetic diversity and differentiation at MHC genes in island populations of tuatara (Sphenodon spp.). Mol Ecol 2010; 19:3894-908. [PMID: 20723045 DOI: 10.1111/j.1365-294x.2010.04771.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Neutral genetic markers are commonly used to understand the effects of fragmentation and population bottlenecks on genetic variation in threatened species. Although neutral markers are useful for inferring population history, the analysis of functional genes is required to determine the significance of any observed geographical differences in variation. The genes of the major histocompatibility complex (MHC) are well-known examples of genes of adaptive significance and are particularly relevant to conservation because of their role in pathogen resistance. In this study, we survey diversity at MHC class I loci across a range of tuatara populations. We compare the levels of MHC variation with that observed at neutral microsatellite markers to determine the relative roles of balancing selection, diversifying selection and genetic drift in shaping patterns of MHC variation in isolated populations. In general, levels of MHC variation within tuatara populations are concordant with microsatellite variation. Tuatara populations are highly differentiated at MHC genes, particularly between the northern and Cook Strait regions, and a trend towards diversifying selection across populations was observed. However, overall our results indicate that population bottlenecks and isolation have a larger influence on patterns of MHC variation in tuatara populations than selection.
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Affiliation(s)
- Hilary C Miller
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
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28
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Burri R, Salamin N, Studer RA, Roulin A, Fumagalli L. Adaptive Divergence of Ancient Gene Duplicates in the Avian MHC Class II. Mol Biol Evol 2010; 27:2360-74. [DOI: 10.1093/molbev/msq120] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Anmarkrud JA, Johnsen A, Bachmann L, Lifjeld JT. Ancestral polymorphism in exon 2 of bluethroat (Luscinia svecica) MHC class II B genes. J Evol Biol 2010; 23:1206-17. [PMID: 20456568 DOI: 10.1111/j.1420-9101.2010.01999.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The genes of the major histocompatibility complex (MHC) are important model genes for understanding selective forces in evolution. Here, we document, using a cloning and sequencing approach, high polymorphism at the exon 2 of the MHC class II B (MHCIIB) genes in the bluethroat (Luscinia svecica); a minimum of 61 unique alleles were detected in 20 individuals, and at least 11 functional loci. In addition, several pseudogenes were revealed. The specimens originated from three different bluethroat subspecies (azuricollis, cyanecula and svecica), and we also analysed four specimens of the closely related thrush nightingale (L. luscinia) for comparison. Phylogenetic analyses of the functional alleles revealed 258 equally parsimonious trees with poor statistical support for the majority of nodes. The distribution of the sequences in the trees point to an ancestral origin of the polymorphism in MHC class II B genes, a portion of which predated the phylogenetic split between the bluethroat and the thrush nightingale. Strong signatures of balancing selection were uncovered for the codons coding for the peptide-binding residues of the functional MHCIIB exon 2 alleles. Our results highlight the importance of duplication and recombination events for shaping passerine MHC and give insights in the evolutionary dynamics of MHC variation among closely related taxa.
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Affiliation(s)
- Jarl A Anmarkrud
- National Centre for Biosystematics, Natural History Museum, University of Oslo, Blindern, Oslo, Norway.
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30
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Bollmer JL, Dunn PO, Whittingham LA, Wimpee C. Extensive MHC Class II B Gene Duplication in a Passerine, the Common Yellowthroat (Geothlypis trichas). J Hered 2010; 101:448-60. [PMID: 20200139 DOI: 10.1093/jhered/esq018] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Jennifer L Bollmer
- Department of Biological Sciences, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA.
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31
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Affiliation(s)
- W. BABIK
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30‐387 Kraków, Poland
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