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Jia Y, Fu Q, Li B, Xu Y, Tariq A. Polymorphism analysis of major histocompatibility complex (MHC) DQB gene in the Asiatic black bear (Ursus thibetanus). MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Sci Rep 2022; 12:17933. [PMID: 36289307 PMCID: PMC9606363 DOI: 10.1038/s41598-022-21658-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/29/2022] [Indexed: 01/20/2023] Open
Abstract
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
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Sá ALAD, Baker PKB, Breaux B, Oliveira JM, Klautau AGCDM, Legatzki K, Luna FDO, Attademo FLN, Hunter ME, Criscitiello MF, Schneider MPC, Sena LDS. Novel insights on aquatic mammal MHC evolution: Evidence from manatee DQB diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 132:104398. [PMID: 35307479 DOI: 10.1016/j.dci.2022.104398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The low diversity in marine mammal major histocompatibility complex (MHC) appears to support the hypothesis of reduced pathogen selective pressure in aquatic systems compared to terrestrial environments. However, the lack of characterization of the aquatic and evolutionarily distant Sirenia precludes drawing more generalized conclusions. Therefore, we aimed to characterize the MHC DQB diversity of two manatee species and compare it with those reported for marine mammals. Our results identified 12 and 6 alleles in T. inunguis and T. manatus, respectively. Alleles show high rates of nonsynonymous substitutions, suggesting loci are evolving under positive selection. Among aquatic mammals, Pinnipeda DQB had smaller numbers of alleles, higher synonymous substitution rate, and a dN/dS ratio closer to 1, suggesting it may be evolving under more relaxed selection compared to fully aquatic mammals. This contradicts one of the predictions of the hypothesis that aquatic environments impose reduced pathogen pressure to mammalian immune system. These results suggest that the unique evolutionary trajectories of mammalian MHC may impose challenges in drawing ecoevolutionary conclusions from comparisons across distant vertebrate lineages.
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Affiliation(s)
- André Luiz Alves de Sá
- Laboratory of Applied Genetics (LGA), Socio-Environmental and Water Resources Institute (ISARH), Federal Rural University of the Amazon (UFRA), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil; Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
| | - Pamela Ketrya Barreiros Baker
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil
| | - Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Jairo Moura Oliveira
- Zoological Park of Santarém - Universidade da Amazônia (ZOOUNAMA), R. Belo Horizonte, 68030-150, Santarém, PA, Brazil
| | - Alex Garcia Cavalleiro de Macedo Klautau
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte (CEPNOR), Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil
| | - Kristian Legatzki
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte (CEPNOR), Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil
| | - Fábia de Oliveira Luna
- National Center for Research and Conservation of Aquatic Mammals, Chico Mendes Institute for Biodiversity Conservation (CMA), ICMBio, Rua Alexandre Herculano 197, 11050-031, Santos, SP, Brazil
| | - Fernanda Löffler Niemeyer Attademo
- National Center for Research and Conservation of Aquatic Mammals, Chico Mendes Institute for Biodiversity Conservation (CMA), ICMBio, Rua Alexandre Herculano 197, 11050-031, Santos, SP, Brazil
| | - Margaret Elizabeth Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA.
| | - Michael Frederick Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
| | - Leonardo Dos Santos Sena
- Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
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Mishra SK, Niranjan SK, Singh R, Kumar P, Kumar SL, Banerjee B, Kataria RS. Diversity analysis at MHC class II DQA locus in buffalo (Bubalus bubalis) indicates extensive duplication and trans-species evolution. Genomics 2020; 112:4417-4426. [PMID: 32738270 DOI: 10.1016/j.ygeno.2020.07.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/06/2020] [Accepted: 07/26/2020] [Indexed: 12/15/2022]
Abstract
Variation at MHC Class II-DQA locus in riverine and swamp buffaloes (Bubu) has been explored in this study. Through sequencing of buffalo DQA, 48 nucleotide variants identified from 17 individuals, reporting 42 novel alleles, including one pseudogene. Individual animal displayed two to seven variants, suggesting the presence of more than two Bubu-DQA loci, as an evidence of extensive duplication. dN values were found to be higher than dS values at peptide binding sites, separately for riverine and swamp buffaloes, indicating locus being under positive selection. Evolutionary analysis revealed numerous trans-species polymorphism with alleles from water buffalo assigned to at least three different loci (Bubu-DQA1, DQA2, DQA3). Alleles of both the sub-species intermixed within the cluster, showing convergent evolution of MHC alleles in bovines. The results thus suggest that both riverine and swamp buffaloes share con-current arrangement of DQA region, comparable to cattle in terms of copy number and population polymorphism.
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Affiliation(s)
- Shailendra Kumar Mishra
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India; School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India.
| | - Ravinder Singh
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - Prem Kumar
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - S Lava Kumar
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India
| | - Bhaswati Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201310, India
| | - Ranjit Singh Kataria
- ICAR-National Bureau of Animal Genetic Resources, GT Road By-Pass, Karnal, 132 001, Haryana, India.
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Becker DJ, Albery GF, Kessler MK, Lunn TJ, Falvo CA, Czirják GÁ, Martin LB, Plowright RK. Macroimmunology: The drivers and consequences of spatial patterns in wildlife immune defence. J Anim Ecol 2020; 89:972-995. [PMID: 31856309 DOI: 10.1111/1365-2656.13166] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 11/06/2019] [Indexed: 01/26/2023]
Abstract
The prevalence and intensity of parasites in wild hosts varies across space and is a key determinant of infection risk in humans, domestic animals and threatened wildlife. Because the immune system serves as the primary barrier to infection, replication and transmission following exposure, we here consider the environmental drivers of immunity. Spatial variation in parasite pressure, abiotic and biotic conditions, and anthropogenic factors can all shape immunity across spatial scales. Identifying the most important spatial drivers of immunity could help pre-empt infectious disease risks, especially in the context of how large-scale factors such as urbanization affect defence by changing environmental conditions. We provide a synthesis of how to apply macroecological approaches to the study of ecoimmunology (i.e. macroimmunology). We first review spatial factors that could generate spatial variation in defence, highlighting the need for large-scale studies that can differentiate competing environmental predictors of immunity and detailing contexts where this approach might be favoured over small-scale experimental studies. We next conduct a systematic review of the literature to assess the frequency of spatial studies and to classify them according to taxa, immune measures, spatial replication and extent, and statistical methods. We review 210 ecoimmunology studies sampling multiple host populations. We show that whereas spatial approaches are relatively common, spatial replication is generally low and unlikely to provide sufficient environmental variation or power to differentiate competing spatial hypotheses. We also highlight statistical biases in macroimmunology, in that few studies characterize and account for spatial dependence statistically, potentially affecting inferences for the relationships between environmental conditions and immune defence. We use these findings to describe tools from geostatistics and spatial modelling that can improve inference about the associations between environmental and immunological variation. In particular, we emphasize exploratory tools that can guide spatial sampling and highlight the need for greater use of mixed-effects models that account for spatial variability while also allowing researchers to account for both individual- and habitat-level covariates. We finally discuss future research priorities for macroimmunology, including focusing on latitudinal gradients, range expansions and urbanization as being especially amenable to large-scale spatial approaches. Methodologically, we highlight critical opportunities posed by assessing spatial variation in host tolerance, using metagenomics to quantify spatial variation in parasite pressure, coupling large-scale field studies with small-scale field experiments and longitudinal approaches, and applying statistical tools from macroecology and meta-analysis to identify generalizable spatial patterns. Such work will facilitate scaling ecoimmunology from individual- to habitat-level insights about the drivers of immune defence and help predict where environmental change may most alter infectious disease risk.
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Affiliation(s)
- Daniel J Becker
- Department of Biology, Indiana University, Bloomington, IN, USA.,Center for the Ecology of Infectious Disease, University of Georgia, Athens, GA, USA
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA
| | | | - Tamika J Lunn
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Caylee A Falvo
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Gábor Á Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Lynn B Martin
- Department of Global and Planetary Health, University of South Florida, Tampa, FL, USA
| | - Raina K Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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Hong Y, Kim KS, Kimura J, Kauhala K, Voloshina I, Goncharuk MS, Yu L, Zhang YP, Sashika M, Lee H, Min MS. Genetic Diversity and Population Structure of East Asian Raccoon Dog (Nyctereutes procyonoides): Genetic Features in Central and Marginal Populations. Zoolog Sci 2019; 35:249-259. [PMID: 29882500 DOI: 10.2108/zs170140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The raccoon dog (Nyctereutes procyonoides) is endemic to East Asia but has been introduced in Europe. Its high adaptability enabled its rapid colonization of European countries, where population growth has been raising concerns regarding ecosystem disturbance and the spread of zoonotic diseases. The genetic diversity and structure of endemic, source, and introduced populations from seven locations across South Korea, China, Russian Far East, Finland (spread to Finland after introduction to European part of Russia from Russian Far East), Vietnam, and Japan (Honshu and Hokkaido) were examined based on 16 microsatellite loci. Two major and significantly different (FST = 0.236) genetic clusters were found: continental (South Korean, Chinese, Russian, Finnish, and Vietnamese) and island (Japanese) populations. The continental raccoon dog population comprises three subpopulations (Chinese_Russian_Finnish, South Korean, and Vietnamese) and the Japanese population consists of Honshu and Hokkaido subpopulations. The genetic diversity and geographic structure of raccoon dogs in East Asia has been influenced by natural barriers to gene flow and reveals a typical central-marginal trend in genetic diversity (continental vs. island, and central vs. marginal or source vs. introduced within continental populations). The detected differences between continental and island populations agree with those reported in previous studies that considered these populations as different species.
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Affiliation(s)
- YoonJee Hong
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kyung Seok Kim
- 2 Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA 50011, USA
| | - Junpei Kimura
- 3 Laboratory of Anatomy and Cell Biology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kaarina Kauhala
- 4 Luonnonvarakeskus (Luke)/Natural Resources Institute Finland, Itäinen Pitkäkatu 3 A, FI-20520 Turku, Finland
| | - Inna Voloshina
- 5 Lazovsky State Nature Reserve, Lazo, Primorsky Krai 692980, Russia
| | - Mikhail S Goncharuk
- 6 Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom
| | - Li Yu
- 7 State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Ya-Ping Zhang
- 8 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Mariko Sashika
- 9 Laboratory of Wildlife Biology and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Hang Lee
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Mi-Sook Min
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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Manczinger M, Boross G, Kemény L, Müller V, Lenz TL, Papp B, Pál C. Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations. PLoS Biol 2019; 17:e3000131. [PMID: 30703088 PMCID: PMC6372212 DOI: 10.1371/journal.pbio.3000131] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/12/2019] [Accepted: 01/15/2019] [Indexed: 02/03/2023] Open
Abstract
Central players of the adaptive immune system are the groups of proteins encoded in the major histocompatibility complex (MHC), which shape the immune response against pathogens and tolerance to self-peptides. The corresponding genomic region is of particular interest, as it harbors more disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Certain MHC molecules can bind to a much wider range of epitopes than others, but the functional implication of such an elevated epitope-binding repertoire has remained largely unclear. It has been suggested that by recognizing more peptide segments, such promiscuous MHC molecules promote immune response against a broader range of pathogens. If so, the geographical distribution of MHC promiscuity level should be shaped by pathogen diversity. Three lines of evidence support the hypothesis. First, we found that in pathogen-rich geographical regions, humans are more likely to carry highly promiscuous MHC class II DRB1 alleles. Second, the switch between specialist and generalist antigen presentation has occurred repeatedly and in a rapid manner during human evolution. Third, molecular positions that define promiscuity level of MHC class II molecules are especially diverse and are under positive selection in human populations. Taken together, our work indicates that pathogen load maintains generalist adaptive immune recognition, with implications for medical genetics and epidemiology. Whereas specialist major histocompatibility complex (MHC) molecules initiate immune response against only relatively few pathogens, generalists provide protection against a broad range. Accordingly, this study shows that the geographical distribution of generalist MHC alleles in human populations reflects exposure to diverse infectious diseases. Variation in the human genome influences our susceptibility to infectious diseases, but the causal link between disease and underlying mutation often remains enigmatic. Major histocompatibility complex II (MHC class II) molecules shape both our immune response against pathogens and our tolerance of self-peptides. The genomic region that encodes MHC molecules is of particular interest, as it is home to more genetic disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Here, we propose that MHC class II molecules can be categorized into two major types; specialists initiate effective immune response against only relatively few pathogens, while generalists provide protection against a broad range of pathogens. As support, we demonstrate that generalist MHC class II variants are more prevalent in human populations residing in pathogen-rich areas.
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Affiliation(s)
- Máté Manczinger
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
- MTA-SZTE Dermatological Research Group, University of Szeged, Szeged, Hungary
| | - Gábor Boross
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Lajos Kemény
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
- MTA-SZTE Dermatological Research Group, University of Szeged, Szeged, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Tobias L. Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail: (CP); (BP)
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail: (CP); (BP)
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Arbanasić H, Konjević D, Vranković L, Bujanić M, Stipoljev S, Balažin M, Šprem N, Škorić D, Galov A. Evolution of MHC class II SLA-DRB1 locus in the Croatian wild boar (Sus scrofa) implies duplication and weak signals of positive selection. Anim Genet 2018; 50:33-41. [PMID: 30357873 DOI: 10.1111/age.12734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2018] [Indexed: 12/22/2022]
Abstract
The wild boar is an ancestor of the domestic pig and an important game species with the widest geographical range of all ungulates. Although a large amount of data are available on major histocompatibility complex (MHC) variability in domestic pigs, only a few studies have been performed on wild boars. Due to their crucial role in appropriate immune responses and extreme polymorphism, MHC genes represent some of the best candidates for studying the processes of adaptive evolution. Here, we present the results on the variability and evolution of the entire MHC class II SLA-DRB1 locus exon 2 in 133 wild boars from Croatia. Using direct sequencing and cloning methods, we identified 20 SLA-DRB1 alleles, including eight new variants, with notable divergence. In some individuals, we documented functional locus duplication, and SLA-DRB1*04:10 was identified as the allele involved in the duplication. The expression of a duplicated locus was confirmed by cloning and sequencing cDNA-derived amplicons. Based on individual genotypes, we were able to assume that alleles SLA-DRB1*04:10 and SLA-DRB1*06:07 are linked as an allelic combination that co-evolves as a two-locus haplotype. Our investigation of evolutionary processes at the SLA-DRB1 locus confirmed the role of intralocus recombination in generating allelic variability, whereas tests of positive selection based on the dN/dS (non-synonymous/synonymous substitution rate ratio) test revealed atypically weak and ambiguous signals.
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Affiliation(s)
- H Arbanasić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - D Konjević
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - L Vranković
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - M Bujanić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - S Stipoljev
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - M Balažin
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - N Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - D Škorić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - A Galov
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
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Mishra SK, Niranjan SK, Banerjee B, Singh R, Kumar P, Kataria RS. Identification of novel allelic variants at the MHC class II DQA
locus in Murrah water buffalo. Anim Genet 2018; 49:497-498. [DOI: 10.1111/age.12704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Shailendra K. Mishra
- ICAR-National Bureau of Animal Genetic Resources; GT Road By-Pass Karnal 132001 Haryana India
- Gautam Buddha University; Yamuna Expressway Gautam Budh Nagar Greater Noida- 201312 Uttar Pradesh India
| | - Saket K. Niranjan
- ICAR-National Bureau of Animal Genetic Resources; GT Road By-Pass Karnal 132001 Haryana India
| | - Bhaswati Banerjee
- Gautam Buddha University; Yamuna Expressway Gautam Budh Nagar Greater Noida- 201312 Uttar Pradesh India
| | - Ravinder Singh
- ICAR-National Bureau of Animal Genetic Resources; GT Road By-Pass Karnal 132001 Haryana India
| | - Prem Kumar
- ICAR-National Bureau of Animal Genetic Resources; GT Road By-Pass Karnal 132001 Haryana India
| | - Ranjit S. Kataria
- ICAR-National Bureau of Animal Genetic Resources; GT Road By-Pass Karnal 132001 Haryana India
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Ishibashi Y, Oi T, Arimoto I, Fujii T, Mamiya K, Nishi N, Sawada S, Tado H, Yamada T. Loss of allelic diversity in the MHC class II DQB gene in western populations of the Japanese black bear Ursus thibetanus japonicus. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0897-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Molecular polymorphism of MHC-DRB gene and genetic diversity analysis of captive forest musk deer (Moschus berezovskii). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Jaeger CP, Duvall MR, Swanson BJ, Phillips CA, Dreslik MJ, Baker SJ, King RB. Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus). Ecol Evol 2016; 6:3991-4003. [PMID: 27516858 PMCID: PMC4874855 DOI: 10.1002/ece3.2159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 01/18/2023] Open
Abstract
Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.
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Affiliation(s)
- Collin P. Jaeger
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinois60115
| | - Melvin R. Duvall
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinois60115
| | - Bradley J. Swanson
- Department of BiologyCentral Michigan UniversityMt. PleasantMichigan48859
| | - Christopher A. Phillips
- Illinois Natural History SurveyUniversity of Illinois Urbana‐ChampaignChampaignIllinois61820
| | - Michael J. Dreslik
- Illinois Natural History SurveyUniversity of Illinois Urbana‐ChampaignChampaignIllinois61820
| | - Sarah J. Baker
- Illinois Natural History SurveyUniversity of Illinois Urbana‐ChampaignChampaignIllinois61820
| | - Richard B. King
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinois60115
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13
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454 screening of individual MHC variation in an endemic island passerine. Immunogenetics 2014; 67:149-62. [PMID: 25515684 PMCID: PMC4325181 DOI: 10.1007/s00251-014-0822-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/28/2014] [Indexed: 11/03/2022]
Abstract
Genes of the major histocompatibility complex (MHC) code for receptors that are central to the adaptive immune response of vertebrates. These genes are therefore important genetic markers with which to study adaptive genetic variation in the wild. Next-generation sequencing (NGS) has increasingly been used in the last decade to genotype the MHC. However, NGS methods are highly prone to sequencing errors, and although several methodologies have been proposed to deal with this, until recently there have been no standard guidelines for the validation of putative MHC alleles. In this study, we used the 454 NGS platform to screen MHC class I exon 3 variation in a population of the island endemic Berthelot's pipit (Anthus berthelotii). We were able to characterise MHC genotypes across 309 individuals with high levels of repeatability. We were also able to determine alleles that had low amplification efficiencies, whose identification within individuals may thus be less reliable. At the population level we found lower levels of MHC diversity in Berthelot's pipit than in its widespread continental sister species the tawny pipit (Anthus campestris), and observed trans-species polymorphism. Using the sequence data, we identified signatures of gene conversion and evidence of maintenance of functionally divergent alleles in Berthelot's pipit. We also detected positive selection at 10 codons. The present study therefore shows that we have an efficient method for screening individual MHC variation across large datasets in Berthelot's pipit, and provides data that can be used in future studies investigating spatio-temporal patterns and scales of selection on the MHC.
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Yasukochi Y, Satta Y. A human-specific allelic group of the MHC DRB1 gene in primates. J Physiol Anthropol 2014; 33:14. [PMID: 24928070 PMCID: PMC4072476 DOI: 10.1186/1880-6805-33-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 05/27/2014] [Indexed: 11/22/2022] Open
Abstract
Background Diversity among human leukocyte antigen (HLA) molecules has been maintained by host-pathogen coevolution over a long period of time. Reflecting this diversity, the HLA loci are the most polymorphic in the human genome. One characteristic of HLA diversity is long-term persistence of allelic lineages, which causes trans-species polymorphisms to be shared among closely related species. Modern humans have disseminated across the world after their exodus from Africa, while chimpanzees have remained in Africa since the speciation event between humans and chimpanzees. It is thought that modern humans have recently acquired resistance to novel pathogens outside Africa. In the present study, we investigated HLA alleles that could contribute to this local adaptation in humans and also studied the contribution of natural selection to human evolution by using molecular data. Results Phylogenetic analysis of HLA-DRB1 genes identified two major groups, HLA Groups A and B. Group A formed a monophyletic clade distinct from DRB1 alleles in other Catarrhini, suggesting that Group A is a human-specific allelic group. Our estimates of divergence time suggested that seven HLA-DRB1 Group A allelic lineages in humans have been maintained since before the speciation event between humans and chimpanzees, while chimpanzees possess only one DRB1 allelic lineage (Patr-DRB1*03), which is a sister group to Group A. Experimental data showed that some Group A alleles bound to peptides derived from human-specific pathogens. Of the Group A alleles, three exist at high frequencies in several local populations outside Africa. Conclusions HLA Group A alleles are likely to have been retained in human lineages for a long period of time and have not expanded since the divergence of humans and chimpanzees. On the other hand, most orthologs of HLA Group A alleles may have been lost in the chimpanzee due to differences in selective pressures. The presence of alleles with high frequency outside of Africa suggests these HLA molecules result from the local adaptations of humans. Our study helps elucidate the mechanism by which the human adaptive immune system has coevolved with pathogens over a long period of time.
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Affiliation(s)
- Yoshiki Yasukochi
- Molecular and Genetic Epidemiology, Faculty of Medicine, University of Tsukuba, 305-8575 Tsukuba, Ibaraki, Japan.
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Chen YY, Zhu Y, Wan QH, Lou JK, Li WJ, Ge YF, Fang SG. Patterns of adaptive and neutral diversity identify the Xiaoxiangling mountains as a refuge for the giant panda. PLoS One 2013; 8:e70229. [PMID: 23894623 PMCID: PMC3716684 DOI: 10.1371/journal.pone.0070229] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 06/18/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic variation plays a significant role in maintaining the evolutionary potential of a species. Comparing the patterns of adaptive and neutral diversity in extant populations is useful for understanding the local adaptations of a species. In this study, we determined the fine-scale genetic structure of 6 extant populations of the giant panda (Ailuropoda melanoleuca) using mtDNA and DNA fingerprints, and then overlaid adaptive variations in 6 functional Aime-MHC class II genes (DRA, DRB3, DQA1, DQA2, DQB1, and DQB2) on this framework. We found that: (1) analysis of the mtDNA and DNA fingerprint-based networks of the 6 populations identified the independent evolutionary histories of the 2 panda subspecies; (2) the basal (ancestral) branches of the fingerprint-based Sichuan-derived network all originated from the smallest Xiaoxiangling (XXL) population, suggesting the status of a glacial refuge in XXL; (3) the MHC variations among the tested populations showed that the XXL population exhibited extraordinary high levels of MHC diversity in allelic richness, which is consistent with the diversity characteristics of a glacial refuge; (4) the phylogenetic tree showed that the basal clades of giant panda DQB sequences were all occupied by XXL-specific sequences, providing evidence for the ancestor-resembling traits of XXL. Finally, we found that the giant panda had many more DQ alleles than DR alleles (33∶13), contrary to other mammals, and that the XXL refuge showed special characteristics in the DQB loci, with 7 DQB members of 9 XXL-unique alleles. Thus, this study identified XXL as a glacial refuge, specifically harboring the most number of primitive DQB alleles.
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Affiliation(s)
- Yi-Yan Chen
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Ying Zhu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Ji-Kang Lou
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Wen-Jing Li
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Yun-Fa Ge
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Sheng-Guo Fang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
- * E-mail:
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