351
|
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.
Collapse
|
352
|
Jan Ejsmond M, Radwan J, Wilson AB. Sexual selection and the evolutionary dynamics of the major histocompatibility complex. Proc Biol Sci 2014; 281:20141662. [PMID: 25339723 PMCID: PMC4213641 DOI: 10.1098/rspb.2014.1662] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/22/2014] [Indexed: 12/27/2022] Open
Abstract
The genes of the major histocompatibility complex (MHC) are a key component of the adaptive immune system and among the most variable loci in the vertebrate genome. Pathogen-mediated natural selection and MHC-based disassortative mating are both thought to structure MHC polymorphism, but their effects have proven difficult to discriminate in natural systems. Using the first model of MHC dynamics incorporating both survival and reproduction, we demonstrate that natural and sexual selection produce distinctive signatures of MHC allelic diversity with critical implications for understanding host-pathogen dynamics. While natural selection produces the Red Queen dynamics characteristic of host-parasite interactions, disassortative mating stabilizes allele frequencies, damping major fluctuations in dominant alleles and protecting functional variants against drift. This subtle difference generates a complex interaction between MHC allelic diversity and population size. In small populations, the stabilizing effects of sexual selection moderate the effects of drift, whereas pathogen-mediated selection accelerates the loss of functionally important genetic diversity. Natural selection enhances MHC allelic variation in larger populations, with the highest levels of diversity generated by the combined action of pathogen-mediated selection and disassortative mating. MHC-based sexual selection may help to explain how functionally important genetic variation can be maintained in populations of conservation concern.
Collapse
Affiliation(s)
- Maciej Jan Ejsmond
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland Department of Arctic Biology, The University Centre in Svalbard, Box 156, 9171 Longyearbyen, Norway
| | - Jacek Radwan
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Anthony B Wilson
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland Department of Biology, Brooklyn College and The Graduate Center, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
| |
Collapse
|
353
|
Kuduk K, Babik W, Bellemain E, Valentini A, Zedrosser A, Taberlet P, Kindberg J, Swenson JE, Radwan J. No evidence for the effect of MHC on male mating success in the brown bear. PLoS One 2014; 9:e113414. [PMID: 25470381 PMCID: PMC4254848 DOI: 10.1371/journal.pone.0113414] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022] Open
Abstract
Mate choice is thought to contribute to the maintenance of the spectacularly high polymorphism of the Major Histocompatibility Complex (MHC) genes, along with balancing selection from parasites, but the relative contribution of the former mechanism is debated. Here, we investigated the association between male MHC genotype and mating success in the brown bear. We analysed fragments of sequences coding for the peptide-binding region of the highly polymorphic MHC class I and class II DRB genes, while controlling for genome-wide effects using a panel of 18 microsatellite markers. Male mating success did not depend on the number of alleles shared with the female or amino-acid distance between potential mates at either locus. Furthermore, we found no indication of female mating preferences for MHC similarity being contingent on the number of alleles the females carried. Finally, we found no significant association between the number of MHC alleles a male carried and his mating success. Thus, our results provided no support for the role of mate choice in shaping MHC polymorphism in the brown bear.
Collapse
Affiliation(s)
- Katarzyna Kuduk
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Eva Bellemain
- SPYGEN, Savoie Technolac - Bât. Koala 17, rue du Lac Saint-André - BP 274, 73375, Le Bourget-du-Lac Cedex, France
| | - Alice Valentini
- SPYGEN, Savoie Technolac - Bât. Koala 17, rue du Lac Saint-André - BP 274, 73375, Le Bourget-du-Lac Cedex, France
| | - Andreas Zedrosser
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway
- Institute for Wildlife Biology and Game Management, University of Natural Resources and Life Sciences, AT-1180, Vienna, Austria
| | - Pierre Taberlet
- CNRS, LECA, F-38000, Grenoble, France
- Université Grenoble Alpes, LECA, F-38000, Grenoble, France
| | - Jonas Kindberg
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Jon E. Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway
- Norwegian Institute for Nature Research, NO-7485, Trondheim, Norway
| | - Jacek Radwan
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
- * E-mail:
| |
Collapse
|
354
|
Real-Monroy MD, Martínez-Méndez N, Ortega J. MHC-DRB Exon 2 Diversity of the Jamaican Fruit-Eating Bat (Artibeus jamaicensis) from Mexico. ACTA CHIROPTEROLOGICA 2014. [DOI: 10.3161/150811014x687260] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
355
|
Radwan J, Kuduk K, Levy E, LeBas N, Babik W. Parasite load and MHC diversity in undisturbed and agriculturally modified habitats of the ornate dragon lizard. Mol Ecol 2014; 23:5966-78. [PMID: 25355141 DOI: 10.1111/mec.12984] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 11/26/2022]
Abstract
Major histocompatibility complex (MHC) gene polymorphism is thought to be driven by host-parasite co-evolution, but the evidence for an association between the selective pressure from parasites and the number of MHC alleles segregating in a population is scarce and inconsistent. Here, we characterized MHC class I polymorphism in a lizard whose habitat preferences (rock outcrops) lead to the formation of well-defined and stable populations. We investigated the association between the load of ticks, which were used as a proxy for the load of pathogens they transmit, and MHC class I polymorphism across populations in two types of habitat: undisturbed reserves and agricultural land. We hypothesized that the association would be positive across undisturbed reserve populations, but across fragmented agricultural land populations, the relationship would be distorted by the loss of MHC variation due to drift. After controlling for habitat, MHC diversity was not associated with tick number, and the habitats did not differ in this respect. Neither did we detect a difference between habitats in the relationship between MHC and neutral diversity, which was positive across all populations. However, there was extensive variation in the number of MHC alleles per individual, and we found that tick number was positively associated with the average number of alleles carried by lizards across reserve populations, but not across populations from disturbed agricultural land. Our results thus indicate that local differences in selection from parasites may contribute to MHC copy number variation within species, but habitat degradation can distort this relationship.
Collapse
Affiliation(s)
- Jacek Radwan
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | | | | | | | | |
Collapse
|
356
|
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]
|
357
|
Mukherjee S, Guha S, Ikeda M, Iwata N, Malhotra AK, Pe'er I, Darvasi A, Lencz T. Excess of homozygosity in the major histocompatibility complex in schizophrenia. Hum Mol Genet 2014; 23:6088-95. [PMID: 24943592 PMCID: PMC4204767 DOI: 10.1093/hmg/ddu308] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 04/11/2014] [Accepted: 06/12/2014] [Indexed: 01/20/2023] Open
Abstract
Genome-wide association studies (GWAS) in schizophrenia have focused on additive allelic effects to identify disease risk loci. In order to examine potential recessive effects, we applied a novel approach to identify regions of excess homozygosity in an ethnically homogenous cohort: 904 schizophrenia cases and 1640 controls drawn from the Ashkenazi Jewish (AJ) population. Genome-wide examination of runs of homozygosity identified an excess in cases localized to the major histocompatibility complex (MHC). To refine this signal, we used the recently developed GERMLINE algorithm to identify chromosomal segments shared identical-by-descent (IBD) and compared homozygosity at such segments in cases and controls. We found a significant excess of homozygosity in schizophrenia cases compared with controls in the MHC (P-value = 0.003). An independent replication cohort of 548 schizophrenia cases from Japan and 542 matched healthy controls demonstrated similar effects. The strongest case-control recessive effects (P = 8.81 × 10(-8)) were localized to a 53-kb region near HLA-A, in a segment encompassing three poorly annotated genes, TRIM10, TRIM15 and TRIM40. At the same time, an adjacent segment in the Class I MHC demonstrated clear additive effects on schizophrenia risk, demonstrating the complexity of association in the MHC and the ability of our IBD approach to refine localization of broad signals derived from conventional GWAS. In sum, homozygosity in the classical MHC region appears to convey significant risk for schizophrenia, consistent with the ecological literature suggesting that homozygosity at the MHC locus may be associated with vulnerability to disease.
Collapse
Affiliation(s)
- Semanti Mukherjee
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA,
| | - Saurav Guha
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA
| | - Masashi Ikeda
- Fujita Health University School of Medicine, 1-98 Kutsukake-cho Dengakugakubo, Toyoake, Aichi 470-1192, Japan
| | - Nakao Iwata
- Fujita Health University School of Medicine, 1-98 Kutsukake-cho Dengakugakubo, Toyoake, Aichi 470-1192, Japan
| | - Anil K Malhotra
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA, Hofstra University School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA and
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Todd Lencz
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA, Hofstra University School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA,
| |
Collapse
|
358
|
Ruiz-López MJ, Monello RJ, Schuttler SG, Lance SL, Gompper ME, Eggert LS. Major Histocompatibility Complex, demographic, and environmental predictors of antibody presence in a free-ranging mammal. INFECTION GENETICS AND EVOLUTION 2014; 28:317-27. [PMID: 25446941 DOI: 10.1016/j.meegid.2014.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/30/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022]
Abstract
Major Histocompatibility Complex (MHC) variability plays a key role in pathogen resistance, but its relative importance compared to environmental and demographic factors that also influence resistance is unknown. We analyzed the MHC II DRB exon 2 for 165 raccoons (Procyon lotor) in Missouri (USA). For each animal we also determined the presence of immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies to two highly virulent pathogens, canine distemper virus (CDV) and parvovirus. We investigated the role of MHC polymorphism and other demographic and environmental factors previously associated with predicting seroconversion. In addition, using an experimental approach, we studied the relative importance of resource availability and contact rates. We found important associations between IgG antibody presence and several MHC alleles and supertypes but not between IgM antibody presence and MHC. No effect of individual MHC diversity was found. For CDV, supertype S8, one allele within S8 (Prlo-DRB(∗)222), and a second allele (Prlo-DRB(∗)204) were positively associated with being IgG+, while supertype S4 and one allele within the supertype (Prlo-DRB(∗)210) were negatively associated with being IgG+. Age, year, and increased food availability were also positively associated with being IgG+, but allele Prlo-DRB(∗)222 was a stronger predictor. For parvovirus, only one MHC allele was negatively associated with being IgG+ and age and site were stronger predictors of seroconversion. Our results show that negative-frequency dependent selection is likely acting on the raccoon MHC and that while the role of MHC in relation to other factors depends on the pathogen of interest, it may be one of the most important factors predicting successful immune response.
Collapse
Affiliation(s)
- María José Ruiz-López
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Ryan J Monello
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Stephanie G Schuttler
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO 65211, USA; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Stacey L Lance
- Savannah River Ecology Laboratory, P O Drawer E, Aiken, SC 29802, USA
| | - Matthew E Gompper
- Department of Fisheries and Wildlife Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Lori S Eggert
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
359
|
Lane-deGraaf KE, Amish SJ, Gardipee F, Jolles A, Luikart G, Ezenwa VO. Signatures of natural and unnatural selection: evidence from an immune system gene in African buffalo. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0658-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
360
|
Pilosof S, Fortuna MA, Cosson JF, Galan M, Kittipong C, Ribas A, Segal E, Krasnov BR, Morand S, Bascompte J. Host-parasite network structure is associated with community-level immunogenetic diversity. Nat Commun 2014; 5:5172. [PMID: 25312328 DOI: 10.1038/ncomms6172] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 09/08/2014] [Indexed: 12/13/2022] Open
Abstract
Genes of the major histocompatibility complex (MHC) encode proteins that recognize foreign antigens and are thus crucial for immune response. In a population of a single host species, parasite-mediated selection drives MHC allelic diversity. However, in a community-wide context, species interactions may modulate selection regimes because the prevalence of a given parasite in a given host may depend on its prevalence in other hosts. By combining network analysis with immunogenetics, we show that host species infected by similar parasites harbour similar alleles with similar frequencies. We further show, using a Bayesian approach, that the probability of mutual occurrence of a functional allele and a parasite in a given host individual is nonrandom and depends on other host-parasite interactions, driving co-evolution within subgroups of parasite species and functional alleles. Therefore, indirect effects among hosts and parasites can shape host MHC diversity, scaling it from the population to the community level.
Collapse
Affiliation(s)
- Shai Pilosof
- Mitrani Department of Desert Ecology and Albert Katz International School for Desert Studies, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| | - Miguel A Fortuna
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - Jean-François Cosson
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France
| | - Maxime Galan
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France
| | - Chaisiri Kittipong
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Alexis Ribas
- Biodiversity Research Group, Faculty of Science, Udon Thani Rajabhat University, Udon Thani 41000, Thailand
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, 76100, Israel
| | - Boris R Krasnov
- Mitrani Department of Desert Ecology and Albert Katz International School for Desert Studies, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| | - Serge Morand
- 1] Centre National de la Recherche Scientifique-Institut des Sciences de l'Évolution, Université Montpellier 2, Montpellier 34095, France [2] Centre de coopération International en Recherche Agronomique pour le Développement, Animal et Gestion Intégrée des Risques, Campus de Baillarguet, F-34093 Montpellier Cedex 5, France [3] Centre d'Infectiologie Christophe Mérieux du Laos, PO Box 3888, Samsenthai Road, Vientiane, Lao PDR
| | - Jordi Bascompte
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| |
Collapse
|
361
|
Kamiya T, O'Dwyer K, Westerdahl H, Senior A, Nakagawa S. A quantitative review of MHC-based mating preference: the role of diversity and dissimilarity. Mol Ecol 2014; 23:5151-63. [DOI: 10.1111/mec.12934] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/04/2014] [Accepted: 09/17/2014] [Indexed: 11/30/2022]
Affiliation(s)
- T. Kamiya
- Laboratoire MIVEGEC (UMR CNRS 5290, UR IRD 224, UM1, UM2); 911 avenue Agropolis, BP 64501 Montpellier Cedex 5 34394 France
| | - K. O'Dwyer
- Department of Zoology; University of Otago; 360 Great King Street Dunedin New Zealand
| | - H. Westerdahl
- Molecular Ecology and Evolution Lab; Department of Biology; Lund University; SE-223 62 Lund Sweden
| | - A. Senior
- The Charles Perkins Center; The University of Sydney; Sydney NSW 2006 Australia
- School of Biological Sciences; The University of Sydney; Sydney NSW 2006 Australia
| | - S. Nakagawa
- Department of Zoology; University of Otago; 360 Great King Street Dunedin New Zealand
| |
Collapse
|
362
|
Sin YW, Annavi G, Dugdale HL, Newman C, Burke T, MacDonald DW. Pathogen burden, co-infection and major histocompatibility complex variability in the European badger (Meles meles). Mol Ecol 2014; 23:5072-88. [PMID: 25211523 DOI: 10.1111/mec.12917] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 09/07/2014] [Accepted: 09/08/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Yung Wa Sin
- Wildlife Conservation Research Unit; Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House, Abingdon Road Tubney Abingdon Oxfordshire OX13 5QL UK
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
- Department of Organismic and Evolutionary Biology; Museum of Comparative Zoology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Geetha Annavi
- Wildlife Conservation Research Unit; Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House, Abingdon Road Tubney Abingdon Oxfordshire OX13 5QL UK
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
- Faculty of Science; Department of Biology; University of Putra Malaysia; UPM 43400 Serdang Selangor Malaysia
| | - Hannah L. Dugdale
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
- Behavioural Ecology and Self-Organization; University of Groningen; PO Box 11103 9700 CC Groningen the Netherlands
- Theoretical Biology; University of Groningen; PO Box 11103 9700 CC Groningen the Netherlands
| | - Chris Newman
- Wildlife Conservation Research Unit; Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House, Abingdon Road Tubney Abingdon Oxfordshire OX13 5QL UK
| | - Terry Burke
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - David W. MacDonald
- Wildlife Conservation Research Unit; Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House, Abingdon Road Tubney Abingdon Oxfordshire OX13 5QL UK
| |
Collapse
|
363
|
Ségurel L, Quintana-Murci L. Preserving immune diversity through ancient inheritance and admixture. Curr Opin Immunol 2014; 30:79-84. [DOI: 10.1016/j.coi.2014.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 08/11/2014] [Accepted: 08/12/2014] [Indexed: 10/24/2022]
|
364
|
Milinski M. Arms races, ornaments and fragrant genes: The dilemma of mate choice in fishes. Neurosci Biobehav Rev 2014; 46 Pt 4:567-72. [DOI: 10.1016/j.neubiorev.2014.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 07/18/2014] [Accepted: 08/12/2014] [Indexed: 11/16/2022]
|
365
|
Jones MR, Cheviron ZA, Carling MD. Variation in positively selected major histocompatibility complex class I loci in rufous-collared sparrows (Zonotrichia capensis). Immunogenetics 2014; 66:693-704. [DOI: 10.1007/s00251-014-0800-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/25/2014] [Indexed: 11/25/2022]
|
366
|
Cutrera AP, Zenuto RR, Lacey EA. Interpopulation differences in parasite load and variable selective pressures on MHC genes inCtenomys talarum. J Mammal 2014. [DOI: 10.1644/13-mamm-a-120] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
367
|
Role of selection versus neutral processes determining genetic variation in a small mammal along a climatic gradient in southern Africa. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9731-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
368
|
Bolnick DI, Snowberg LK, Caporaso JG, Lauber C, Knight R, Stutz WE. Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. Mol Ecol 2014; 23:4831-45. [PMID: 24975397 DOI: 10.1111/mec.12846] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 12/13/2022]
Abstract
Animals harbour diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge: distinguishing between mutualistic and pathogenic members of diverse and host-specific microbial communities. We propose that Major Histocompatibility class II (MHC) genotypes contribute to recognition and regulation of gut microbes, and thus, MHC polymorphism contributes to microbial variation among hosts. Here, we show that MHC IIb polymorphism is associated with among-individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. We sampled stickleback from Cedar Lake, on Vancouver Island, and used next-generation sequencing to genotype the sticklebacks' gut microbiota (16S sequencing) and their MHC class IIb exon 2 sequences. The presence of certain MHC motifs was associated with altered relative abundance (increase or decrease) of some microbial Families. The effect sizes are modest and entail a minority of microbial taxa, but these results represent the first indication that MHC genotype may affect gut microbiota composition in natural populations (MHC-microbe associations have also been found in a few studies of lab mice). Surprisingly, these MHC effects were frequently sex-dependent. Finally, hosts with more diverse MHC motifs had less diverse gut microbiota. One implication is that MHC might influence the efficacy of therapeutic strategies to treat dysbiosis-associated disease, including the outcome of microbial transplants between healthy and diseased patients. We also speculate that macroparasite-driven selection on MHC has the potential to indirectly alter the host gut microbiota, and vice versa.
Collapse
Affiliation(s)
- Daniel I Bolnick
- Howard Hughes Medical Institute and Section of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | | | | | | | | | | |
Collapse
|
369
|
Li L, Wang BB, Ge YF, Wan QH. Major histocompatibility complex class II polymorphisms in forest musk deer (Moschus berezovskii) and their probable association with purulent disease. Int J Immunogenet 2014; 41:401-12. [PMID: 25053118 DOI: 10.1111/iji.12135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/20/2014] [Accepted: 06/12/2014] [Indexed: 11/26/2022]
Abstract
Genes of the major histocompatibility complex (MHC) family are crucial in immune responses because they present pathogenic peptides to T cells. In this study, we analysed the genetic variation in forest musk deer (Moschus berezovskii) MHC II genes and its potential association with musk deer purulent disease. In total, 53 purulent disease-susceptible and 46 purulent disease-resistant individuals were selected for MHC II exon 2 fragment analysis. Among them, 16 DQ alleles and four additional DR alleles were identified, with DQ exon 2 fragments displaying a low level of polymorphism. The nonsynonymous substitutions exceeded the synonymous substitutions in the peptide-binding sites of DQA2, DQB1 and DQB2. Then, 28 MHC II alleles were used to analyse the distribution patterns of purulent disease between the susceptible and resistant groups. Among them, three alleles (DQA1*01, DQA1*02 and DQA2*04) were found to be resistant, and five alleles (DRB3*07, DQA1*03, DQA1*04, DQA2*05 and DQA2*06) were found to increase susceptibility. Additionally, three haplotypes were found to be putatively associated with musk deer purulent disease. However, these three haplotypes were only found in the resistant or susceptible group, and their frequencies were low. The results from our study support a contributory role of MHC II polymorphisms in the development of purulent disease in forest musk deer.
Collapse
Affiliation(s)
- L Li
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | | | | | | |
Collapse
|
370
|
Kyle CJ, Rico Y, Castillo S, Srithayakumar V, Cullingham CI, White BN, Pond BA. Spatial patterns of neutral and functional genetic variations reveal patterns of local adaptation in raccoon (Procyon lotor) populations exposed to raccoon rabies. Mol Ecol 2014; 23:2287-98. [PMID: 24655158 DOI: 10.1111/mec.12726] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/14/2014] [Accepted: 03/14/2014] [Indexed: 12/26/2022]
Abstract
Local adaptation is necessary for population survival and depends on the interplay between responses to selective forces and demographic processes that introduce or retain adaptive and maladaptive attributes. Host-parasite systems are dynamic, varying in space and time, where both host and parasites must adapt to their ever-changing environment in order to survive. We investigated patterns of local adaptation in raccoon populations with varying temporal exposure to the raccoon rabies virus (RRV). RRV infects approximately 85% of the population when epizootic and has been presumed to be completely lethal once contracted; however, disease challenge experiments and varying spatial patterns of RRV spread suggest some level of immunity may exist. We first assessed patterns of local adaptation in raccoon populations along the eastern seaboard of North America by contrasting spatial patterns of neutral (microsatellite loci) and functional, major histocompatibility complex (MHC) genetic diversity and structure. We explored variation of MHC allele frequencies in the light of temporal population exposure to RRV (0-60 years) and specific RRV strains in infected raccoons. Our results revealed high levels of MHC variation (66 DRB exon 2 alleles) and pronounced genetic structure relative to neutral microsatellite loci, indicative of local adaptation. We found a positive association linking MHC genetic diversity and temporal RRV exposure, but no association with susceptibility and resistance to RRV strains. These results have implications for landscape epidemiology studies seeking to predict the spread of RRV and present an example of how population demographics influence the degree to which populations adapt to local selective pressures.
Collapse
Affiliation(s)
- Christopher J Kyle
- Forensic Science Department, Trent University, Peterborough, ON, Canada, K9J 7B8; Natural Resources DNA Profiling and Forensics Centre, Trent University, Peterborough, ON, Canada, K9J 7B8
| | | | | | | | | | | | | |
Collapse
|
371
|
Lighten J, van Oosterhout C, Bentzen P. Critical review of NGS analyses for de novo genotyping multigene families. Mol Ecol 2014; 23:3957-72. [DOI: 10.1111/mec.12843] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/08/2014] [Accepted: 06/17/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Jackie Lighten
- Department of Biology; Marine Gene Probe Laboratory; Dalhousie University; Halifax Nova Scotia Canada
| | - Cock van Oosterhout
- School of Environmental Sciences; University of East Anglia; Norwich Research Park; Norwich UK
| | - Paul Bentzen
- Department of Biology; Marine Gene Probe Laboratory; Dalhousie University; Halifax Nova Scotia Canada
| |
Collapse
|
372
|
Stutz WE, Bolnick DI. Stepwise threshold clustering: a new method for genotyping MHC loci using next-generation sequencing technology. PLoS One 2014; 9:e100587. [PMID: 25036866 PMCID: PMC4103772 DOI: 10.1371/journal.pone.0100587] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/26/2014] [Indexed: 12/26/2022] Open
Abstract
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems:1) a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci--Stepwise Threshold Clustering (STC)--that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.
Collapse
Affiliation(s)
- William E. Stutz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
| | - Daniel I. Bolnick
- Howard Hughes Medical Institute & Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| |
Collapse
|
373
|
TURNER AK, BELDOMENICO PM, BOWN K, BURTHE SJ, JACKSON JA, LAMBIN X, BEGON M. Host-parasite biology in the real world: the field voles of Kielder. Parasitology 2014; 141:997-1017. [PMID: 24612619 PMCID: PMC4047648 DOI: 10.1017/s0031182014000171] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/20/2013] [Accepted: 01/22/2014] [Indexed: 12/21/2022]
Abstract
Research on the interactions between the field voles (Microtus agrestis) of Kielder Forest and their natural parasites dates back to the 1930s. These early studies were primarily concerned with understanding how parasites shape the characteristic cyclic population dynamics of their hosts. However, since the early 2000s, research on the Kielder field voles has expanded considerably and the system has now been utilized for the study of host-parasite biology across many levels, including genetics, evolutionary ecology, immunology and epidemiology. The Kielder field voles therefore represent one of the most intensely and broadly studied natural host-parasite systems, bridging theoretical and empirical approaches to better understand the biology of infectious disease in the real world. This article synthesizes the body of work published on this system and summarizes some important insights and general messages provided by the integrated and multidisciplinary study of host-parasite interactions in the natural environment.
Collapse
Affiliation(s)
- A. K. TURNER
- Institute of Integrative Biology, University of
Liverpool, UK
| | - P. M. BELDOMENICO
- Institute of Integrative Biology, University of
Liverpool, UK
- National Centre for Zoonosis Research, University
of Liverpool, UK
- Laboratorio de Ecología de Enfermedades,
Instituto de Ciencias Veterinarias del Litoral, Universidad Nacional del
Litoral – Consejo de Investigaciones Científicas y Técnicas (UNL – CONICET),
Esperanza, Argentina
| | - K. BOWN
- Institute of Integrative Biology, University of
Liverpool, UK
- School of Environment & Life Sciences,
University of Salford, UK
| | - S. J. BURTHE
- Institute of Integrative Biology, University of
Liverpool, UK
- National Centre for Zoonosis Research, University
of Liverpool, UK
- Centre for Ecology & Hydrology, Natural
Environmental Research Council, Edinburgh,
UK
| | - J. A. JACKSON
- Institute of Integrative Biology, University of
Liverpool, UK
- Institute of Biological, Environmental and Rural
Sciences, University of Aberystwyth, UK
| | - X. LAMBIN
- School of Biological Sciences, University of
Aberdeen, UK
| | - M. BEGON
- Institute of Integrative Biology, University of
Liverpool, UK
| |
Collapse
|
374
|
Lamaze FC, Pavey SA, Normandeau E, Roy G, Garant D, Bernatchez L. Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis). Mol Ecol 2014; 23:1730-48. [PMID: 24795997 DOI: 10.1111/mec.12684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The capacity of an individual to battle infection is an important fitness determinant in wild vertebrate populations. The major histocompatibility complex (MHC) genes are crucial for a host's adaptive immune system to detect pathogens. However, anthropogenic activities may disrupt natural cycles of co-evolution between hosts and pathogens. In this study, we investigated the dynamic sequence and expression variation of host parasite interactions in brook charr (Salvelinus fontinalis) in a context of past human disturbance via population supplementation from domestic individuals. To do so, we developed a new method to examine selection shaping MHC diversity within and between populations and found a complex interplay between neutral and selective processes that varied between lakes that were investigated. We provided evidence for a lower introgression rate of domestic alleles and found that parasite infection increased with domestic genomic background of individuals. We also documented an association between individual MHC alleles and parasite taxa. Finally, longer cis-regulatory minisatellites were positively correlated with MHC II down-regulation and domestic admixture, suggesting that inadvertent selection during domestication resulted in a lower immune response capacity, through a trade-off between growth and immunity, which explained the negative selection of domestic alleles at least under certain circumstances.
Collapse
|
375
|
Grossen C, Keller L, Biebach I, Croll D. Introgression from domestic goat generated variation at the major histocompatibility complex of Alpine ibex. PLoS Genet 2014; 10:e1004438. [PMID: 24945814 PMCID: PMC4063738 DOI: 10.1371/journal.pgen.1004438] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 04/30/2014] [Indexed: 12/30/2022] Open
Abstract
The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection. The major histocompatibility complex (MHC), a crucial component of the defense against pathogens, contains the most polymorphic functional genes in vertebrate genomes. The extraordinary genetic variation is generally considered to be ancient. We investigated whether a previously neglected mechanism, introgression from related species, provides an additional source of MHC variation. We show that introgression from domestic goat dramatically increased genetic variation at the MHC of Alpine ibex, a species that had nearly gone extinct during the 18th century, but has been restored to large numbers since. We show that Alpine ibex share one of only two alleles at a generally highly polymorphic MHC locus with domestic goats and that the chromosomal region containing the goat-type allele has a signature of recent introgression. Our finding contradicts the long-standing view that ancient trans-species polymorphism is the sole source of the extraordinary genetic variability at the MHC. Instead, we show that in Alpine ibex introgression generated genetic diversity at a MHC locus. Our study supports the view that loci favoring genetic polymorphism may be susceptible to adaptive introgression from related species and will encourage future research to identify unexpected signatures of introgression.
Collapse
Affiliation(s)
- Christine Grossen
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Department of Zoology, University of British Columbia, Vancouver, Canada
- * E-mail:
| | - Lukas Keller
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Iris Biebach
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - The International Goat Genome Consortium
- Kunming Institute of Zoology, Chinese Academy of Sciences, State Key Laboratory of Genetic Resources and Evolution, Kunming, China
- INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Daniel Croll
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| |
Collapse
|
376
|
Yao YF, Dai QX, Li J, Ni QY, Zhang MW, Xu HL. Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles. BMC Evol Biol 2014; 14:130. [PMID: 24930092 PMCID: PMC4070090 DOI: 10.1186/1471-2148-14-130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 06/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even with a low level of neutral variability in some species. However, in small and isolated or bottlenecked populations, balancing selection may be overwhelmed by genetic drift. To estimate microevolutionary forces acting on the isolated rhesus macaque populations, we examined genetic variation at Mhc-DQB1 loci in 119 wild rhesus macaques from five geographically isolated populations in western Sichuan, China, and compared the levels of MHC variation and differentiation among populations with that previously observed at neutral microsatellite markers. RESULTS 23 Mamu-DQB1 alleles were identified in 119 rhesus macaques in western Sichuan, China. These macaques exhibited relatively high levels of genetic diversity at Mamu-DQB1. The Hanyuan population presented the highest genetic variation, whereas the Heishui population was the lowest. Analysis of molecular variance (AMOVA) and pairwise FST values showed moderate genetic differentiation occurring among the five populations at the Mhc-DQB1 locus. Non-synonymous substitutions occurred at a higher frequency than synonymous substitutions in the peptide binding region. Levels of MHC variation within rhesus macaque populations are concordant with microsatellite variation. On the phylogenetic tree for the rhesus and crab-eating macaques, extensive allele or allelic lineage sharing is observed between the two species. CONCLUSIONS Phylogenetic analyses confirm the apparent trans-species model of evolution of the Mhc-DQB1 genes in these macaques. Balancing selection plays an important role in sharing allelic lineages between species, but genetic drift may share balancing selection dominance to maintain MHC diversity. Great divergence at neutral or adaptive markers showed that moderate genetic differentiation had occurred in rhesus macaque populations in western Sichuan, China, due to the habitat fragmentation caused by long-term geographic barriers and human activity. The Heishui population should be paid more attention for its lowest level of genetic diversity and relatively great divergence from others.
Collapse
Affiliation(s)
- Yong-Fang Yao
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
| | - Qiu-Xia Dai
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
| | - Jing Li
- College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Qing-Yong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
| | - Ming-Wang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
| | - Huai-Liang Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
- Experimental Animal Engineering Center/National Experimental Macaque Reproduce Laboratory, Sichuan Agricultural Universiy, Ya′an 625014, China
| |
Collapse
|
377
|
Immunogenetic factors affecting susceptibility of humans and rodents to hantaviruses and the clinical course of hantaviral disease in humans. Viruses 2014; 6:2214-41. [PMID: 24859344 PMCID: PMC4036553 DOI: 10.3390/v6052214] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/17/2014] [Accepted: 05/16/2014] [Indexed: 12/11/2022] Open
Abstract
We reviewed the associations of immunity-related genes with susceptibility of humans and rodents to hantaviruses, and with severity of hantaviral diseases in humans. Several class I and class II HLA haplotypes were linked with severe or benign hantavirus infections, and these haplotypes varied among localities and hantaviruses. The polymorphism of other immunity-related genes including the C4A gene and a high-producing genotype of TNF gene associated with severe PUUV infection. Additional genes that may contribute to disease or to PUUV infection severity include non-carriage of the interleukin-1 receptor antagonist (IL-1RA) allele 2 and IL-1β (-511) allele 2, polymorphisms of plasminogen activator inhibitor (PAI-1) and platelet GP1a. In addition, immunogenetic studies have been conducted to identify mechanisms that could be linked with the persistence/clearance of hantaviruses in reservoirs. Persistence was associated during experimental infections with an upregulation of anti-inflammatory responses. Using natural rodent population samples, polymorphisms and/or expression levels of several genes have been analyzed. These genes were selected based on the literature of rodent or human/hantavirus interactions (some Mhc class II genes, Tnf promoter, and genes encoding the proteins TLR4, TLR7, Mx2 and β3 integrin). The comparison of genetic differentiation estimated between bank vole populations sampled over Europe, at neutral and candidate genes, has allowed to evidence signatures of selection for Tnf, Mx2 and the Drb Mhc class II genes. Altogether, these results corroborated the hypothesis of an evolution of tolerance strategies in rodents. We finally discuss the importance of these results from the medical and epidemiological perspectives.
Collapse
|
378
|
Nonsynonymous substitution rate heterogeneity in the peptide-binding region among different HLA-DRB1 lineages in humans. G3-GENES GENOMES GENETICS 2014; 4:1217-26. [PMID: 24793785 PMCID: PMC4455771 DOI: 10.1534/g3.114.011726] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An extraordinary diversity of amino acid sequences in the peptide-binding region (PBR) of human leukocyte antigen [HLA; human major histocompatibility complex (MHC)] molecules has been maintained by balancing selection. The process of accumulation of amino acid diversity in the PBR for six HLA genes (HLA-A, B, C, DRB1, DQB1, and DPB1) shows that the number of amino acid substitutions in the PBR among alleles does not linearly correlate with the divergence time of alleles at the six HLA loci. At these loci, some pairs of alleles show significantly less nonsynonymous substitutions at the PBR than expected from the divergence time. The same phenomenon was observed not only in the HLA but also in the rat MHC. To identify the cause for this, DRB1 sequences, a representative case of a typical nonlinear pattern of substitutions, were examined. When the amino acid substitutions in the PBR were placed with maximum parsimony on a maximum likelihood tree based on the non-PBR substitutions, heterogeneous rates of nonsynonymous substitutions in the PBR were observed on several branches. A computer simulation supported the hypothesis that allelic pairs with low PBR substitution rates were responsible for the stagnation of accumulation of PBR nonsynonymous substitutions. From these observations, we conclude that the nonsynonymous substitution rate at the PBR sites is not constant among the allelic lineages. The deceleration of the rate may be caused by the coexistence of certain pathogens for a substantially long time during HLA evolution.
Collapse
|
379
|
Wright DJ, Spurgin LG, Collar NJ, Komdeur J, Burke T, Richardson DS. The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler. Mol Ecol 2014; 23:2165-77. [PMID: 24689851 PMCID: PMC4237152 DOI: 10.1111/mec.12740] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 01/10/2023]
Abstract
Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool.
Collapse
Affiliation(s)
- David J Wright
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK; NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | | | | | | | | | | |
Collapse
|
380
|
Winternitz JC, Wares JP, Yabsley MJ, Altizer S. Wild cyclic voles maintain high neutral and MHC diversity without strong evidence for parasite-mediated selection. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9709-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
381
|
Scherman K, Råberg L, Westerdahl H. Positive selection on MHC class II DRB and DQB genes in the bank vole (Myodes glareolus). J Mol Evol 2014; 78:293-305. [PMID: 24748547 DOI: 10.1007/s00239-014-9618-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/30/2014] [Indexed: 10/25/2022]
Abstract
The major histocompatibility complex (MHC) class IIB genes show considerable sequence similarity between loci. The MHC class II DQB and DRB genes are known to exhibit a high level of polymorphism, most likely maintained by parasite-mediated selection. Studies of the MHC in wild rodents have focused on DRB, whilst DQB has been given much less attention. Here, we characterised DQB genes in Swedish bank voles Myodes glareolus, using full-length transcripts. We then designed primers that specifically amplify exon 2 from DRB (202 bp) and DQB (205 bp) and investigated molecular signatures of natural selection on DRB and DQB alleles. The presence of two separate gene clusters was confirmed using BLASTN and phylogenetic analysis, where our seven transcripts clustered according to either DQB or DRB homologues. These gene clusters were again confirmed on exon 2 data from 454-amplicon sequencing. Our DRB primers amplify a similar number of alleles per individual as previously published DRB primers, though our reads are longer. Traditional d N/d S analyses of DRB sequences in the bank vole have not found a conclusive signal of positive selection. Using a more advanced substitution model (the Kumar method) we found positive selection in the peptide binding region (PBR) of both DRB and DQB genes. Maximum likelihood models of codon substitutions detected positively selected sites located in the PBR of both DQB and DRB. Interestingly, these analyses detected at least twice as many positively selected sites in DQB than DRB, suggesting that DQB has been under stronger positive selection than DRB over evolutionary time.
Collapse
Affiliation(s)
- Kristin Scherman
- Department of Biology, MEMEG, Lund University, Sölvegatan 37, 223 62, Lund, Sweden,
| | | | | |
Collapse
|
382
|
Kamath PL, Turner WC, Küsters M, Getz WM. Parasite-mediated selection drives an immunogenetic trade-off in plains zebras (Equus quagga). Proc Biol Sci 2014; 281:20140077. [PMID: 24718761 DOI: 10.1098/rspb.2014.0077] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pathogen evasion of the host immune system is a key force driving extreme polymorphism in genes of the major histocompatibility complex (MHC). Although this gene family is well characterized in structure and function, there is still much debate surrounding the mechanisms by which MHC diversity is selectively maintained. Many studies have investigated relationships between MHC variation and specific pathogens, and have found mixed support for and against the hypotheses of heterozygote advantage, frequency-dependent or fluctuating selection. Few, however, have focused on the selective effects of multiple parasite types on host immunogenetic patterns. Here, we examined relationships between variation in the equine MHC gene, ELA-DRA, and both gastrointestinal (GI) and ectoparasitism in plains zebras (Equus quagga). Specific alleles present at opposing population frequencies had antagonistic effects, with rare alleles associated with increased GI parasitism and common alleles with increased tick burdens. These results support a frequency-dependent mechanism, but are also consistent with fluctuating selection. Maladaptive GI parasite 'susceptibility alleles' were reduced in frequency, suggesting that these parasites may play a greater selective role at this locus. Heterozygote advantage, in terms of allele mutational divergence, also predicted decreased GI parasite burden in genotypes with a common allele. We conclude that an immunogenetic trade-off affects resistance/susceptibility to parasites in this system. Because GI and ectoparasites do not directly interact within hosts, our results uniquely show that antagonistic parasite interactions can be indirectly modulated through the host immune system. This study highlights the importance of investigating the role of multiple parasites in shaping patterns of host immunogenetic variation.
Collapse
Affiliation(s)
- Pauline L Kamath
- US Geological Survey, Northern Rocky Mountain Science Center, , 2327 University Way, Bozeman, MT 59715, USA, Department of Environmental Science, Policy, and Management, University of California, , 130 Mulford Hall No. 3114, Berkeley, CA 94720, USA, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, , PO Box 1066 Blindern, Oslo 0361, Norway, Berkeley Etosha Anthrax Research Project, , Swakopmund, Namibia, School of Mathematical Sciences, University of KwaZulu-Natal, , Private Bag X54001, 14, Durban 4000, South Africa
| | | | | | | |
Collapse
|
383
|
A review of molecular approaches for investigating patterns of coevolution in marine host-parasite relationships. ADVANCES IN PARASITOLOGY 2014; 84:209-52. [PMID: 24480315 DOI: 10.1016/b978-0-12-800099-1.00004-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Parasites and their relationships with hosts play a crucial role in the evolutionary pathways of every living organism. One method of investigating host-parasite systems is using a molecular approach. This is particularly important as analyses based solely on morphology or laboratory studies of parasites and their hosts do not take into account historical evolutionary interactions that can shape the distribution, abundance and population structure of parasites and their hosts. However, the predominant host-parasite coevolution literature has focused on terrestrial hosts and their parasites, and there still is a lack of studies in marine environments. Given that marine systems are generally more open than terrestrial ones, they provide fascinating opportunities for large-scale (as well as small-scale) geographic studies. Further, patterns and processes of genetic structuring and systematics are becoming more available across many different taxa (but especially fishes) in many marine systems, providing an excellent basis for examining whether parasites follow host population/species structure. In this chapter, we first highlight the factors and processes that challenge our ability to interpret evolutionary patterns of coevolution of hosts and their parasites in marine systems at different spatial, temporal and taxonomic scales. We then review the use of the most commonly utilized genetic markers in studying marine host-parasite systems. We give an overview and discuss which molecular methodologies resolve evolutionary relationships best and also discuss the applicability of new approaches, such as next-generation sequencing and studies utilizing functional markers to gain insights into more contemporary processes shaping host-parasite relationships.
Collapse
|
384
|
Alcaide M, Muñoz J, Martínez-de la Puente J, Soriguer R, Figuerola J. Extraordinary MHC class II B diversity in a non-passerine, wild bird: the Eurasian Coot Fulica atra (Aves: Rallidae). Ecol Evol 2014; 4:688-98. [PMID: 24683452 PMCID: PMC3967895 DOI: 10.1002/ece3.974] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/30/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022] Open
Abstract
The major histocompatibility complex (MHC) hosts the most polymorphic genes ever described in vertebrates. The MHC triggers the adaptive branch of the immune response, and its extraordinary variability is considered an evolutionary consequence of pathogen pressure. The last few years have witnessed the characterization of the MHC multigene family in a large diversity of bird species, unraveling important differences in its polymorphism, complexity, and evolution. Here, we characterize the first MHC class II B sequences isolated from a Rallidae species, the Eurasian Coot Fulica atra. A next-generation sequencing approach revealed up to 265 alleles that translated into 251 different amino acid sequences (β chain, exon 2) in 902 individuals. Bayesian inference identified up to 19 codons within the presumptive peptide-binding region showing pervasive evidence of positive, diversifying selection. Our analyses also detected a significant excess of high-frequency segregating sites (average Tajima's D = 2.36, P < 0.05), indicative of balancing selection. We found one to six different alleles per individual, consistent with the occurrence of at least three MHC class II B gene duplicates. However, the genotypes comprised of three alleles were by far the most abundant in the population investigated (49.4%), followed by those with two (29.6%) and four (17.5%) alleles. We suggest that these proportions are in agreement with the segregation of MHC haplotypes differing in gene copy number. The most widespread segregating haplotypes, according to our findings, would contain one single gene or two genes. The MHC class II of the Eurasian Coot is a valuable system to investigate the evolutionary implications of gene copy variation and extensive variability, the greatest ever found, to the best of our knowledge, in a wild population of a non-passerine bird.
Collapse
Affiliation(s)
- Miguel Alcaide
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Joaquin Muñoz
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
- The University of Oklahoma Biological Station15389 Station Road, Kingston, Oklahoma, 73439
| | | | - Ramón Soriguer
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Jordi Figuerola
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| |
Collapse
|
385
|
Zhu R, Chen ZY, Wang J, Yuan JD, Liao XY, Gui JF, Zhang QY. Extensive diversification of MHC in Chinese giant salamanders Andrias davidianus (Anda-MHC) reveals novel splice variants. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 42:311-322. [PMID: 24135718 DOI: 10.1016/j.dci.2013.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/02/2013] [Accepted: 10/03/2013] [Indexed: 06/02/2023]
Abstract
A series of MHC alleles (including 26 class IA, 27 class IIA, and 17 class IIB) were identified from Chinese giant salamander Andrias davidianus (Anda-MHC). These genes are similar to classical MHC molecules in terms of characteristic domains, functional residues, deduced tertiary structures and genetic diversity. The majority of variation between alleles is found in the putative peptide-binding region (PBR), which is driven by positive Darwinian selection. The coexistence of two isoforms in MHC IA, IIA, and IIB alleles are shown: one full-length transcript and one novel splice variant. Despite lake of the external domains, these variants exhibit similar subcellular localization with the full-length transcripts. Moreover, the expression of MHC isoforms are up-regulated upon in vivo and in vitro stimulation with Andrias davidianus ranavirus (ADRV), suggesting their potential roles in the immune response. The results provide insights into understanding MHC variation and function in this ancient and endangered urodele amphibian.
Collapse
Affiliation(s)
- Rong Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | | | | | | | | | | | | |
Collapse
|
386
|
Salie M, van der Merwe L, Möller M, Daya M, van der Spuy GD, van Helden PD, Martin MP, Gao XJ, Warren RM, Carrington M, Hoal EG. Associations between human leukocyte antigen class I variants and the Mycobacterium tuberculosis subtypes causing disease. J Infect Dis 2014; 209:216-23. [PMID: 23945374 PMCID: PMC3873786 DOI: 10.1093/infdis/jit443] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/17/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The development of active tuberculosis disease has been shown to be multifactorial. Interactions between host and bacterial genotype may influence disease outcome, with some studies indicating the adaptation of M. tuberculosis strains to specific human populations. Here we investigate the role of the human leukocyte antigen (HLA) class I genes in this biological process. METHODS Three hundred patients with tuberculosis from South Africa were typed for their HLA class I alleles by direct sequencing. Mycobacterium tuberculosis genotype classification was done by IS6110 restriction fragment length polymorphism genotyping and spoligotyping. RESULTS We showed that Beijing strain occurred more frequently in individuals with multiple disease episodes (P < .001) with the HLA-B27 allele lowering the odds of having an additional episode (odds ratio, 0.21; P = .006). Associations were also identified for specific HLA types and disease caused by the Beijing, LAM, LCC, and Quebec strains. HLA types were also associated with disease caused by strains from the Euro-American or East Asian lineages, and the frequencies of these alleles in their sympatric human populations identified potential coevolutionary events between host and pathogen. CONCLUSIONS This is the first report of the association of human HLA types and M. tuberculosis strain genotype, highlighting that both host and pathogen genetics need to be taken into consideration when studying tuberculosis disease development.
Collapse
Affiliation(s)
- Muneeb Salie
- MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg
| | - Lize van der Merwe
- MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg
- MRC Biostatistics Unit, Medical Research Council, Tygerberg
- Department of Statistics, University of Western Cape, Bellville,South Africa
| | - Marlo Möller
- MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg
| | - Michelle Daya
- MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg
| | - Gian D. van der Spuy
- MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg
| | - Paul D. van Helden
- MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg
| | - Maureen P. Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge
| | - Xiao-jiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge
| | - Robin M. Warren
- MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge
| | - Eileen G. Hoal
- MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg
| |
Collapse
|
387
|
Rimer J, Cohen IR, Friedman N. Do all creatures possess an acquired immune system of some sort? Bioessays 2014; 36:273-81. [DOI: 10.1002/bies.201300124] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jacob Rimer
- Department of Immunology; Weizmann Institute of Science; Rehovot Israel
| | - Irun R. Cohen
- Department of Immunology; Weizmann Institute of Science; Rehovot Israel
| | - Nir Friedman
- Department of Immunology; Weizmann Institute of Science; Rehovot Israel
| |
Collapse
|
388
|
Ekblom R, Wennekes P, Horsburgh GJ, Burke T. Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics. Mol Ecol Resour 2014; 14:636-46. [PMID: 24345231 DOI: 10.1111/1755-0998.12213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/04/2013] [Accepted: 12/11/2013] [Indexed: 11/30/2022]
Abstract
The house sparrow (Passer domesticus) is an important model species in ecology and evolution. However, until recently, genomic resources for molecular ecological projects have been lacking in this species. Here, we present transcriptome sequencing data (RNA-Seq) from three different house sparrow tissues (spleen, blood and bursa). These tissues were specifically chosen to obtain a diverse representation of expressed genes and to maximize the yield of immune-related gene functions. After de novo assembly, 15,250 contigs were identified, representing sequence data from a total of 8756 known avian genes (as inferred from the closely related zebra finch). The transcriptome assembly contain sequence data from nine manually annotated MHC genes, including an almost complete MHC class I coding sequence. There were 407, 303 and 68 genes overexpressed in spleen, blood and bursa, respectively. Gene ontology terms related to ribosomal function were associated with overexpression in spleen and oxygen transport functions with overexpression in blood. In addition to the transcript sequences, we provide 327 gene-linked microsatellites (SSRs) with sufficient flanking sequences for primer design, and 3177 single-nucleotide polymorphisms (SNPs) within genes, that can be used in follow-up molecular ecology studies of this ecological well-studied species.
Collapse
Affiliation(s)
- Robert Ekblom
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, Uppsala, SE-75236, Sweden; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | | | | | | |
Collapse
|
389
|
Bauer MM, Miller MM, Briles WE, Reed KM. Genetic variation at the MHC in a population of introduced wild turkeys. Anim Biotechnol 2013; 24:210-28. [PMID: 23777350 DOI: 10.1080/10495398.2013.767267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Genetic variation in the major histocompatibility complex (MHC) is known to affect disease resistance in many species. Investigations of MHC diversity in populations of wild species have focused on the antigen presenting class IIβ molecules due to the known polymorphic nature of these genes and the role these molecules play in pathogen recognition. Studies of MHC haplotype variation in the turkey ( Meleagris gallopavo ) are limited. This study was designed to examine MHC diversity in a group of Eastern wild turkeys ( Meleagris gallopavo silvestris ) collected during population expansion following reintroduction of the species in southern Wisconsin, USA. Southern blotting with BG and class IIβ probes and single nucleotide polymorphism (SNP) genotyping was used to measure MHC variation. SNP analysis focused on single copy MHC genes flanking the highly polymorphic class IIβ genes. Southern blotting identified 27 class IIβ phenotypes, whereas SNP analysis identified 13 SNP haplotypes occurring in 28 combined genotypes. Results show that genetic diversity estimates based on RFLP (Southern blot) analysis underestimate the level of variation detected by SNP analysis. Sequence analysis of the mitochondrial D-loop identified 7 mitochondrial haplotypes (mitotypes) in the sampled birds. Results show that wild turkeys located in southern Wisconsin have a genetically diverse MHC and originate from several maternal lineages.
Collapse
Affiliation(s)
- Miranda M Bauer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | | | | | | |
Collapse
|
390
|
Vásquez-Carrillo C, Friesen V, Hall L, Peery MZ. Variation in MHC class II B genes in marbled murrelets: implications for delineating conservation units. Anim Conserv 2013. [DOI: 10.1111/acv.12089] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- C. Vásquez-Carrillo
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI USA
| | - V. Friesen
- Department of Biology; Queen's University; Kingston Ontario Canada
| | - L. Hall
- Department of Environmental Science, Policy, and Management; University of California-Berkeley; Berkeley CA USA
| | - M. Z. Peery
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI USA
| |
Collapse
|
391
|
Wang Y, Qiu M, Yang J, Zhao X, Wang Y, Zhu Q, Liu Y. Sequence variations of the MHC class I gene exon 2 and exon 3 between infected and uninfected chickens challenged with Marek's disease virus. INFECTION GENETICS AND EVOLUTION 2013; 21:103-9. [PMID: 24200589 DOI: 10.1016/j.meegid.2013.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 11/17/2022]
Abstract
The major histocompatibility complex (MHC) among chickens has been well established as being associated with disease resistance and pathogens infection, but the genetic differences in MHC between chickens susceptible to certain infections and those chickens that remain uninfected have not been sufficiently determined. In this study, we sought the genetic basis that may underlie differences in susceptibility to infection among chickens by challenging four groups of broilers with Marek's disease virus (MDV). Over the course of the experiment, lesions began to appear between 21 and 35 days post challenge (dpc), and commercial broilers were not necessarily better than indigenous chickens in terms of disease resistance. The four groups showed neutral resistance to MDV infection validated by challenge results and evolutionary analysis of exons 2 and 3 of the MHC class I region. Several variable sites in exon 2 and exon 3 were exclusively appeared in infected chickens. Exon 3 was likely more crucial than exon 2 in disease resistance. Our observations offered a support for a potential association between promiscuous pathogens and conspicuous genetic diversity in the MHC class I region.
Collapse
Affiliation(s)
- Ye Wang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China
| | - Mohan Qiu
- Sichuan Animal Science Academy, Chengdu, Sichuan 610066, China
| | - Jiandong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xiaoling Zhao
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China
| | - Yan Wang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China
| | - Qing Zhu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China
| | - Yiping Liu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu Campus, Chengdu, Sichuan 611130, China.
| |
Collapse
|
392
|
Mating advantage for rare males in wild guppy populations. Nature 2013; 503:108-10. [PMID: 24172904 DOI: 10.1038/nature12717] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/26/2013] [Indexed: 11/08/2022]
Abstract
To understand the processes that maintain genetic diversity is a long-standing challenge in evolutionary biology, with implications for predicting disease resistance, response to environmental change, and population persistence. Simple population genetic models are not sufficient to explain the high levels of genetic diversity sometimes observed in ecologically important traits. In guppies (Poecilia reticulata), male colour pattern is both diverse and heritable, and is arguably one of the most extreme examples of morphological polymorphism known. Negative frequency-dependent selection (NFDS), a form of selection in which genotypes are favoured when they are rare, can potentially maintain such extensive polymorphism, but few experimental studies have confirmed its operation in nature. Here we use highly replicated experimental manipulations of natural populations to show that males with rare colour patterns have higher reproductive fitness, demonstrating NFDS mediated by sexual selection. Rare males acquired more mates and sired more offspring compared to common males and, as previously reported, had higher rates of survival. Orange colour, implicated in other studies of sexual selection in guppies, did predict male reproductive success, but only in one of three populations. These data support the hypothesis that NFDS maintains diversity in the colour patterns of male guppies through two selective agents, mates and predators. Similar field-based manipulations of genotype frequencies could provide a powerful approach to reveal the underlying ecological and behavioural mechanisms that maintain genetic and phenotypic diversity.
Collapse
|
393
|
Winternitz JC, Minchey SG, Garamszegi LZ, Huang S, Stephens PR, Altizer S. Sexual selection explains more functional variation in the mammalian major histocompatibility complex than parasitism. Proc Biol Sci 2013; 280:20131605. [PMID: 23966643 PMCID: PMC3768310 DOI: 10.1098/rspb.2013.1605] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 07/23/2013] [Indexed: 12/31/2022] Open
Abstract
Understanding drivers of genetic diversity at the major histocompatibility complex (MHC) is vitally important for predicting how vertebrate immune defence might respond to future selection pressures and for preserving immunogenetic diversity in declining populations. Parasite-mediated selection is believed to be the major selective force generating MHC polymorphism, and while MHC-based mating preferences also exist for multiple species including humans, the general importance of mate choice is debated. To investigate the contributions of parasitism and sexual selection in explaining among-species variation in MHC diversity, we applied comparative methods and meta-analysis across 112 mammal species, including carnivores, bats, primates, rodents and ungulates. We tested whether MHC diversity increased with parasite richness and relative testes size (as an indicator of the potential for mate choice), while controlling for phylogenetic autocorrelation, neutral mutation rate and confounding ecological variables. We found that MHC nucleotide diversity increased with parasite richness for bats and ungulates but decreased with parasite richness for carnivores. By contrast, nucleotide diversity increased with relative testes size for all taxa. This study provides support for both parasite-mediated and sexual selection in shaping functional MHC polymorphism across mammals, and importantly, suggests that sexual selection could have a more general role than previously thought.
Collapse
Affiliation(s)
- J C Winternitz
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA.
| | | | | | | | | | | |
Collapse
|
394
|
Harrison XA, York JE, Cram DL, Young AJ. Extra-group mating increases inbreeding risk in a cooperatively breeding bird. Mol Ecol 2013; 22:5700-15. [DOI: 10.1111/mec.12505] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/15/2013] [Accepted: 08/24/2013] [Indexed: 01/11/2023]
Affiliation(s)
- X. A. Harrison
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
- Centre for Ecology & Conservation; University of Exeter; Tremough Campus; Penryn Cornwall TR10 9EZ UK
| | - J. E. York
- Centre for Ecology & Conservation; University of Exeter; Tremough Campus; Penryn Cornwall TR10 9EZ UK
| | - D. L. Cram
- Centre for Ecology & Conservation; University of Exeter; Tremough Campus; Penryn Cornwall TR10 9EZ UK
| | - A. J. Young
- Centre for Ecology & Conservation; University of Exeter; Tremough Campus; Penryn Cornwall TR10 9EZ UK
| |
Collapse
|
395
|
Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE). BMC Evol Biol 2013; 13:194. [PMID: 24028551 PMCID: PMC3848458 DOI: 10.1186/1471-2148-13-194] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/06/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs). RESULTS We sequenced genes encoding Toll-like receptor 4 (Tlr4) and 7 (Tlr7), two of the key bacterial- and viral-sensing receptors of innate immunity, across 23 species within the subfamily Murinae. Although we have shown that the phylogeny of both Tlr genes is largely congruent with the phylogeny of rodents based on a comparably sized non-immune sequence dataset, we also identified several potentially important discrepancies. The sequence analyses revealed that major parts of both Tlrs are evolving under strong purifying selection, likely due to functional constraints. Yet, also several signatures of positive selection have been found in both genes, with more intense signal in the bacterial-sensing Tlr4 than in the viral-sensing Tlr7. 92% and 100% of sites evolving under positive selection in Tlr4 and Tlr7, respectively, were located in the extracellular domain. Directly in the Ligand-Binding Region (LBR) of TLR4 we identified two rapidly evolving amino acid residues and one site under positive selection, all three likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In contrast, all putative sites of LBRTLR7 involved in the detection of viral nucleic acids were highly conserved across rodents. Interspecific differences in the predicted 3D-structure of the LBR of both Tlrs were not related to phylogenetic history, while analyses of protein charges clearly discriminated Rattini and Murini clades. CONCLUSIONS In consequence of the constraints given by the receptor protein function purifying selection has been a dominant force in evolution of Tlrs. Nevertheless, our results show that episodic diversifying parasite-mediated selection has shaped the present species-specific variability in rodent Tlrs. The intensity of diversifying selection was higher in Tlr4 than in Tlr7, presumably due to structural properties of their ligands.
Collapse
|
396
|
McClelland EK, Ming TJ, Tabata A, Kaukinen KH, Beacham TD, Withler RE, Miller KM. Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka). Mol Ecol 2013; 22:4783-800. [DOI: 10.1111/mec.12424] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Erin K. McClelland
- Fisheries and Oceans Canada; Pacific Biological Station 3190 Hammond Bay Rd Nanaimo BC V9T 6N7 Canada
| | - Tobi J. Ming
- Fisheries and Oceans Canada; Pacific Biological Station 3190 Hammond Bay Rd Nanaimo BC V9T 6N7 Canada
| | - Amy Tabata
- Fisheries and Oceans Canada; Pacific Biological Station 3190 Hammond Bay Rd Nanaimo BC V9T 6N7 Canada
| | - Karia H. Kaukinen
- Fisheries and Oceans Canada; Pacific Biological Station 3190 Hammond Bay Rd Nanaimo BC V9T 6N7 Canada
| | - Terry D. Beacham
- Fisheries and Oceans Canada; Pacific Biological Station 3190 Hammond Bay Rd Nanaimo BC V9T 6N7 Canada
| | - Ruth E. Withler
- Fisheries and Oceans Canada; Pacific Biological Station 3190 Hammond Bay Rd Nanaimo BC V9T 6N7 Canada
| | - Kristina M. Miller
- Fisheries and Oceans Canada; Pacific Biological Station 3190 Hammond Bay Rd Nanaimo BC V9T 6N7 Canada
| |
Collapse
|
397
|
Cochran SD, Cole JB, Null DJ, Hansen PJ. Single Nucleotide Polymorphisms in Candidate Genes Associated with Fertilizing Ability of Sperm and Subsequent Embryonic Development in Cattle1. Biol Reprod 2013; 89:69. [DOI: 10.1095/biolreprod.113.111260] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
398
|
Westerdahl H, Stjernman M, Råberg L, Lannefors M, Nilsson JÅ. MHC-I affects infection intensity but not infection status with a frequent avian malaria parasite in blue tits. PLoS One 2013; 8:e72647. [PMID: 24023631 PMCID: PMC3758318 DOI: 10.1371/journal.pone.0072647] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/12/2013] [Indexed: 12/23/2022] Open
Abstract
Host resistance against parasites depends on three aspects: the ability to prevent, control and clear infections. In vertebrates the immune system consists of innate and adaptive immunity. Innate immunity is particularly important for preventing infection and eradicating established infections at an early stage while adaptive immunity is slow, but powerful, and essential for controlling infection intensities and eventually clearing infections. Major Histocompatibility Complex (MHC) molecules are central in adaptive immunity, and studies on parasite resistance and MHC in wild animals have found effects on both infection intensity (parasite load) and infection status (infected or not). It seems MHC can affect both the ability to control infection intensities and the ability to clear infections. However, these two aspects have rarely been considered simultaneously, and their relative importance in natural populations is therefore unclear. Here we investigate if MHC class I genotype affects infection intensity and infection status with a frequent avian malaria infection Haemoproteus majoris in a natural population of blue tits Cyanistes caeruleus. We found a significant negative association between a single MHC allele and infection intensity but no association with infection status. Blue tits that carry a specific MHC allele seem able to suppress H. majoris infection intensity, while we have no evidence that this allele also has an effect on clearance of the H. majoris infection, a result that is in contrast with some previous studies of MHC and avian malaria. A likely explanation could be that the clearance rate of avian malaria parasites differs between avian malaria lineages and/or between avian hosts.
Collapse
Affiliation(s)
| | | | - Lars Råberg
- Department of Biology, Lund University, Lund, Sweden
| | | | | |
Collapse
|
399
|
Monzón-Argüello C, Garcia de Leaniz C, Gajardo G, Consuegra S. Less can be more: loss of MHC functional diversity can reflect adaptation to novel conditions during fish invasions. Ecol Evol 2013; 3:3359-68. [PMID: 24223274 PMCID: PMC3797483 DOI: 10.1002/ece3.701] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 06/26/2013] [Accepted: 07/01/2013] [Indexed: 12/02/2022] Open
Abstract
The ability of invasive species to adapt to novel conditions depends on population size and environmental mismatch, but also on genetic variation. Away from their native range, invasive species confronted with novel selective pressures may display different levels of neutral versus functional genetic variation. However, the majority of invasion studies have only examined genetic variation at neutral markers, which may reveal little about how invaders adapt to novel environments. Salmonids are good model systems to examine adaptation to novel pressures because they have been translocated all over the world and represent major threats to freshwater biodiversity in the Southern Hemisphere, where they have become invasive. We examined patterns of genetic differentiation at seven putatively neutral (microsatellites) loci and one immune-related major histocompatibility complex (MHC class II-β) locus among introduced rainbow trout living in captivity (farmed) or under natural conditions (naturalized) in Chilean Patagonia. A significant positive association was found between differentiation at neutral and functional markers, highlighting the role of neutral evolutionary forces in shaping genetic variation at immune-related genes in salmonids. However, functional (MHC) genetic diversity (but not microsatellite diversity) decreased with time spent in the wild since introduction, suggesting that there was selection against alleles associated with captive rearing of donor populations that do not provide an advantage in the wild. Thus, although high genetic diversity may initially enhance fitness in translocated populations, it does not necessarily reflect invasion success, as adaptation to novel conditions may result in rapid loss of functional MHC diversity.
Collapse
Affiliation(s)
- Catalina Monzón-Argüello
- Department of Biosciences, Swansea University Swansea, SA2 8PP, United Kingdom ; IBERS, Aberystwyth University Penglais Campus, Aberystwyth, SY23 3DA, United Kingdom
| | | | | | | |
Collapse
|
400
|
Lifjeld JT, Gohli J, Johnsen A. Promiscuity, sexual selection, and genetic diversity: a reply to Spurgin. Evolution 2013; 67:3073-4. [PMID: 24094357 DOI: 10.1111/evo.12211] [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: 06/07/2013] [Accepted: 07/13/2013] [Indexed: 11/27/2022]
Abstract
We recently reported a positive association between female promiscuity and genetic diversity across passerine birds, and launched the hypothesis that female promiscuity acts as a balancing selection, pressure maintaining genetic diversity in populations (Gohli et al.2013). Spurgin (2013) questions both our analyses and interpretations. While we agree that the hypothesis needs more comprehensive empirical testing, we find his specific points of criticism unjustified. In a more general perspective, we call for a more explicit recognition of female mating preferences as mechanisms of selection in population genetics theory.
Collapse
Affiliation(s)
- Jan T Lifjeld
- Natural History Museum, University of Oslo, 0318, Oslo, Norway.
| | | | | |
Collapse
|