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Cortazar-Chinarro M, Richter-Boix A, Rödin-Mörch P, Halvarsson P, Logue JB, Laurila A, Höglund J. Association between the skin microbiome and MHC class II diversity in an amphibian. Mol Ecol 2024; 33:e17198. [PMID: 37933583 DOI: 10.1111/mec.17198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.
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Affiliation(s)
- M Cortazar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- MEMEG/Department of Biology, Lund University, Lund, Sweden
- Department of Earth Ocean and Atmospheric Sciences, Faculty of Science 2020-2207, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Richter-Boix
- Department of Political and Social Science, Pompeu Fabra University, Barcelona, Spain
| | - P Rödin-Mörch
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - P Halvarsson
- Parasitology/Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J B Logue
- Aquatic Ecology/Department of Biology, Lund University, Lund, Sweden
- SLU University Library, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - J Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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2
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Wang QL, Wang TM, Deng CM, Zhang WL, He YQ, Xue WQ, Liao Y, Yang DW, Zheng MQ, Jia WH. Association of HLA diversity with the risk of 25 cancers in the UK Biobank. EBioMedicine 2023; 92:104588. [PMID: 37148584 DOI: 10.1016/j.ebiom.2023.104588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/17/2023] [Accepted: 04/11/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND The human leukocyte antigen (HLA) is a highly polymorphic region, and HLA diversity may play a role in presenting tumour-associated peptides and inducing immune responses. However, the effect of HLA diversity on cancers has not been fully assessed. We aimed to explore the role of HLA diversity on cancer development. METHODS A pan-cancer analysis was performed to evaluate the effect of HLA diversity, measured by HLA heterozygosity and HLA evolutionary divergence (HED), on the susceptibility of 25 cancers in the UK Biobank. FINDINGS We observed that the diversity of HLA class II locus was associated with a lower risk of lung cancer (ORhetero = 0.94, 95% CI = 0.90-0.97, P = 1.29 × 10-4) and head and neck cancer (ORhetero = 0.91, 95% CI = 0.86-0.96, P = 1.56 × 10-3). Besides, a lower risk of non-Hodgkin lymphoma was associated with an increased diversity of HLA class I (ORhetero = 0.92, 95% CI = 0.87-0.98, P = 8.38 × 10-3) and class II locus (ORhetero = 0.89, 95% CI = 0.86-0.92, P = 1.65 × 10-10). A lower risk of Hodgkin lymphoma was associated with the HLA class I diversity (ORhetero = 0.85, 95% CI = 0.75-0.96, P = 0.011). The protective effect of HLA diversity was mainly observed in pathological subtypes with higher tumour mutation burden, such as lung squamous cell carcinoma (P = 9.39 × 10-3) and diffuse large B cell lymphoma (Pclass I = 4.12 × 10-4; Pclass Ⅱ = 4.71 × 10-5), as well as the smoking subgroups of lung cancer (P = 7.45 × 10-5) and head and neck cancer (P = 4.55 × 10-3). INTERPRETATION We provided a systematic insight into the effect of HLA diversity on cancers, which might help to understand the etiological role of HLA on cancer development. FUNDING This study was supported by grants from the National Natural Science Foundation of China (82273705, 82003520); the Basic and Applied Basic Research Foundation of Guangdong Province, China (2021B1515420007); the Science and Technology Planning Project of Guangzhou, China (201804020094); Sino-Sweden Joint Research Programme (81861138006); the National Natural Science Foundation of China (81973131, 81903395, 81803319, 81802708).
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Affiliation(s)
- Qiao-Ling Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China; School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Da-Wei Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China; School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Mei-Qi Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China; School of Public Health, Sun Yat-sen University, Guangzhou, China.
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3
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Fu M, Eimes JA, Waldman B. Divergent allele advantage in the MHC and amphibian emerging infectious disease. INFECTION, GENETICS AND EVOLUTION 2023; 111:105429. [PMID: 36990307 DOI: 10.1016/j.meegid.2023.105429] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Genetic variation in the major histocompatibility complex (MHC) may be associated with resistance to the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). The pathogen originated in Asia, then spread worldwide, causing amphibian population declines and species extinctions. We compared the expressed MHC IIβ1 alleles of a Bd-resistant toad species, Bufo gargarizans, from South Korea with those of a Bd-susceptible Australasian frog species, Litoria caerulea. We found at least six expressed MHC IIβ1 loci in each of the two species. Amino acid diversity encoded by these MHC alleles was similar between species, but the genetic divergence of those alleles known for broader pathogen-derived peptide binding was greater in the Bd-resistant species. In addition, we found a potentially rare allele in one resistant individual from the Bd-susceptible species. Deep next-generation sequencing recovered approximately triple the genetic resolution accessible from traditional cloning-based genotyping. Targeting more than one MHC IIβ1 expressed locus enables us to better understand how host MHC may adapt to emerging infectious diseases.
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Pagliuca S, Gurnari C, Rubio MT, Visconte V, Lenz TL. Individual HLA heterogeneity and its implications for cellular immune evasion in cancer and beyond. Front Immunol 2022; 13:944872. [PMID: 36131910 PMCID: PMC9483928 DOI: 10.3389/fimmu.2022.944872] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023] Open
Abstract
Structural and functional variability of human leukocyte antigen (HLA) is the foundation for competent adaptive immune responses against pathogen and tumor antigens as it assures the breadth of the presented immune-peptidome, theoretically sustaining an efficient and diverse T cell response. This variability is presumably the result of the continuous selection by pathogens, which over the course of evolution shaped the adaptive immune system favoring the assortment of a hyper-polymorphic HLA system able to elaborate efficient immune responses. Any genetic alteration affecting this diversity may lead to pathological processes, perturbing antigen presentation capabilities, T-cell reactivity and, to some extent, natural killer cell functionality. A highly variable germline HLA genotype can convey immunogenetic protection against infections, be associated with tumor surveillance or influence response to anti-neoplastic treatments. In contrast, somatic aberrations of HLA loci, rearranging the original germline configuration, theoretically decreasing its variability, can facilitate mechanisms of immune escape that promote tumor growth and immune resistance. The purpose of the present review is to provide a unified and up-to-date overview of the pathophysiological consequences related to the perturbations of the genomic heterogeneity of HLA complexes and their impact on human diseases, with a special focus on cancer.
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Affiliation(s)
- Simona Pagliuca
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
- Service d’hématologie Clinique, Hôpital Brabois, CHRU Nancy and CNRS UMR 7365 IMoPa, Biopole de l’Université de Loarraine, Vandoeuvre les Nancy, France
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Marie Thérèse Rubio
- Service d’hématologie Clinique, Hôpital Brabois, CHRU Nancy and CNRS UMR 7365 IMoPa, Biopole de l’Université de Loarraine, Vandoeuvre les Nancy, France
| | - Valeria Visconte
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
| | - Tobias L. Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
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Jennings SL, Hoover BA, Wa Sin SY, Ebeler SE. Feather chemicals contain information about the major histocompatibility complex in a highly scented seabird. Proc Biol Sci 2022; 289:20220567. [PMID: 35611538 PMCID: PMC9130785 DOI: 10.1098/rspb.2022.0567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mate choice informed by the immune genes of the major histocompatibility complex (MHC) may provide fitness benefits including offspring with increased immunocompetence. Olfactory cues are considered the primary mechanism organisms use to evaluate the MHC of potential mates, yet this idea has received limited attention in birds. Motivated by a finding of MHC-dependent mate choice in the Leach's storm-petrel (Oceanodroma leucorhoa), we examined whether the chemical profiles of this highly scented seabird contain information about MHC genes. Whereas previous studies in birds examined non-volatile compounds, we used gas chromatography-mass spectrometry to measure the volatile compounds emitted from feathers that potentially serve as olfactory infochemicals about MHC and coupled this with locus-specific genotyping of MHC IIB genes. We found that feather chemicals reflected individual MHC diversity through interactions with sex and breeding status. Furthermore, similarity in MHC genotype was correlated with similarity in chemical profiles within female-female and male-female dyads. We provide the first evidence that volatile chemicals from bird feathers can encode information about the MHC. Our findings suggest that olfaction likely aids MHC-based mate choice in this species and highlight a role for chemicals in mediating genetic mate choice in birds where this mode of communication has been largely overlooked.
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Affiliation(s)
- Sarah L. Jennings
- Graduate Group in Ecology, University of California Davis, Davis CA 95616, USA
| | - Brian A. Hoover
- Graduate Group in Ecology, University of California Davis, Davis CA 95616, USA,Schmid College of Science and Technology, Chapman University, Orange, CA 92886, USA
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR
| | - Susan E. Ebeler
- Graduate Group in Ecology, University of California Davis, Davis CA 95616, USA,Department of Viticulture and Enology, University of California Davis, Davis CA 95616, USA
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Daull AM, Dubois V, Labussière-Wallet H, Venet F, Barraco F, Ducastelle-Lepretre S, Larcher MV, Balsat M, Gilis L, Fossard G, Ghesquières H, Heiblig M, Ader F, Alcazer V. Class I/Class II HLA Evolutionary Divergence Ratio Is an Independent Marker Associated With Disease-Free and Overall Survival After Allogeneic Hematopoietic Stem Cell Transplantation for Acute Myeloid Leukemia. Front Immunol 2022; 13:841470. [PMID: 35309346 PMCID: PMC8931406 DOI: 10.3389/fimmu.2022.841470] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Class I Human Leukocyte Antigen (HLA) evolutionary divergence (HED) is a metric which reflects immunopeptidome diversity and has been associated with immune checkpoint inhibitor responses in solid tumors. Its impact and interest in allogeneic hematopoietic stem cell transplantation (HCT) have not yet been thoroughly studied. This study analyzed the clinical and immune impact of class I and II HED in 492 acute myeloid leukemia (AML) recipients undergoing HCT. The overall cohort was divided into a training (n=338) and a testing (n=132) set. Univariate cox screening found a positive impact of a high class I HED and a negative impact of a high class II HED on both disease-free (DFS) and overall survival (OS). These results were combined in a unique marker, class I/class II HED ratio, and assessed in the testing cohort. The final multivariate cox model confirmed the positive impact of a high versus low class I/class II HED ratio on both DFS (Hazard Ratio (HR) 0.41 [95% CI 0.2-0.83]; p=0.01) and OS (HR 0.34 [0.19-0.59]; p<0.001), independently of HLA matching and other HCT parameters. No significant association was found between the ratio and graft-versus-host disease (GvHD) nor with neutrophil and platelet recovery. A high class I HED was associated with a tendency for an increase in NK, CD8 T-cell, and B cell recovery at 12 months. These results introduce HED as an original and independent prognosis marker reflecting immunopeptidome diversity and alloreactivity after HCT.
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Affiliation(s)
- Anne-Marie Daull
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Valérie Dubois
- Laboratory of histocompatibility, Etablissement Français du Sang, Lyon, France
| | - Hélène Labussière-Wallet
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Fabienne Venet
- Hospices Civils de Lyon, Immunology laboratory, Edouard Herriot Hospital, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard-Lyon 1, Lyon, France
| | - Fiorenza Barraco
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | | | - Marie-Virginie Larcher
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Marie Balsat
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Lila Gilis
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Gaëlle Fossard
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Hervé Ghesquières
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Maël Heiblig
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
- UR LIB “Lymphoma Immuno-Biology”, Université Claude Bernard Lyon I, Lyon, France
| | - Florence Ader
- Hospices Civils de Lyon, Immunology laboratory, Edouard Herriot Hospital, Lyon, France
- Hospices Civils de Lyon, Department of infectious diseases, Croix-Rousse hospital, Lyon, France
- LegioPath team, CIRI INSERM U1111 CNRS UMR 5308, Lyon, France
| | - Vincent Alcazer
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
- UR LIB “Lymphoma Immuno-Biology”, Université Claude Bernard Lyon I, Lyon, France
- *Correspondence: Vincent Alcazer,
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7
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Pagliuca S, Gurnari C, Awada H, Kishtagari A, Kongkiatkamon S, Terkawi L, Zawit M, Guan Y, LaFramboise T, Jha BK, Patel BJ, Hamilton BK, Majhail NS, Lundgren S, Mustjoki S, Saunthararajah Y, Visconte V, Chan TA, Yang CY, Lenz TL, Maciejewski JP. The similarity of class II HLA genotypes defines patterns of autoreactivity in idiopathic bone marrow failure disorders. Blood 2021; 138:2781-2798. [PMID: 34748628 PMCID: PMC8718627 DOI: 10.1182/blood.2021012900] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Idiopathic aplastic anemia (IAA) is a rare autoimmune bone marrow failure (BMF) disorder initiated by a human leukocyte antigen (HLA)-restricted T-cell response to unknown antigens. As in other autoimmune disorders, the predilection for certain HLA profiles seems to represent an etiologic factor; however, the structure-function patterns involved in the self-presentation in this disease remain unclear. Herein, we analyzed the molecular landscape of HLA complexes of a cohort of 300 IAA patients and almost 3000 healthy and disease controls by deeply dissecting their genotypic configurations, functional divergence, self-antigen binding capabilities, and T-cell receptor (TCR) repertoire specificities. Specifically, analysis of the evolutionary divergence of HLA genotypes (HED) showed that IAA patients carried class II HLA molecules whose antigen-binding sites were characterized by a high level of structural homology, only partially explained by specific risk allele profiles. This pattern implies reduced HLA binding capabilities, confirmed by binding analysis of hematopoietic stem cell (HSC)-derived self-peptides. IAA phenotype was associated with the enrichment in a few amino acids at specific positions within the peptide-binding groove of DRB1 molecules, affecting the interface HLA-antigen-TCR β and potentially constituting the basis of T-cell dysfunction and autoreactivity. When analyzing associations with clinical outcomes, low HED was associated with risk of malignant progression and worse survival, underlying reduced tumor surveillance in clearing potential neoantigens derived from mechanisms of clonal hematopoiesis. Our data shed light on the immunogenetic risk associated with IAA etiology and clonal evolution and on general pathophysiological mechanisms potentially involved in other autoimmune disorders.
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Affiliation(s)
- Simona Pagliuca
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
- University of Paris, Paris, France
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Hassan Awada
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Ashwin Kishtagari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Sunisa Kongkiatkamon
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Laila Terkawi
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Misam Zawit
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Yihong Guan
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Babal K Jha
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Bhumika J Patel
- Leukemia Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Betty K Hamilton
- Blood and Marrow Transplant Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Navneet S Majhail
- Blood and Marrow Transplant Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Sofie Lundgren
- Hematology Research Unit Helsinki, University of Helsinki-Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki-Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Yogen Saunthararajah
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Valeria Visconte
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany; and
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
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8
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Naito‐Liederbach AM, Sato Y, Nakajima N, Maeda T, Inoue T, Yamazaki T, Ogden R, Inoue‐Murayama M. Genetic diversity of the endangered Japanese golden eagle at neutral and functional loci. Ecol Res 2021. [DOI: 10.1111/1440-1703.12246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Yu Sato
- Wildlife Research Center Kyoto University Kyoto Japan
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Roslin UK
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies National Institute for Environmental Studies Tsukuba Japan
| | - Taku Maeda
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health Morioka Japan
| | - Takehiko Inoue
- Asian Raptor Research and Conservation Network Yasu Japan
| | - Toru Yamazaki
- Asian Raptor Research and Conservation Network Yasu Japan
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Roslin UK
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9
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Sawada A, Ando H, Takagi M. Evaluating the existence and benefit of major histocompatibility complex-based mate choice in an isolated owl population. J Evol Biol 2020; 33:762-772. [PMID: 32281698 DOI: 10.1111/jeb.13629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/16/2020] [Accepted: 04/01/2020] [Indexed: 11/28/2022]
Abstract
How mate preferences evolve in the first place has been a major conundrum for sexual selection. Some hypotheses explaining this assume fitness benefit derived from subsequent generations. Major histocompatibility complex (MHC)-based mate choice is a representative example of the mate choice that is associated with such trans-generational mechanisms. To provide evidences for fitness benefit of MHC-based mate choice, previous studies assessed the association between own MHC genotype and own fitness components. However, the association between MHC-based mate choice in the parental generation and fitness components in the resultant offspring generation has only rarely been measured in wild populations. Focusing on the isolated population of the monogamous Ryukyu Scops Owl (Otus elegans interpositus) on Minami-daito Island, Japan, we found evidence of MHC-based mate choice. However, we found no evidence of MHC-based mate choice increasing own reproductive success or offspring survival. This is a rare case study that directly examines the existence of the trans-generational indirect benefit of MHC-based mate choice for genetic compatibility from trans-generational data in a wild bird population. By investigating the fitness benefits of mate choice, this study serves to facilitate our understanding of the evolution of MHC-based mate choice.
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Affiliation(s)
- Akira Sawada
- Department of Natural History Science, Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Haruko Ando
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masaoki Takagi
- Department of Natural History Science, Graduate School of Science, Hokkaido University, Sapporo, Japan
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10
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Arora J, Pierini F, McLaren PJ, Carrington M, Fellay J, Lenz TL. HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation. Mol Biol Evol 2020; 37:639-650. [PMID: 31651980 PMCID: PMC7038656 DOI: 10.1093/molbev/msz249] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote advantage is still elusive. HLA heterozygotes may present a broader array of antigenic viral peptides to immune cells, possibly resulting in a more efficient cytotoxic T-cell response. Alternatively, heterozygosity may simply increase the chance to carry the most protective HLA alleles, as individual HLA alleles are known to differ substantially in their association with HIV-1 control. Here, we used data from 6,311 HIV-1-infected individuals to explore the relative contribution of quantitative and qualitative aspects of peptide presentation in HLA heterozygote advantage against HIV. Screening the entire HIV-1 proteome, we observed that heterozygous individuals exhibited a broader array of HIV-1 peptides presented by their HLA class I alleles. In addition, viral load was negatively correlated with the breadth of the HIV-1 peptide repertoire bound by an individual's HLA variants, particularly at HLA-B. This suggests that heterozygote advantage at HLA-B is at least in part mediated by quantitative peptide presentation. We also observed higher HIV-1 sequence diversity among HLA-B heterozygous individuals, suggesting stronger evolutionary pressure from HLA heterozygosity. However, HLA heterozygotes were also more likely to carry certain HLA alleles, including the highly protective HLA-B*57:01 variant, indicating that HLA heterozygote advantage ultimately results from a combination of quantitative and qualitative effects in antigen presentation.
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Affiliation(s)
- Jatin Arora
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Center, National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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11
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Pierini F, Lenz TL. Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection. Mol Biol Evol 2020; 35:2145-2158. [PMID: 29893875 PMCID: PMC6106954 DOI: 10.1093/molbev/msy116] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The highly polymorphic genes of the major histocompatibility complex (MHC) play a key role in adaptive immunity. Divergent allele advantage, a mechanism of balancing selection, is proposed to contribute to their exceptional polymorphism. It assumes that MHC genotypes with more divergent alleles allow for broader antigen-presentation to immune effector cells, by that increasing immunocompetence. However, the direct correlation between pairwise sequence divergence and the corresponding repertoire of bound peptides has not been studied systematically across different MHC genes. Here, we investigated this relationship for five key classical human MHC genes (human leukocyte antigen; HLA-A, -B, -C, -DRB1, and -DQB1), using allele-specific computational binding prediction to 118,097 peptides derived from a broad range of human pathogens. For all five human MHC genes, the genetic distance between two alleles of a heterozygous genotype was positively correlated with the total number of peptides bound by these two alleles. In accordance with the major antigen-presentation pathway of MHC class I molecules, HLA-B and HLA-C alleles showed particularly strong correlations for peptides derived from intracellular pathogens. Intriguingly, this bias coincides with distinct protein compositions between intra- and extracellular pathogens, possibly suggesting adaptation of MHC I molecules to present specifically intracellular peptides. Eventually, we observed significant positive correlations between an allele’s average divergence and its population frequency. Overall, our results support the divergent allele advantage as a meaningful quantitative mechanism through which pathogen-mediated selection leads to the evolution of MHC diversity.
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Affiliation(s)
- Federica Pierini
- Research Group for Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Ploen, Germany
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12
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Chowell D, Krishna C, Pierini F, Makarov V, Rizvi NA, Kuo F, Morris LGT, Riaz N, Lenz TL, Chan TA. Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy. Nat Med 2019; 25:1715-1720. [PMID: 31700181 DOI: 10.1038/s41591-019-0639-4] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022]
Abstract
Functional diversity of the highly polymorphic human leukocyte antigen class I (HLA-I) genes underlies successful immunologic control of both infectious disease and cancer. The divergent allele advantage hypothesis dictates that an HLA-I genotype with two alleles with sequences that are more divergent enables presentation of more diverse immunopeptidomes1-3. However, the effect of sequence divergence between HLA-I alleles-a quantifiable measure of HLA-I evolution-on the efficacy of immune checkpoint inhibitor (ICI) treatment for cancer remains unknown. In the present study the germline HLA-I evolutionary divergence (HED) of patients with cancer treated with ICIs was determined by quantifying the physiochemical sequence divergence between HLA-I alleles of each patient's genotype. HED was a strong determinant of survival after treatment with ICIs. Even among patients fully heterozygous at HLA-I, patients with an HED in the upper quartile respond better to ICIs than patients with a low HED. Furthermore, HED strongly impacts the diversity of tumor, viral and self-immunopeptidomes and intratumoral T cell receptor clonality. Similar to tumor mutation burden, HED is a fundamental metric of diversity at the major histocompatibility complex-peptide complex, which dictates ICI efficacy. The data link divergent HLA allele advantage to immunotherapy efficacy and unveil how ICI response relies on the evolved efficiency of HLA-mediated immunity.
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Affiliation(s)
- Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Naiyer A Rizvi
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell School of Medicine, New York, NY, USA.
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13
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Lan H, Zhou T, Wan QH, Fang SG. Genetic Diversity and Differentiation at Structurally Varying MHC Haplotypes and Microsatellites in Bottlenecked Populations of Endangered Crested Ibis. Cells 2019; 8:E377. [PMID: 31027280 PMCID: PMC6523929 DOI: 10.3390/cells8040377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022] Open
Abstract
Investigating adaptive potential and understanding the relative roles of selection and genetic drift in populations of endangered species are essential in conservation. Major histocompatibility complex (MHC) genes characterized by spectacular polymorphism and fitness association have become valuable adaptive markers. Herein we investigate the variation of all MHC class I and II genes across seven populations of an endangered bird, the crested ibis, of which all current individuals are offspring of only two pairs. We inferred seven multilocus haplotypes from linked alleles in the Core Region and revealed structural variation of the class II region that probably evolved through unequal crossing over. Based on the low polymorphism, structural variation, strong linkage, and extensive shared alleles, we applied the MHC haplotypes in population analysis. The genetic variation and population structure at MHC haplotypes are generally concordant with those expected from microsatellites, underlining the predominant role of genetic drift in shaping MHC variation in the bottlenecked populations. Nonetheless, some populations showed elevated differentiation at MHC, probably due to limited gene flow. The seven populations were significantly differentiated into three groups and some groups exhibited genetic monomorphism, which can be attributed to founder effects. We therefore propose various strategies for future conservation and management.
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Affiliation(s)
- Hong Lan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Department of Agriculture, Zhejiang Open University, Hangzhou 310012, China.
| | - Tong Zhou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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14
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Banerjee N, Polushina T, Bettella F, Steen VM, Andreassen OA, Le Hellard S. Analysis of differentially methylated regions in great apes and extinct hominids provides support for the evolutionary hypothesis of schizophrenia. Schizophr Res 2019; 206:209-216. [PMID: 30545758 DOI: 10.1016/j.schres.2018.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 10/12/2018] [Accepted: 11/22/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The persistence of schizophrenia in human populations separated by geography and time led to the evolutionary hypothesis that proposes schizophrenia as a by-product of the higher cognitive abilities of modern humans. To explore this hypothesis, we used here an evolutionary epigenetics approach building on differentially methylated regions (DMRs) of the genome. METHODS We implemented a polygenic enrichment testing pipeline using the summary statistics of genome-wide association studies (GWAS) of schizophrenia and 12 other phenotypes. We investigated the enrichment of association of these traits across genomic regions with variable methylation between modern humans and great apes (orangutans, chimpanzees and gorillas; great ape DMRs) and between modern humans and recently extinct hominids (Neanderthals and Denisovans; hominid DMRs). RESULTS Regions that are hypo-methylated in humans compared to great apes show enrichment of association with schizophrenia only if the major histocompatibility complex (MHC) region is included. With the MHC region removed from the analysis, only a modest enrichment for SNPs of low effect persists. The INRICH pipeline confirms this finding after rigorous permutation and bootstrapping procedures. CONCLUSION The analyses of regions with differential methylation changes in humans and great apes do not provide compelling evidence of enrichment of association with schizophrenia, in contrast to our previous findings on more recent methylation differences between modern humans, Neanderthals and Denisovans. Our results further support the evolutionary hypothesis of schizophrenia and indicate that the origin of some of the genetic susceptibility factors of schizophrenia may lie in recent human evolution.
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Affiliation(s)
- Niladri Banerjee
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Tatiana Polushina
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Francesco Bettella
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
| | - Vidar M Steen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Ole A Andreassen
- NORMENT - K.G. Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; NORMENT - K.G. Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
| | - Stephanie Le Hellard
- NORMENT - K.G. Jebsen Center for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
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15
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Roved J, Hansson B, Tarka M, Hasselquist D, Westerdahl H. Evidence for sexual conflict over major histocompatibility complex diversity in a wild songbird. Proc Biol Sci 2018; 285:rspb.2018.0841. [PMID: 30068671 PMCID: PMC6111173 DOI: 10.1098/rspb.2018.0841] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/06/2018] [Indexed: 12/24/2022] Open
Abstract
Sex differences in parasite load and immune responses are found across a wide range of animals, with females generally having lower parasite loads and stronger immune responses than males. Intrigued by these general patterns, we investigated if there was any sign of sex-specific selection on an essential component of adaptive immunity that is known to affect fitness, the major histocompatibility complex class I (MHC-I) genes, in a 20-year study of great reed warblers. Our analyses on fitness related to MHC-I diversity showed a highly significant interaction between MHC-I diversity and sex, where males with higher, and females with lower, MHC-I diversity were more successful in recruiting offspring. Importantly, mean MHC-I diversity did not differ between males and females, and consequently neither sex reached its MHC-I fitness optimum. Thus, there is an unresolved genetic sexual conflict over MHC-I diversity in great reed warblers. Selection from pathogens is known to maintain MHC diversity, but previous theory ignores that the immune environments are considerably different in males and females. Our results suggest that sexually antagonistic selection is an important, previously neglected, force in the evolution of vertebrate adaptive immunity, and have implications for evolutionary understanding of costs of immune responses and autoimmune diseases.
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Affiliation(s)
- Jacob Roved
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Maja Tarka
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Dennis Hasselquist
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Helena Westerdahl
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62 Lund, Sweden
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16
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Hoover B, Alcaide M, Jennings S, Sin SYW, Edwards SV, Nevitt GA. Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach's storm-petrels (Oceanodroma leucorhoa). Mol Ecol 2018; 27:3371-3385. [PMID: 30010226 DOI: 10.1111/mec.14801] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/31/2018] [Accepted: 06/20/2018] [Indexed: 01/03/2023]
Abstract
Studies of MHC-based mate choice in wild populations often test hypotheses on species exhibiting female choice and male-male competition, which reflects the general prevalence of females as the choosy sex in natural systems. Here, we examined mutual mate-choice patterns in a small burrow-nesting seabird, the Leach's storm-petrel (Oceanodroma leucorhoa), using the major histocompatibility complex (MHC). The life history and ecology of this species are extreme: both partners work together to fledge a single chick during the breeding season, a task that requires regularly travelling hundreds of kilometres to and from foraging grounds over a 6- to 8-week provisioning period. Using a 5-year data set unprecedented for this species (n = 1078 adults and 925 chicks), we found a positive relationship between variation in the likelihood of female reproductive success and heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous reports rejecting disassortative mating as a mechanism for maintaining genetic polymorphism in this species, here we show that males make significant disassortative mate-choice decisions. Variability in female reproductive success suggests that the most common homozygous females (Ocle-DAB2*01/Ocle-DAB2*01) may be physiologically disadvantaged and, therefore, less preferred as lifelong partners for choosy males. The results from this study support the role of mate choice in maintaining high levels of MHC variability in a wild seabird species and highlight the need to incorporate a broader ecological framework and sufficient sample sizes into studies of MHC-based mating patterns in wild populations in general.
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Affiliation(s)
- Brian Hoover
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
| | - Miguel Alcaide
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sarah Jennings
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Gabrielle A Nevitt
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
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17
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Krause ET, Bischof HJ, Engel K, Golüke S, Maraci Ö, Mayer U, Sauer J, Caspers BA. Olfaction in the Zebra Finch ( Taeniopygia guttata ): What Is Known and Further Perspectives. ADVANCES IN THE STUDY OF BEHAVIOR 2018. [DOI: 10.1016/bs.asb.2017.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Characterization of major histocompatibility complex class I, and class II DRB loci of captive and wild Indian leopards (Panthera pardus fusca). Genetica 2017; 145:541-558. [DOI: 10.1007/s10709-017-9979-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/14/2017] [Indexed: 10/19/2022]
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19
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Grosberg RK, Levitan DR, Cameron BB. EVOLUTIONARY GENETICS OF ALLORECOGNITION IN THE COLONIAL HYDROID HYDRACTINIA SYMBIOLONGICARPUS. Evolution 2017; 50:2221-2240. [PMID: 28565652 DOI: 10.1111/j.1558-5646.1996.tb03612.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/1995] [Accepted: 05/14/1996] [Indexed: 12/01/2022]
Abstract
Many sedentary, clonal marine invertebrates compete intensively with conspecifics for habitable space. Allorecognition systems mediate the nature and outcome of these intraspecific competitive interactions, such that the initiation of agonistic behavior and the potential for intergenotypic fusion depend strongly on the relatedness of the contestants. The dependence of these behaviors on relatedness, along with the extraordinary precision with which self can be discriminated from nonself, suggest that allorecognition systems are highly polymorphic genetically. However, allotypic specificity of this sort could be produced by any number of genetic scenarios, ranging from relatively few loci with abundant allelic variation to numerous loci with relatively few alleles per locus. At this point, virtually nothing is known of the formal genetics of allorecognition in marine invertebrates; consequently, the evolutionary dynamics of such systems remain poorly understood. In this paper, we characterize the formal genetics of allorecognition in the marine hydrozoan Hydractinia symbiolongicarpus. Hydractinia symbiolongicarpus colonizes gastropod shells occupied by hermit crabs. When two or more individuals grow into contact, one of three outcomes ensues: fusion (compatibility), transitory fusion (a temporary state of compatibility), and rejection (incompatibility, often accompanied by the production of agonistic structures termed hyperplastic stolons). Observed patterns of compatibility between unrelated, half-sib pairs, and full-sib pairs show that unrelated and half-sib pairs under laboratory culture have a very low probability of being fusible, whereas full sibs have a roughly 30% rate of fusion in experimental pairings. The genetic simulations indicate that roughly five loci, with 5-7 alleles per locus, confer specificity in this species. In ecological terms, the reproductive ecology of H. symbiolongicarpus should promote the cosettlement of kin, some of which should be full sibs, and some half sibs. Thus, there is potential for kin selection to play a major role in the evolution of the H. symbiolongicarpus allorecognition system. In genetic terms, this system conforms to theoretical predictions for a recognition system selected to distinguish among classes of kin, in addition to self from nonself.
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Affiliation(s)
- Richard K Grosberg
- Center for Population Biology, University of California, Davis, California, 95616
| | - Don R Levitan
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, 32306-2043
| | - Brenda B Cameron
- Center for Population Biology, University of California, Davis, California, 95616
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20
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Bensch S, Hasselquist D, von Schantz T. GENETIC SIMILARITY BETWEEN PARENTS PREDICTS HATCHING FAILURE: NONINCESTUOUS INBREEDING IN THE GREAT REED WARBLER? Evolution 2017; 48:317-326. [PMID: 28568307 DOI: 10.1111/j.1558-5646.1994.tb01314.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/1992] [Accepted: 04/13/1993] [Indexed: 12/01/2022]
Abstract
The DNA-fingerprinting technique was used to find the true pedigrees and to detect the overall genetic similarity between mates of great reed warblers (Acrocephalus arundinaceus) at an isolated breeding site in Sweden. The study covered 4 yr preceded by 3 yr when almost all adults and nestlings in the study area had been banded. DNA fingerprinting revealed that the putative father had sired 97% of the young (N = 455). The mate's genetic similarity, revealed as the proportion of bands shared in restriction fragment length polymorphism (RFLP) patterns, was high compared with other species of wild birds. Also, band sharing was higher between mates native to the area than between pairs in which the female was experimentally introduced from a distant breeding site. Hatching success of eggs was negatively correlated with the degree of genetic similarity between the mates, whereas pedigree data, up to the level of great-grandparents, clearly demonstrated an absence of close inbreeding. These are the first data showing a significant fitness cost associated with the choice of a mate that has high genetic similarity, even if it is not a close kin. This cost might be caused by generalized negative consequences of genomewide inbreeding in the present study, possibly accentuated by recent population bottlenecks.
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Affiliation(s)
- Staffan Bensch
- Department of Ecology, Animal Ecology, University of Lund, Ecology Building, S-223 62 Lund, Sweden.,Molecular Population Biology, Wallenberg Laboratory, University of Lund, Box 7031, S-220 07 Lund, Sweden
| | - Dennis Hasselquist
- Department of Ecology, Animal Ecology, University of Lund, Ecology Building, S-223 62 Lund, Sweden.,Molecular Population Biology, Wallenberg Laboratory, University of Lund, Box 7031, S-220 07 Lund, Sweden
| | - Torbjörn von Schantz
- Department of Ecology, Animal Ecology, University of Lund, Ecology Building, S-223 62 Lund, Sweden.,Molecular Population Biology, Wallenberg Laboratory, University of Lund, Box 7031, S-220 07 Lund, Sweden
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21
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Cohen CS, Saito Y, Weissman IL. EVOLUTION OF ALLORECOGNITION IN BOTRYLLID ASCIDIANS INFERRED FROM A MOLECULAR PHYLOGENY. Evolution 2017; 52:746-756. [PMID: 28565254 DOI: 10.1111/j.1558-5646.1998.tb03699.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/1997] [Accepted: 03/06/1998] [Indexed: 11/26/2022]
Abstract
Despite the functional and phyletic ubiquity of highly polymorphic genetic recognition systems, the evolution and maintenance of these remarkable loci remain an empirical and theoretical puzzle. Many clonal invertebrates use polymorphic genetic recognition systems to discriminate kin from unrelated individuals during behavioral interactions that mediate competition for space. Space competition may have been a selective force promoting the evolution of highly polymorphic recognition systems, or preexisting polymorphic loci may have been coopted for the purpose of mediating space competition. Ascidian species in the family Botryllidae have an allorecognition system in which fusion or rejection between neighboring colonies is controlled by allele-sharing at a single, highly polymorphic locus. The behavioral sequence involved in allorecognition varies in a species-specific fashion with some species requiring extensive intercolony tissue integration prior to the allorecognition response, while other species contact opposing colonies at only a few points on the outer surface before resolving space conflicts. Due to an apparent species-specific continuum of behavioral variation in the degree of intercolony tissue integration required for allorecognition, this system lends itself to a phylogenetic analysis of the evolution of an allorecognition system. We constructed a molecular phylogeny of the botryllids based on 18S rDNA sequence and mapped allorecognition behavioral variation onto the phylogeny. Our phylogeny shows the basal allorecognition condition for the group is the most internal form of the recognition reaction. More derived species show progressively more external allorecognition responses, and in some cases loss of some features of internal function. We suggest that external allorecognition appears to be a secondary function of a polymorphic discriminatory system that was already in place due to other selective pressures such as gamete, pathogen, or developmental cell lineage recognition.
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Affiliation(s)
- C Sarah Cohen
- Department of Developmental Biology and Hopkins Marine Station, Stanford University, Stanford, California, 94305
| | - Yasunori Saito
- Shimoda Marine Research Station, University of Tsukuba, 5-10-1 Shimoda, Shizuoka 415, Japan
| | - Irving L Weissman
- Department of Developmental Biology and Hopkins Marine Station, Stanford University, Stanford, California, 94305
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22
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Positive selection in cathelicidin host defense peptides: adaptation to exogenous pathogens or endogenous receptors? Heredity (Edinb) 2016; 118:453-465. [PMID: 27925615 PMCID: PMC5564380 DOI: 10.1038/hdy.2016.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/28/2016] [Accepted: 10/03/2016] [Indexed: 11/24/2022] Open
Abstract
The cause of adaptive protein evolution includes internal (for example, co-evolution of ligand-receptor pairs) and external (for example, adaptation to different ecological niches) mechanisms. Host defense peptides (HDPs) are a class of vertebrate-specific cationic antimicrobial peptides evolving under positive selection. Besides their antibiotic activity, HDPs also exert an effect on multiple host immune cells, thus providing an ideal model to study selective agents driving their evolution. On the basis of a combination of computational and experimental approaches, we studied the evolution of LL-37-type HDPs in mammals, the mature peptide of cathelicidin CAP18 (herein termed CAP18-MP) and investigated the driving force behind the evolution. Using codon-substitution maximum likelihood models, we analyzed CAP18-MPs in 40 species belonging to nine mammalian Orders and identified four positively selected sites (PSSs) that all are located on two terminal unordered regions of CAP18-MPs. Grafting the two positively selected regions of human or whale CAP18-MP to the α-helical scaffold of a rabbit homolog (substituting its corresponding parts) led to no alterations in antibacterial activity, spectrum and action mode. Likewise, further deletion of the two terminal regions did not alter its functional features. Evolutionary conservation analysis of mammalian FPR2, a receptor known to interact with the C-terminal positively selected region of LL-37, revealed high evolutionary variability in its ligand-binding extracellular loop domains, matching sequence diversity of the unordered regions in CAP18-MPs. This is the first report describing that the signature of positive selection of cathelicidins is not associated with their direct bactericidal activity, but rather with the evolutionary variability of their endogenous receptors.
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23
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Winternitz J, Abbate JL, Huchard E, Havlíček J, Garamszegi LZ. Patterns of MHC-dependent mate selection in humans and nonhuman primates: a meta-analysis. Mol Ecol 2016; 26:668-688. [DOI: 10.1111/mec.13920] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 12/27/2022]
Affiliation(s)
- J. Winternitz
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 24306 Ploen Germany
- Institute of Vertebrate Biology; Czech Academy of Sciences; v.v.i. Květná 8 603 65 Brno Czech Republic
- Institute of Botany; Czech Academy of Sciences; v.v.i. Lidická 25/27 657 20 Brno Czech Republic
| | - J. L. Abbate
- Institute of Ecology and Evolution; University of Bern; Balterstrasse 6 3006 Bern Switzerland
- INRA - UMR 1062 CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); 755 Avenue du campus Agropolis 34988 Montferrier-sur-Lez France
| | - E. Huchard
- CEFE UMR5175; CNRS - Université de Montpellier - EPHE; 1919 Route de Mende 34295 Montpellier Cedex 5 France
| | - J. Havlíček
- Department of Zoology; Faculty of Science; Charles University; Viničná 7 128 44 Prague 2 Czech Republic
| | - L. Z. Garamszegi
- Department of Evolutionary Ecology; Estación Biológica de Doñana-CSIC; c/Americo Vespucio s/n 41092 Seville Spain
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Burger D, Meuwly C, Marti E, Sieme H, Oberthür M, Janda J, Meinecke-Tillmann S, Wedekind C. MHC-correlated preferences in diestrous female horses (Equus caballus). Theriogenology 2016; 89:318-323.e1. [PMID: 27842717 DOI: 10.1016/j.theriogenology.2016.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 12/29/2022]
Abstract
Genes of the major histocompatibility complex (MHC) have been shown to influence communication in many vertebrates, possibly with context-specific MHC-correlated reactions. Here we test for MHC-linked female preferences in the polygynous horse (Equus caballus) by repeatedly exposing 19 mares to a group of seven sexually experienced stallions. Each mare was tested four times during two consecutive reproductive cycles, twice during estrus and twice during diestrus. Male plasma testosterone concentrations were determined from weekly blood samples, and equine leukocyte antigen (ELA) class I and II alleles were determined serologically at the end of the experiments. Perception of male attractiveness was strongly dependent on estrous cycle: mean preference scores did not correlate for mares in diestrus and estrus and varied more during estrus than during diestrus. We found elevated female interests for MHC-dissimilar stallions, but only during diestrus, not during estrus. Female preferences were not significantly predicted by mean male testosterone plasma concentrations. However, testosterone concentrations changed during the 11 weeks of the experiment. By the end of the experiment, average testosterone concentration was significantly correlated to the average number of MHC alleles the stallions shared with the mares. We conclude that the MHC affects female preferences for stallions, but non-MHC linked male characteristics can overshadow effects of the MHC during estrus.
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Affiliation(s)
- D Burger
- Swiss Institute of Equine Medicine, Agroscope and University of Bern, Avenches, Switzerland.
| | - C Meuwly
- Swiss Institute of Equine Medicine, Agroscope and University of Bern, Avenches, Switzerland
| | - E Marti
- Department of Clinical Research, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - H Sieme
- Institute for Reproductive Biology, University of Veterinary Medicine Hanover, Hanover, Germany
| | - M Oberthür
- Unit for Reproductive Medicine-Clinic for Horses, University of Veterinary Medicine Hanover, Hanover, Germany
| | - J Janda
- Department of Clinical Research, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - S Meinecke-Tillmann
- Unit for Reproductive Medicine-Clinic for Horses, University of Veterinary Medicine Hanover, Hanover, Germany
| | - C Wedekind
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
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25
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Pearson SK, Bradford TM, Ansari TH, Bull CM, Gardner MG. MHC genotyping from next-generation sequencing: detailed methodology for the gidgee skink, Egernia stokesii. T ROY SOC SOUTH AUST 2016. [DOI: 10.1080/03721426.2016.1216735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- S. K. Pearson
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
| | - T. M. Bradford
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
| | - T. H. Ansari
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
| | - C. M. Bull
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
| | - M. G. Gardner
- School of Biological Sciences, Flinders University of South Australia, Bedford Park, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
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26
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Ferrandiz-Rovira M, Allainé D, Callait-Cardinal MP, Cohas A. Mate choice for neutral and MHC genetic characteristics in Alpine marmots: different targets in different contexts? Ecol Evol 2016; 6:4243-57. [PMID: 27386072 PMCID: PMC4930977 DOI: 10.1002/ece3.2189] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/11/2016] [Accepted: 04/26/2016] [Indexed: 01/16/2023] Open
Abstract
Sexual selection through female mate choice for genetic characteristics has been suggested to be an important evolutionary force maintaining genetic variation in animal populations. However, the genetic targets of female mate choice are not clearly identified and whether female mate choice is based on neutral genetic characteristics or on particular functional loci remains an open question. Here, we investigated the genetic targets of female mate choice in Alpine marmots (Marmota marmota), a socially monogamous mammal where extra‐pair paternity (EPP) occurs. We used 16 microsatellites to describe neutral genetic characteristics and two MHC loci belonging to MHC class I and II as functional genetic characteristics. Our results reveal that (1) neutral and MHC genetic characteristics convey different information in this species, (2) social pairs show a higher MHC class II dissimilarity than expected under random mate choice, and (3) the occurrence of EPP increases when social pairs present a high neutral genetic similarity or dissimilarity but also when they present low MHC class II dissimilarity. Thus, female mate choice is based on both neutral and MHC genetic characteristics, and the genetic characteristics targeted seem to be context dependent (i.e., the genes involved in social mate choice and genetic mate choice differ). We emphasize the need for empirical studies of mate choice in the wild using both neutral and MHC genetic characteristics because whether neutral and functional genetic characteristics convey similar information is not universal.
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Affiliation(s)
- Mariona Ferrandiz-Rovira
- Laboratoire Biométrie et Biologie Evolutive Université de Lyon CNRS UMR 5558 Université Lyon 1 F-69622 Villeurbanne F-69000 Lyon France; Université of Lyon VetAgro Sup Campus Vet F-69280 Marcy-L'Étoile France; CREAF Cerdanyola del Vallès 08193 Catalonia Spain; Univ Autònoma de Barcelona Cerdanyola del Vallès 08193 Catalonia Spain
| | - Dominique Allainé
- Laboratoire Biométrie et Biologie Evolutive Université de Lyon CNRS UMR5558 Université Lyon 1 F-69622 Villeurbanne F-69000 Lyon France
| | - Marie-Pierre Callait-Cardinal
- Laboratoire Biométrie et Biologie Evolutive Université de Lyon CNRS UMR 5558 Université Lyon 1 F-69622 Villeurbanne F-69000 Lyon France; Université of Lyon VetAgro Sup Campus Vet F-69280 Marcy-L'Étoile France
| | - Aurélie Cohas
- Laboratoire Biométrie et Biologie Evolutive Université de Lyon CNRS UMR5558 Université Lyon 1 F-69622 Villeurbanne F-69000 Lyon France
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27
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Cobble KR, Califf KJ, Stone NE, Shuey MM, Birdsell DN, Colman RE, Schupp JM, Aziz M, Van Andel R, Rocke TE, Wagner DM, Busch JD. Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history. Ecol Evol 2016; 6:2624-51. [PMID: 27066243 PMCID: PMC4798151 DOI: 10.1002/ece3.2077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 01/16/2023] Open
Abstract
Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague‐related die‐offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67–0.87) in all colonies. Two other DRB1 alleles appear to be trans‐species polymorphisms shared with the black‐tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (FST = 0.033) than at microsatellite markers (FST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an FST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.
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Affiliation(s)
- Kacy R Cobble
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Katy J Califf
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Nathan E Stone
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Megan M Shuey
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Dawn N Birdsell
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Rebecca E Colman
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - James M Schupp
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Maliha Aziz
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Roger Van Andel
- University of California Berkeley MC 7150 Berkeley California 94720 USA
| | - Tonie E Rocke
- United States Geological Survey National Wildlife Health Center 6006 Schroeder Road Madison Wisconsin 53711 USA
| | - David M Wagner
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
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Zeng QQ, He K, Sun DD, Ma MY, Ge YF, Fang SG, Wan QH. Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes. BMC Evol Biol 2016; 16:42. [PMID: 26892934 PMCID: PMC4758006 DOI: 10.1186/s12862-016-0609-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 02/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) genes are vital partners in the acquired immune processes of vertebrates. MHC diversity may be directly associated with population resistance to infectious pathogens. Here, we screened for polymorphisms in exons 2 and 3 of the IA1 and IA2 genes in 12 golden pheasant populations across the Chinese mainland to characterize their genetic variation levels, to understand the effects of historical positive selection and recombination in shaping class I diversity, and to investigate the genetic structure of wild golden pheasant populations. RESULTS Among 339 individual pheasants, we identified 14 IA1 alleles in exon 2 (IA1-E2), 11 IA1-E3 alleles, 27 IA2-E2 alleles, and 28 IA2-E3 alleles. The non-synonymous substitution rate was significantly greater than the synonymous substitution rate at sequences in the IA2 gene encoding putative peptide-binding sites but not in the IA1 gene; we also found more positively selected sites in IA2 than in IA1. Frequent recombination events resulted in at least 9 recombinant IA2 alleles, in accordance with the intermingling pattern of the phylogenetic tree. Although some IA alleles are widely shared among studied populations, large variation occurs in the number of IA alleles across these populations. Allele frequency analysis across 2 IA loci showed low levels of genetic differentiation among populations on small geographic scales; however, significant genetic differentiation was observed between pheasants from the northern and southern regions of the Yangtze River. Both STRUCTURE analysis and F-statistic (F ST ) value comparison classified those populations into 2 major groups: the northern region of the Yangtze River (NYR) and the southern region of the Yangtze River (SYR). CONCLUSIONS More extensive polymorphisms in IA2 than IA1 indicate that IA2 has undergone much stronger positive-selection pressure during evolution. Moreover, the recombination events detected between the genes and the intermingled phylogenetic pattern indicate that interlocus recombination accounts for much of the allelic variation in IA2. Analysis of the population differentiation implied that homogenous balancing selection plays an important part in maintaining an even distribution of MHC variations. The natural barrier of the Yangtze River and heterogeneous balancing selection might help shape the NYR-SYR genetic structure in golden pheasants.
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Affiliation(s)
- Qian-Qian Zeng
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Ke He
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang, 311300, China.
| | - Dan-Dan Sun
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Mei-Ying Ma
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Yun-Fa Ge
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Sheng-Guo Fang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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29
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Buczek M, Okarma H, Demiaszkiewicz AW, Radwan J. MHC, parasites and antler development in red deer: no support for the Hamilton & Zuk hypothesis. J Evol Biol 2016; 29:617-32. [PMID: 26687843 DOI: 10.1111/jeb.12811] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 12/08/2015] [Accepted: 12/11/2015] [Indexed: 12/28/2022]
Abstract
The Hamilton-Zuk hypothesis proposes that the genetic benefits of preferences for elaborated secondary sexual traits have their origins in the arms race between hosts and parasites, which maintains genetic variance in parasite resistance. Infection, in turn, can be reflected in the expression of costly sexual ornaments. However, the link between immune genes, infection and the expression of secondary sexual traits has rarely been investigated. Here, we explored whether the presence and identity of functional variants (supertypes) of the highly polymorphic major histocompatibility complex (MHC), which is responsible for the recognition of parasites, predict the load of lung and gut parasites and antler development in the red deer (Cervus elaphus). While we found MHC supertypes to be associated with infection by a number of parasite species, including debilitating lung nematodes, we did not find support for the Hamilton-Zuk hypothesis. On the contrary, we found that lung nematode load was positively associated with antler development. We also found that the supertypes that were associated with resistance to certain parasites at the same time cause susceptibility to others. Such trade-offs may undermine the potential genetic benefits of mate choice for resistant partners.
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Affiliation(s)
- M Buczek
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - H Okarma
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | | | - J Radwan
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland.,Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Poland
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30
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Galaverni M, Caniglia R, Milanesi P, Lapalombella S, Fabbri E, Randi E. Choosy Wolves? Heterozygote Advantage But No Evidence of MHC-Based Disassortative Mating. J Hered 2015; 107:134-42. [PMID: 26610365 DOI: 10.1093/jhered/esv090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/27/2015] [Indexed: 11/13/2022] Open
Abstract
A variety of nonrandom mate choice strategies, including disassortative mating, are used by vertebrate species to avoid inbreeding, maintain heterozygosity and increase fitness. Disassortative mating may be mediated by the major histocompatibility complex (MHC), an important gene cluster controlling immune responses to pathogens. We investigated the patterns of mate choice in 26 wild-living breeding pairs of gray wolf (Canis lupus) that were identified through noninvasive genetic methods and genotyped at 3 MHC class II and 12 autosomal microsatellite (STR) loci. We tested for deviations from random mating and evaluated the covariance of genetic variables at functional and STR markers with fitness proxies deduced from pedigree reconstructions. Results did not show evidences of MHC-based disassortative mating. Rather we found a higher peptide similarity between mates at MHC loci as compared with random expectations. Fitness values were positively correlated with heterozygosity of the breeders at both MHC and STR loci, whereas they decreased with relatedness at STRs. These findings may indicate fitness advantages for breeders that, while avoiding highly related mates, are more similar at the MHC and have high levels of heterozygosity overall. Such a pattern of MHC-assortative mating may reflect local coadaptation of the breeders, while a reduction in genetic diversity may be balanced by heterozygote advantages.
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Affiliation(s)
- Marco Galaverni
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi).
| | - Romolo Caniglia
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
| | - Pietro Milanesi
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
| | - Silvana Lapalombella
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
| | - Elena Fabbri
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
| | - Ettore Randi
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
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Yang B, Ren B, Xiang Z, Yang J, Yao H, Garber PA, Li M. Major histocompatibility complex and mate choice in the polygynous primate: the Sichuan snub-nosed monkey (Rhinopithecus roxellana). Integr Zool 2015; 9:598-612. [PMID: 24382257 DOI: 10.1111/1749-4877.12084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The highly polymorphic genes within the major histocompatibility complex (MHC) not only play a major role in immunity resistance, but also seem to provide hints for mate choice in some animal populations. In the present study we investigated MHC-related mate choice in a small natural population (group size 40-55 individuals) of a polygynous primate, the Sichuan snub-nosed monkey (Rhinopithecus roxellana). We found that there was no evidence either for MHC-disassortative mating, or for females to mate with males based on MHC heterozygosity or specific alleles. Nevertheless, of the 11 alleles identified, we found that the frequencies of 2 alleles, Rhro-DRB2 (P < 0.01) and Rhro-DRB5 (P < 0.05) were higher in offspring than in their parents. These findings suggest that MHC-DRB in this population of R. roxellana is unlikely to be associated with mating preferences. Limited female opportunities for mate choice are likely due, in part, to the harem breeding structure present in R. roxellana, and the relatively small number of resident adult males in our study band (N = 4-6). In addition, we suggest that differences in the frequency of particular alleles across generations may be linked to parasite resistance in a fluctuating environment; however, confirmation of this finding requires further study.
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Affiliation(s)
- Banghe Yang
- Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Graduate School of the University of Chinese Academy of Sciences, Beijing, China
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Sepil I, Radersma R, Santure AW, De Cauwer I, Slate J, Sheldon BC. No evidence for MHC class I-based disassortative mating in a wild population of great tits. J Evol Biol 2015; 28:642-54. [DOI: 10.1111/jeb.12600] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 01/07/2015] [Accepted: 01/23/2015] [Indexed: 11/28/2022]
Affiliation(s)
- I. Sepil
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
| | - R. Radersma
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
| | - A. W. Santure
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- School of Biological Sciences; The University of Auckland; Auckland New Zealand
| | - I. De Cauwer
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Laboratoire de Génétique et Evolution des Populations Végétales; UMR CNRS 8198; Université des Sciences et Technologies de Lille-Lille 1; Villeneuve d'Ascq Cedex France
| | - J. Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - B. C. Sheldon
- Department of Zoology; Edward Grey Institute; University of Oxford; Oxford UK
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454 screening of individual MHC variation in an endemic island passerine. Immunogenetics 2014; 67:149-62. [PMID: 25515684 PMCID: PMC4325181 DOI: 10.1007/s00251-014-0822-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/28/2014] [Indexed: 11/03/2022]
Abstract
Genes of the major histocompatibility complex (MHC) code for receptors that are central to the adaptive immune response of vertebrates. These genes are therefore important genetic markers with which to study adaptive genetic variation in the wild. Next-generation sequencing (NGS) has increasingly been used in the last decade to genotype the MHC. However, NGS methods are highly prone to sequencing errors, and although several methodologies have been proposed to deal with this, until recently there have been no standard guidelines for the validation of putative MHC alleles. In this study, we used the 454 NGS platform to screen MHC class I exon 3 variation in a population of the island endemic Berthelot's pipit (Anthus berthelotii). We were able to characterise MHC genotypes across 309 individuals with high levels of repeatability. We were also able to determine alleles that had low amplification efficiencies, whose identification within individuals may thus be less reliable. At the population level we found lower levels of MHC diversity in Berthelot's pipit than in its widespread continental sister species the tawny pipit (Anthus campestris), and observed trans-species polymorphism. Using the sequence data, we identified signatures of gene conversion and evidence of maintenance of functionally divergent alleles in Berthelot's pipit. We also detected positive selection at 10 codons. The present study therefore shows that we have an efficient method for screening individual MHC variation across large datasets in Berthelot's pipit, and provides data that can be used in future studies investigating spatio-temporal patterns and scales of selection on the MHC.
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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: 26] [Impact Index Per Article: 2.6] [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.
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Affiliation(s)
- Jacek Radwan
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
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35
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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
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36
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Miller KM, Teffer A, Tucker S, Li S, Schulze AD, Trudel M, Juanes F, Tabata A, Kaukinen KH, Ginther NG, Ming TJ, Cooke SJ, Hipfner JM, Patterson DA, Hinch SG. Infectious disease, shifting climates, and opportunistic predators: cumulative factors potentially impacting wild salmon declines. Evol Appl 2014; 7:812-55. [PMID: 25469162 PMCID: PMC4227861 DOI: 10.1111/eva.12164] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 03/06/2014] [Indexed: 12/23/2022] Open
Abstract
Emerging diseases are impacting animals under high-density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.
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Affiliation(s)
- Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
- Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Amy Teffer
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Strahan Tucker
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Marc Trudel
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Francis Juanes
- Biology Department, University of VictoriaVictoria, BC, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Norma G Ginther
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimo, BC, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton UniverisyOttawa, ON, Canada
| | - J Mark Hipfner
- Environment Canada, Wildlife Research DivisionDelta, BC, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Science BranchBurnaby, BC, Canada
| | - Scott G Hinch
- Forest and Conservation Sciences, University of British ColumbiaVancouver, BC, Canada
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37
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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.
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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
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38
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Norén K, Angerbjörn A. Genetic perspectives on northern population cycles: bridging the gap between theory and empirical studies. Biol Rev Camb Philos Soc 2013; 89:493-510. [PMID: 24779519 DOI: 10.1111/brv.12070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 01/13/2023]
Abstract
Many key species in northern ecosystems are characterised by high-amplitude cyclic population demography. In 1924, Charles Elton described the ecology and evolution of cyclic populations in a classic paper and, since then, a major focus has been the underlying causes of population cycles. Elton hypothesised that fluctuations reduced population genetic variation and influenced the direction of selection pressures. In concordance with Elton, present theories concern the direct consequences of population cycles for genetic structure due to the processes of genetic drift and selection, but also include feedback models of genetic composition on population dynamics. Most of these theories gained mathematical support during the 1970s and onwards, but due to methodological drawbacks, difficulties in long-term sampling and a complex interplay between microevolutionary processes, clear empirical data allowing the testing of these predictions are still scarce. Current genetic tools allow for estimates of genetic variation and identification of adaptive genomic regions, making this an ideal time to revisit this subject. Herein, we attempt to contribute towards a consensus regarding the enigma described by Elton almost 90 years ago. We present nine predictions covering the direct and genetic feedback consequences of population cycles on genetic variation and population structure, and review the empirical evidence. Generally, empirical support for the predictions was low and scattered, with obvious gaps in the understanding of basic population processes. We conclude that genetic variation in northern cyclic populations generally is high and that the geographic distribution and amount of diversity are usually suggested to be determined by various forms of context- and density-dependent dispersal exceeding the impact of genetic drift. Furthermore, we found few clear signatures of selection determining genetic composition in cyclic populations. Dispersal is assumed to have a strong impact on genetic structuring and we suggest that the signatures of other microevolutionary processes such as genetic drift and selection are weaker and have been over-shadowed by density-dependent dispersal. We emphasise that basic biological and demographical questions still need to be answered and stress the importance of extensive sampling, appropriate choice of tools and the value of standardised protocols.
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Affiliation(s)
- Karin Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
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39
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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.
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Affiliation(s)
- J C Winternitz
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA.
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40
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Liu HY, Xue F, Wan QH, Ge YF. MHC Class II Genes in the Endangered Hainan Eld's Deer (Cervus eldi hainanus). J Hered 2013; 104:874-80. [DOI: 10.1093/jhered/est062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Characteristics of MHC class I genes in house sparrows Passer domesticus as revealed by long cDNA transcripts and amplicon sequencing. J Mol Evol 2013; 77:8-21. [PMID: 23877344 DOI: 10.1007/s00239-013-9575-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
In birds the major histocompatibility complex (MHC) organization differs both among and within orders; chickens Gallus gallus of the order Galliformes have a simple arrangement, while many songbirds of the order Passeriformes have a more complex arrangement with larger numbers of MHC class I and II genes. Chicken MHC genes are found at two independent loci, classical MHC-B and non-classical MHC-Y, whereas non-classical MHC genes are yet to be verified in passerines. Here we characterize MHC class I transcripts (α1 to α3 domain) and perform amplicon sequencing using a next-generation sequencing technique on exon 3 from house sparrow Passer domesticus (a passerine) families. Then we use phylogenetic, selection, and segregation analyses to gain a better understanding of the MHC class I organization. Trees based on the α1 and α2 domain revealed a distinct cluster with short terminal branches for transcripts with a 6-bp deletion. Interestingly, this cluster was not seen in the tree based on the α3 domain. 21 exon 3 sequences were verified in a single individual and the average numbers within an individual were nine and five for sequences with and without a 6-bp deletion, respectively. All individuals had exon 3 sequences with and without a 6-bp deletion. The sequences with a 6-bp deletion have many characteristics in common with non-classical MHC, e.g., highly conserved amino acid positions were substituted compared with the other alleles, low nucleotide diversity and just a single site was subject to positive selection. However, these alleles also have characteristics that suggest they could be classical, e.g., complete linkage and absence of a distinct cluster in a tree based on the α3 domain. Thus, we cannot determine for certain whether or not the alleles with a 6-bp deletion are non-classical based on our present data. Further analyses on segregation patterns of these alleles in combination with dating the 6-bp deletion through MHC characterization across the genus Passer may solve this matter in the future.
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42
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Heber S, Varsani A, Kuhn S, Girg A, Kempenaers B, Briskie J. The genetic rescue of two bottlenecked South Island robin populations using translocations of inbred donors. Proc Biol Sci 2012; 280:20122228. [PMID: 23235701 DOI: 10.1098/rspb.2012.2228] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Populations forced through bottlenecks typically lose genetic variation and exhibit inbreeding depression. 'Genetic rescue' techniques that introduce individuals from outbred populations can be highly effective in reversing the deleterious effects of inbreeding, but have limited application for the majority of endangered species, which survive only in a few bottlenecked populations. We tested the effectiveness of using highly inbred populations as donors to rescue two isolated and bottlenecked populations of the South Island robin (Petroica australis). Reciprocal translocations significantly increased heterozygosity and allelic diversity. Increased genetic diversity was accompanied by increased juvenile survival and recruitment, sperm quality, and immunocompetence of hybrid individuals (crosses between the two populations) compared with inbred control individuals (crosses within each population). Our results confirm that the implementation of 'genetic rescue' using bottlenecked populations as donors provides a way of preserving endangered species and restoring their viability when outbred donor populations no longer exist.
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Affiliation(s)
- S Heber
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand.
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43
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Sepil I, Lachish S, Sheldon BC. Mhc-linked survival and lifetime reproductive success in a wild population of great tits. Mol Ecol 2012. [DOI: 10.1111/mec.12123] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Irem Sepil
- Department of Zoology; Edward Grey Institute; University of Oxford; South Parks Road Oxford OX1 3PS UK
| | - Shelly Lachish
- Department of Zoology; Edward Grey Institute; University of Oxford; South Parks Road Oxford OX1 3PS UK
| | - Ben C. Sheldon
- Department of Zoology; Edward Grey Institute; University of Oxford; South Parks Road Oxford OX1 3PS UK
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44
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Arbanasić H, Huber Đ, Kusak J, Gomerčić T, Hrenović J, Galov A. Extensive polymorphism and evidence of selection pressure on major histocompatibility complex DLA-DRB1, DQA1 and DQB1 class II genes in Croatian grey wolves. ACTA ACUST UNITED AC 2012; 81:19-27. [PMID: 23134500 DOI: 10.1111/tan.12029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 10/04/2012] [Accepted: 10/15/2012] [Indexed: 11/29/2022]
Abstract
The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for measuring fitness-related genetic variation in wildlife populations. Because of human persecution and habitat fragmentation, the grey wolf has become extinct from a large part of Western and Central Europe, and remaining populations have become isolated. In Croatia, the grey wolf population, part of the Dinaric-Balkan population, shrank nearly to extinction during the 20th century, and is now legally protected. Using the cloning-sequencing method, we investigated the genetic diversity and evolutionary history of exon 2 of MHC class II DLA-DRB1, DQA1 and DQB1 genes in 77 individuals. We identified 13 DRB1, 7 DQA1 and 11 DQB1 highly divergent alleles, and 13 DLA-DRB1/DQA1/DQB1 haplotypes. Selection analysis comparing the relative rates of non-synonymous to synonymous mutations (d(N)/d(S)) showed evidence of positive selection pressure acting on all three loci. Trans-species polymorphism was found, suggesting the existence of balancing selection. Evolutionary codon models detected considerable difference between alpha and beta chain gene selection patterns: DRB1 and DQB1 appeared to be under stronger selection pressure, while DQA1 showed signs of moderate selection. Our results suggest that, despite the recent contraction of the Croatian wolf population, genetic variability in selectively maintained immune genes has been preserved.
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Affiliation(s)
- H Arbanasić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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45
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Wutzler R, Foerster K, Kempenaers B. MHC class I variation in a natural blue tit population (Cyanistes caeruleus). Genetica 2012; 140:349-64. [PMID: 23073914 DOI: 10.1007/s10709-012-9679-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 09/03/2012] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is central to the vertebrate immune system and its highly polymorphic genes are considered to influence several life-history traits of individuals. To characterize the MHC in a natural population of blue tits (Cyanistes caeruleus) we investigated the class I exon 3 diversity of more than 900 individuals. We designed two pairs of motif-specific primers that reliably amplify independent subsets of MHC alleles. Applying denaturing gradient gel electrophoresis (DGGE) we obtained 48 independently inherited units of unique band patterns (DGGE-haplogroups), which were validated in a segregation analysis within 105 families. In a second approach, we extensively sequenced 6 unrelated individuals to confirm that DGGE-haplogroup composition reflects individual allelic variation. The highest number of different DGGE-haplogroups in a single individual corresponded in 19 MHC exon 3 sequences, suggesting a minimum of 10 amplified MHC class I loci in the blue tit. In total, we identified 50 unique functional and 3 non-functional sequences. Functional sequences showed high levels of recombination and strong positive selection in the antigen binding region, whereas nucleotide diversity was comparatively low in the range of all passerine species. Finally, in a phylogenetic comparison of passerine MHC class I exon 3 sequences we discuss conflicting evolutionary signals possibly due to recent gene duplication, recombination events and concerted evolution. Our results indicate that the described method is suitable to effectively explore the MHC diversity and its ecological impacts in blue tits in future studies.
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Affiliation(s)
- R Wutzler
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82305 Seewiesen, Germany.
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46
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Evolution of the MHC-DQB exon 2 in marine and terrestrial mammals. Immunogenetics 2012; 65:47-61. [PMID: 23064401 DOI: 10.1007/s00251-012-0647-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 08/13/2012] [Indexed: 10/27/2022]
Abstract
On the basis of a general low polymorphism, several studies suggest that balancing selection in the class II major histocompatibility complex (MHC) is weaker in marine mammals as compared with terrestrial mammals. We investigated such differential selection among Cetacea, Artiodactyla, and Primates at exon 2 of MHC-DQB gene by contrasting indicators of molecular evolution such as occurrence of transpecific polymorphisms, patterns of phylogenetic branch lengths by codon position, rates of nonsynonymous and synonymous substitutions as well as accumulation of variable sites on the sampling of alleles. These indicators were compared between the DQB and the mitochondrial cytochrome b gene (cytb) as a reference of neutral expectations and differences between molecular clocks resulting from life history and historical demography. All indicators showed that the influence of balancing selection on the DQB is more variable and overall weaker for cetaceans. In our sampling, ziphiids, the sperm whale, monodontids and the finless porpoise formed a group with lower DQB polymorphism, while mysticetes exhibited a higher DQB variation similar to that of terrestrial mammals as well as higher occurrence of transpecific polymorphisms. Different dolphins appeared in the two groups. Larger variation of selection on the cetacean DQB could be related to greater stochasticity in their historical demography and thus, to a greater complexity of the general ecology and disease processes of these animals.
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47
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Natsopoulou ME, Pálsson S, Ólafsdóttir GÁ. Parasites and parallel divergence of the number of individual MHC alleles between sympatric three-spined stickleback Gasterosteus aculeatus morphs in Iceland. JOURNAL OF FISH BIOLOGY 2012; 81:1696-1714. [PMID: 23020569 DOI: 10.1111/j.1095-8649.2012.03430.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Two pairs of sympatric three-spined stickleback Gasterosteus aculeatus morphs and two single morph populations inhabiting mud and lava or rocky benthic habitats in four Icelandic lakes were screened for parasites and genotyped for MHC class IIB diversity. Parasitic infection differed consistently between G. aculeatus from different benthic habitats. Gasterosteus aculeatus from the lava or rocky habitats were more heavily infected in all lakes. A parallel pattern was also found in individual MHC allelic variation with lava G. aculeatus morphs exhibiting lower levels of variation than the mud morphs. Evidence for selective divergence in MHC allele number is ambiguous but supported by two findings in addition to the parallel pattern observed. MHC allele diversity was not consistent with diversity reported at neutral markers (microsatellites) and in Þingvallavatn the most common number of alleles in each morph was associated with lower infection levels. In the Þingvallavatn lava morph, lower infection levels by the two most common parasites, Schistocephalus solidus and Diplostomum baeri, were associated with different MHC allele numbers.
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Affiliation(s)
- M E Natsopoulou
- Research Centre of the Westfjords, University of Iceland, Adalstraeti 21, 415 Bolungarvík, Iceland
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48
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Baratti M, Dessì-Fulgheri F, Ambrosini R, Bonisoli-Alquati A, Caprioli M, Goti E, Matteo A, Monnanni R, Ragionieri L, Ristori E, Romano M, Rubolini D, Scialpi A, Saino N. MHC genotype predicts mate choice in the ring-necked pheasant Phasianus colchicus. J Evol Biol 2012; 25:1531-42. [PMID: 22591334 DOI: 10.1111/j.1420-9101.2012.02534.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Females of several vertebrate species selectively mate with males on the basis of the major histocompatibility complex (MHC) genes. As androgen-mediated maternal effects have long-lasting consequences for the adult phenotype, both mating and reproductive success may depend on the combined effect of MHC genotype and exposure to androgens during early ontogeny. We studied how MHC-based mate choice in ring-necked pheasants (Phasianus colchicus) was influenced by an experimental in ovo testosterone (T) increase. There was no conclusive evidence of in ovo T treatment differentially affecting mate choice in relation to MHC genotype. However, females avoided mating with males with a wholly different MHC genotype compared with males sharing at least one MHC allele. Females also tended to avoid mating with MHC-identical males, though not significantly so. These findings suggest that female pheasants preferred males with intermediate MHC dissimilarity. Male MHC heterozygosity or diversity did not predict the expression of ornaments or male dominance rank. Thus, MHC-based mating preferences in the ring-necked pheasant do not seem to be mediated by ornaments' expression and may have evolved mainly to reduce the costs of high heterozygosity at MHC loci for the progeny, such as increased risk of autoimmune diseases or disruption of coadapted gene pools.
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Affiliation(s)
- M Baratti
- Istituto per lo Studio degli Ecosistemi, Sesto Fiorentino, via Madonna del Piano 10, Florence, Italy.
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49
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Sepil I, Moghadam HK, Huchard E, Sheldon BC. Characterization and 454 pyrosequencing of major histocompatibility complex class I genes in the great tit reveal complexity in a passerine system. BMC Evol Biol 2012; 12:68. [PMID: 22587557 PMCID: PMC3483247 DOI: 10.1186/1471-2148-12-68] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 05/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The critical role of Major Histocompatibility Complex (Mhc) genes in disease resistance and their highly polymorphic nature make them exceptional candidates for studies investigating genetic effects on survival, mate choice and conservation. Species that harbor many Mhc loci and high allelic diversity are particularly intriguing as they are potentially under strong selection and studies of such species provide valuable information as to the mechanisms maintaining Mhc diversity. However comprehensive genotyping of complex multilocus systems has been a major challenge to date with the result that little is known about the consequences of this complexity in terms of fitness effects and disease resistance. RESULTS In this study, we genotyped the Mhc class I exon 3 of the great tit (Parus major) from two nest-box breeding populations near Oxford, UK that have been monitored for decades. Characterization of Mhc class I exon 3 was adopted and bidirectional sequencing was carried using the 454 sequencing platform. Full analysis of sequences through a stepwise variant validation procedure allowed reliable typing of more than 800 great tits based on 214,357 reads; from duplicates we estimated the repeatability of typing as 0.94. A total of 862 alleles were detected, and the presence of at least 16 functional loci was shown - the highest number characterized in a wild bird species. Finally, the functional alleles were grouped into 17 supertypes based on their antigen binding affinities. CONCLUSIONS We found extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. The presence of many functional loci was shown, together with a pseudogene family and putatively non-functional alleles; there was clear evidence that functional alleles were under strong balancing selection. This study is the first step towards an in-depth analysis of this gene complex in this species, which will help understanding how parasite-mediated and sexual selection shape and maintain host genetic variation in nature. We believe that study systems like ours can make important contributions to the field of evolutionary biology and emphasize the necessity of integrating long-term field-based studies with detailed genetic analysis to unravel complex evolutionary processes.
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Affiliation(s)
- Irem Sepil
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, OX1 3PS, UK.
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50
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MALÉ PIERREJEANG, MARTIN JEANFRANÇOIS, GALAN MAXIME, DEFFONTAINE VALÉRIE, BRYJA JOSEF, COSSON JEANFRANÇOIS, MICHAUX JOHAN, CHARBONNEL NATHALIE. Discongruence of Mhc and cytochrome b phylogeographical patterns in Myodes glareolus (Rodentia: Cricetidae). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01799.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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