1
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Million KM, Lively CM. Trans-specific polymorphism and the convergent evolution of supertypes in major histocompatibility complex class II genes in darters ( Etheostoma). Ecol Evol 2022; 12:e8485. [PMID: 36311547 PMCID: PMC9601779 DOI: 10.1002/ece3.8485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/24/2022] Open
Abstract
Major Histocompatibility Complex (MHC) genes are one of the most polymorphic gene groups known in vertebrates. MHC genes also exhibit allelic variants that are shared among taxa, referred to as trans-specific polymorphism (TSP). The role that selection plays in maintaining such high diversity within species, as well as TSP, is an ongoing discussion in biology. In this study, we used deep-sequencing techniques to characterize MHC class IIb gene diversity in three sympatric species of darters. We found at least 5 copies of the MHC gene in darters, with 126 genetic variants encoding 122 unique amino acid sequences. We identified four supertypes based on the binding properties of proteins encoded by the sequences. Although each species had a unique pool of variants, many variants were shared between species pairs and across all three species. Phylogenetic analysis showed that the variants did not group together monophyletically based on species identity or on supertype. An expanded phylogenetic analysis showed that some darter alleles grouped together with alleles from other percid fishes. Our findings show that TSP occurs in darters, which suggests that balancing selection is acting at the genotype level. Supertypes, however, are most likely evolving convergently, as evidenced by the fact that alleles do not form monophyletic groups based on supertype. Our research demonstrates that selection may be acting differently on MHC genes at the genotype and supertype levels, selecting for the maintenance of high genotypic diversity while driving the convergent evolution of similar MHC phenotypes across different species.
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Affiliation(s)
- Kara M. Million
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
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2
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Gahr CL, Boehm T, Milinski M. Male validation factor for three-spined stickleback ( Gasterosteus aculeatus) mate choice likely evolutionarily conserved since 50 thousand years. ETHOL ECOL EVOL 2021. [DOI: 10.1080/03949370.2020.1789748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Christoph L. Gahr
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max-Planck-Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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3
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Gahr CL, Boehm T, Milinski M. Female assortative mate choice functionally validates synthesized male odours of evolving stickleback river-lake ecotypes. Biol Lett 2018; 14:20180730. [PMID: 30958253 PMCID: PMC6303515 DOI: 10.1098/rsbl.2018.0730] [Citation(s) in RCA: 8] [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: 10/16/2018] [Accepted: 11/22/2018] [Indexed: 12/16/2022] Open
Abstract
During mate choice decisions, females of many vertebrates use male olfactory cues to achieve immunogenetic optimality of their offspring. Three-spined sticklebacks ( Gasterosteus aculeatus) populating habitats that differ in their parasite communities evolve locally adapted combinations of genetic variants encoded at the major histocompatibility complex (MHC). Such adaptation confers optimal resistance to the local parasite fauna. Immunogenetic signatures co-evolved with local parasites favour population-specific assortative mate choice behaviour. Previous studies have shown that female sticklebacks evaluate male MHC-associated olfactory cues during the process of mate choice, but how habitat-specific information is exchanged between males and females has remained elusive. Here, we directly demonstrate the molecular nature of the olfactory cue providing habitat-specific information. Under controlled laboratory conditions, females that are ready to mate prefer mixtures of synthetic MHC peptide ligands mimicking the optimal allele number of their original population. These results imply that female sticklebacks can determine the number of MHC alleles of their prospective mates, compare it to their own immunogenetic status, and, if optimal with respect to the immunogenetic complementarity, accept the male as mate. Our results suggest a potentially common mechanism of ecological speciation in vertebrates that is based on the olfactory assessment of habitat-specific immunogenetic diversity.
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Affiliation(s)
- Christoph L. Gahr
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Plön, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max-Planck-Institute for Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Manfred Milinski
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Plön, Germany
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4
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Lenz TL, Hafer N, Samonte IE, Yeates SE, Milinski M. Cryptic haplotype-specific gamete selection yields offspring with optimal MHC immune genes. Evolution 2018; 72:2478-2490. [PMID: 30246285 PMCID: PMC6282957 DOI: 10.1111/evo.13591] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022]
Abstract
Females choose specific mates in order to produce fitter offspring. However, several factors interfere with females' control over fertilization of their eggs, including sneaker males and phenotypically unpredictable allele segregation during meiosis. Mate choice at the individual level thus provides only a poor approximation for obtaining the best genetic match. Consequently, postcopulatory sperm selection by female oocytes has been proposed as a mechanism to achieve complementary combinations of parental haplotypes. Here, using controlled in vitro fertilization of three‐spined stickleback eggs, we find haplotype‐specific fertilization bias toward gametes with complementary major histocompatibility complex (MHC) immunogenes. The resulting zygote (and thus offspring) genotypes exhibit an intermediate level of individual MHC diversity that was previously shown to confer highest pathogen resistance. Our finding of haplotype‐specific gamete selection thus represents an intriguing mechanism for fine‐tuned optimization of the offspring's immune gene composition and an evolutionary advantage in the Red Queen dynamics of host‐parasite coevolution.
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Affiliation(s)
- Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Nina Hafer
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Irene E Samonte
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Sarah E Yeates
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany.,Current Address: School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
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5
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Abduriyim S, Nishita Y, Kosintsev PA, Raichev E, Väinölä R, Kryukov AP, Abramov AV, Kaneko Y, Masuda R. Diversity and evolution of MHC class II DRB gene in the Eurasian badger genus Meles (Mammalia: Mustelidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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6
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Andreou D, Eizaguirre C, Boehm T, Milinski M. Mate choice in sticklebacks reveals that immunogenes can drive ecological speciation. Behav Ecol 2017; 28:953-961. [PMID: 29622924 PMCID: PMC5873247 DOI: 10.1093/beheco/arx074] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/27/2017] [Accepted: 05/08/2017] [Indexed: 11/14/2022] Open
Abstract
Adaptation to ecologically contrasting niches can lead to the formation of new species. Theoretically, this process of ecological speciation can be driven by pleiotropic "magic traits" that genetically link natural and sexual selection. To qualify as a true magic trait, the pleiotropic function of a gene must be reflected in biologically relevant mechanisms underlying both local adaptation and mate choice. The immune genes of the major histocompatibility complex (MHC) contribute to parasite resistance and also play a major role in sexual selection. Hence, the MHC may encode a candidate magic trait. Using diverging 3-spined stickleback populations from a connected lake-river habitat, we show with mate choice experiments in a flow channel that polymorphic MHC genes probably underlie assortative mating with respect to particular habitat-adapted ecotypes, potentially resulting in reproductive isolation. By manipulating olfactory cues in controlled experiments, we show that female sticklebacks employ MHC-dependent male olfactory signals to select mates with which they can achieve a habitat-specific MHC gene structure that optimally protects their offspring against local parasites. By using MHC-based olfactory signals, females thus select individuals of their own population as mates. Our results demonstrate how mate choice and parasite resistance may be functionally linked. These findings suggest that MHC genes are pleiotropic and encode a true magic trait of biologically significant effect.
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Affiliation(s)
- Demetra Andreou
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August- Thienemann- Str. 2, D-24306, Ploen, Germany
- Department of Life and Environmental Science, Faculty of Science and Technology, Talbot Campus, Poole, BH12 5BB, UK
| | - Christophe Eizaguirre
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August- Thienemann- Str. 2, D-24306, Ploen, Germany
- GEOMAR| Helmholtz Centre for Ocean Research, Department of Evolutionary Ecology of Marine Fishes, D-24105, Kiel, Germany
- Present address: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK, and
| | - Thomas Boehm
- Max Planck Institute of Immunobiology and Epigenetics, Department of Developmental Immunology, Stuebeweg 51, D-79108 Freiburg, Germany
| | - Manfred Milinski
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August- Thienemann- Str. 2, D-24306, Ploen, Germany
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7
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Kaufmann J, Lenz TL, Kalbe M, Milinski M, Eizaguirre C. A field reciprocal transplant experiment reveals asymmetric costs of migration between lake and river ecotypes of three-spined sticklebacks (Gasterosteus aculeatus
). J Evol Biol 2017; 30:938-950. [DOI: 10.1111/jeb.13057] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/15/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022]
Affiliation(s)
- J. Kaufmann
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
- DEE; University of Lausanne; Lausanne Switzerland
| | - T. L. Lenz
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - M. Kalbe
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - M. Milinski
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; Plön Germany
| | - C. Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research; Kiel Germany
- School of Biological and Chemical Sciences; Queen Mary University of London; London UK
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8
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Hofmann MJ, Bracamonte SE, Eizaguirre C, Barluenga M. Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids. BMC Genet 2017; 18:15. [PMID: 28201988 PMCID: PMC5310070 DOI: 10.1186/s12863-017-0474-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes. RESULTS Here, we characterized the genes of MHC class IIB chain of the Midas cichlid species complex (Amphilophus cf. citrinellus) including fish from five lakes in Nicaragua. We designed 19 new specific primers anchored in a stepwise fashion in order to detect all alleles present. We obtained 866 genomic DNA (gDNA) sequences from thirteen individuals and 756 additional sequences from complementary DNA (cDNA) of seven of those individuals. We identified 69 distinct alleles with up to 25 alleles per individual. We also found considerable intron length variation and mismatches of alleles detected in cDNA and gDNA suggesting that some loci have undergone pseudogenization. Lastly, we created a model of protein structure homology for each allele and identified their key structural components. CONCLUSIONS Overall, the Midas cichlid has one of the most diverse repertoires of MHC class IIB genes known, which could serve as a powerful tool to elucidate the process of divergent radiations, colonization and speciation in sympatry.
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Affiliation(s)
- Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Seraina E Bracamonte
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker weg 20, 24105, Kiel, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Christophe Eizaguirre
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker weg 20, 24105, Kiel, Germany
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006, Madrid, Spain.
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9
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Gaigher A, Burri R, Gharib WH, Taberlet P, Roulin A, Fumagalli L. Family-assisted inference of the genetic architecture of major histocompatibility complex variation. Mol Ecol Resour 2016; 16:1353-1364. [DOI: 10.1111/1755-0998.12537] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 04/07/2016] [Accepted: 04/18/2016] [Indexed: 12/13/2022]
Affiliation(s)
- A. Gaigher
- Laboratory for Conservation Biology; Department of Ecology and Evolution; University of Lausanne; Biophore Lausanne CH-1015 Switzerland
| | - R. Burri
- Department of Evolutionary Biology; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - W. H. Gharib
- Interfaculty Bioinformatics Unit; University of Bern; CH-3012 Bern Switzerland
| | - P. Taberlet
- CNRS; Laboratoire d'Ecologie Alpine (LECA); 38000 Grenoble France
- Laboratoire d'Ecologie Alpine (LECA); University of Grenoble Alpes; 38000 Grenoble France
| | - A. Roulin
- Laboratory for Conservation Biology; Department of Ecology and Evolution; University of Lausanne; Biophore Lausanne CH-1015 Switzerland
| | - L. Fumagalli
- Laboratory for Conservation Biology; Department of Ecology and Evolution; University of Lausanne; Biophore Lausanne CH-1015 Switzerland
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10
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Bracamonte SE, Smith S, Hammer M, Pavey SA, Sunnucks P, Beheregaray LB. Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations. FISH & SHELLFISH IMMUNOLOGY 2015; 46:468-476. [PMID: 26093210 DOI: 10.1016/j.fsi.2015.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/04/2015] [Accepted: 06/07/2015] [Indexed: 06/04/2023]
Abstract
Genetic diversity is an essential aspect of species viability, and assessments of neutral genetic diversity are regularly implemented in captive breeding and conservation programs. Despite their importance, information from adaptive markers is rarely included in such programs. A promising marker of significance in fitness and adaptive potential is the major histocompatibility complex (MHC), a key component of the adaptive immune system. Populations of Australian freshwater fishes are generally declining in numbers due to human impacts and the introduction of exotic species, a scenario of particular concern for members of the family Percichthyidae, several of which are listed as nationally vulnerable or endangered, and hence subject to management plans, captive breeding, and restoration plans. We used a next-generation sequencing approach to characterize the MHC IIB locus and provide a conservative description of its levels of diversity in four endangered percichthyids: Gadopsis marmoratus, Macquaria australasica, Nannoperca australis, and Nannoperca obscura. Evidence is presented for a duplicated MHC IIB locus, positively selected sites and recombination of MHC alleles. Relatively moderate levels of diversity were detected in the four species, as well as in different ecotypes within each species. Phylogenetic analyses revealed genus specific clustering of alleles and no allele sharing among species. There were also no shared alleles observed between two ecotypes within G. marmoratus and within M. australasica, which might be indicative of ecologically-driven divergence and/or long divergence times. This represents the first characterization and assessment of MHC diversity for Percichthyidae, and also for Australian freshwater fishes in general, providing key genetic resources for a vertebrate group of increasing conservation concern.
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Affiliation(s)
- Seraina E Bracamonte
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Steve Smith
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia; Department of Integrative Biology and Evolution, University of Veterinary Medicine, 1160 Vienna, Austria
| | - Michael Hammer
- Evolutionary Biology Unit, South Australian Museum, North Terrace Adelaide, South Australia 5000 and Curator of Fishes, Museum and Art Gallery of the Northern Territory, PO Box 4646, Darwin, Northern Territory 0801, Australia
| | - Scott A Pavey
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec QC G1V 0A6, Canada
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne 3800, Victoria, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Lab, Flinders University, Adelaide 5001, South Australia, Australia.
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11
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Sin YW, Annavi G, Newman C, Buesching C, Burke T, Macdonald DW, Dugdale HL. MHC class II-assortative mate choice in European badgers (Meles meles). Mol Ecol 2015; 24:3138-50. [DOI: 10.1111/mec.13217] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Yung Wa Sin
- Wildlife Conservation Research Unit (WildCRU); Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House Abingdon Road Abingdon Oxfordshire OX13 5QL UK
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield South Yorkshire S10 2TN UK
- Department of Organismic and Evolutionary Biology; Museum of Comparative Zoology; Harvard University; 26 Oxford Street Cambridge MA 02138 USA
| | - Geetha Annavi
- Wildlife Conservation Research Unit (WildCRU); Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House Abingdon Road Abingdon Oxfordshire OX13 5QL UK
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield South Yorkshire S10 2TN UK
- Biology Department; Faculty of Science; Universiti Putra Malaysia; 43400 UPM Serdang Selangor Darul Ehsan Malaysia
| | - Chris Newman
- Wildlife Conservation Research Unit (WildCRU); Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House Abingdon Road Abingdon Oxfordshire OX13 5QL UK
| | - Christina Buesching
- Wildlife Conservation Research Unit (WildCRU); Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House Abingdon Road Abingdon Oxfordshire OX13 5QL UK
| | - Terry Burke
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield South Yorkshire S10 2TN UK
| | - David W. Macdonald
- Wildlife Conservation Research Unit (WildCRU); Department of Zoology; Recanati-Kaplan Centre; University of Oxford; Tubney House Abingdon Road Abingdon Oxfordshire OX13 5QL UK
| | - Hannah L. Dugdale
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield South Yorkshire S10 2TN UK
- Groningen Institute for Evolutionary Life Sciences; University of Groningen; PO Box 11103 9700CC Groningen the Netherlands
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12
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Björklund M, Aho T, Behrmann-Godel J. Isolation over 35 years in a heated biotest basin causes selection on MHC class IIß genes in the European perch (Perca fluviatilis L.). Ecol Evol 2015; 5:1440-55. [PMID: 25897384 PMCID: PMC4395174 DOI: 10.1002/ece3.1426] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 01/20/2015] [Accepted: 01/28/2015] [Indexed: 01/15/2023] Open
Abstract
Genes that play key roles in host immunity such as the major histocompatibility complex (MHC) in vertebrates are expected to be major targets of selection. It is well known that environmental conditions can have an effect on host–parasite interactions and may thus influence the selection on MHC. We analyzed MHC class IIß variability over 35 years in a population of perch (Perca fluviatilis) from the Baltic Sea that was split into two populations separated from each other. One population was subjected to heating from cooling water of a nuclear power plant and was isolated from the surrounding environment in an artificial lake, while the other population was not subjected to any change in water temperature (control). The isolated population experienced a change of the allelic composition and a decrease in allelic richness of MHC genes compared to the control population. The two most common MHC alleles showed cyclic patterns indicating ongoing parasite–host coevolution in both populations, but the alleles that showed a cyclic behavior differed between the two populations. No such patterns were observed at alleles from nine microsatellite loci, and no genetic differentiation was found between populations. We found no indications for a genetic bottleneck in the isolated population during the 35 years. Additionally, differences in parasitism of the current perch populations suggest that a change of the parasite communities has occurred over the isolation period, although the evidence in form of in-depth knowledge of the change of the parasite community over time is lacking. Our results are consistent with the hypothesis of a selective sweep imposed by a change in the parasite community.
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Affiliation(s)
- Mats Björklund
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University Uppsala, Sweden
| | - Teija Aho
- Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences Skolgatan 6, Öregrund, SE-742 42, Sweden
| | - Jasminca Behrmann-Godel
- Limnological Institute, University of Konstanz Mainaustrasse 252, D-78464, Konstanz, Germany
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13
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Bolnick DI, Snowberg LK, Caporaso JG, Lauber C, Knight R, Stutz WE. Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. Mol Ecol 2014; 23:4831-45. [PMID: 24975397 DOI: 10.1111/mec.12846] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 12/13/2022]
Abstract
Animals harbour diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge: distinguishing between mutualistic and pathogenic members of diverse and host-specific microbial communities. We propose that Major Histocompatibility class II (MHC) genotypes contribute to recognition and regulation of gut microbes, and thus, MHC polymorphism contributes to microbial variation among hosts. Here, we show that MHC IIb polymorphism is associated with among-individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. We sampled stickleback from Cedar Lake, on Vancouver Island, and used next-generation sequencing to genotype the sticklebacks' gut microbiota (16S sequencing) and their MHC class IIb exon 2 sequences. The presence of certain MHC motifs was associated with altered relative abundance (increase or decrease) of some microbial Families. The effect sizes are modest and entail a minority of microbial taxa, but these results represent the first indication that MHC genotype may affect gut microbiota composition in natural populations (MHC-microbe associations have also been found in a few studies of lab mice). Surprisingly, these MHC effects were frequently sex-dependent. Finally, hosts with more diverse MHC motifs had less diverse gut microbiota. One implication is that MHC might influence the efficacy of therapeutic strategies to treat dysbiosis-associated disease, including the outcome of microbial transplants between healthy and diseased patients. We also speculate that macroparasite-driven selection on MHC has the potential to indirectly alter the host gut microbiota, and vice versa.
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Affiliation(s)
- Daniel I Bolnick
- Howard Hughes Medical Institute and Section of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
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14
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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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15
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Sommer S, Courtiol A, Mazzoni CJ. MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout. BMC Genomics 2013; 14:542. [PMID: 23937623 PMCID: PMC3750822 DOI: 10.1186/1471-2164-14-542] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 07/30/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is the most important genetic marker to study patterns of adaptive genetic variation determining pathogen resistance and associated life history decisions. It is used in many different research fields ranging from human medical, molecular evolutionary to functional biodiversity studies. Correct assessment of the individual allelic diversity pattern and the underlying structural sequence variation is the basic requirement to address the functional importance of MHC variability. Next-generation sequencing (NGS) technologies are likely to replace traditional genotyping methods to a great extent in the near future but first empirical studies strongly indicate the need for a rigorous quality control pipeline. Strict approaches for data validation and allele calling to distinguish true alleles from artefacts are required. RESULTS We developed the analytical methodology and validated a data processing procedure which can be applied to any organism. It allows the separation of true alleles from artefacts and the evaluation of genotyping reliability, which in addition to artefacts considers for the first time the possibility of allelic dropout due to unbalanced amplification efficiencies across alleles. Finally, we developed a method to assess the confidence level per genotype a-posteriori, which helps to decide which alleles and individuals should be included in any further downstream analyses. The latter method could also be used for optimizing experiment designs in the future. CONCLUSIONS Combining our workflow with the study of amplification efficiency offers the chance for researchers to evaluate enormous amounts of NGS-generated data in great detail, improving confidence over the downstream analyses and subsequent applications.
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Affiliation(s)
- Simone Sommer
- Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, D-10315 Berlin, Germany
| | - Alexandre Courtiol
- Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, D-10315 Berlin, Germany
| | - Camila J Mazzoni
- Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, D-10315 Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Koenigin-Luise-Straße 6-8, D-14195 Berlin, Germany
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Lenz TL, Mueller B, Trillmich F, Wolf JBW. Divergent allele advantage at MHC-DRB through direct and maternal genotypic effects and its consequences for allele pool composition and mating. Proc Biol Sci 2013; 280:20130714. [PMID: 23677346 DOI: 10.1098/rspb.2013.0714] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
It is still debated whether main individual fitness differences in natural populations can be attributed to genome-wide effects or to particular loci of outstanding functional importance such as the major histocompatibility complex (MHC). In a long-term monitoring project on Galápagos sea lions (Zalophus wollebaeki), we collected comprehensive fitness and mating data for a total of 506 individuals. Controlling for genome-wide inbreeding, we find strong associations between the MHC locus and nearly all fitness traits. The effect was mainly attributable to MHC sequence divergence and could be decomposed into contributions of own and maternal genotypes. In consequence, the population seems to have evolved a pool of highly divergent alleles conveying near-optimal MHC divergence even by random mating. Our results demonstrate that a single locus can significantly contribute to fitness in the wild and provide conclusive evidence for the 'divergent allele advantage' hypothesis, a special form of balancing selection with interesting evolutionary implications.
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Affiliation(s)
- Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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Lenz TL, Eizaguirre C, Kalbe M, Milinski M. EVALUATING PATTERNS OF CONVERGENT EVOLUTION AND TRANS-SPECIES POLYMORPHISM AT MHC IMMUNOGENES IN TWO SYMPATRIC STICKLEBACK SPECIES. Evolution 2013; 67:2400-12. [DOI: 10.1111/evo.12124] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/26/2013] [Indexed: 01/15/2023]
Affiliation(s)
- Tobias L. Lenz
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; August-Thienemann-Str 2 24306 Plön Germany
| | - Christophe Eizaguirre
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; August-Thienemann-Str 2 24306 Plön Germany
- Department of Evolutionary Ecology of Marine Fishes; GEOMAR
- Helmholtz Center for Ocean Research; Düsternbrooker Weg 20 24105 Kiel Germany
| | - Martin Kalbe
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; August-Thienemann-Str 2 24306 Plön Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; August-Thienemann-Str 2 24306 Plön Germany
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18
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Stiebens VA, Merino SE, Chain FJJ, Eizaguirre C. Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing. BMC Evol Biol 2013; 13:95. [PMID: 23627726 PMCID: PMC3655109 DOI: 10.1186/1471-2148-13-95] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 04/17/2013] [Indexed: 11/17/2022] Open
Abstract
Background In evolutionary and conservation biology, parasitism is often highlighted as a major selective pressure. To fight against parasites and pathogens, genetic diversity of the immune genes of the major histocompatibility complex (MHC) are particularly important. However, the extensive degree of polymorphism observed in these genes makes it difficult to conduct thorough population screenings. Methods We utilized a genotyping protocol that uses 454 amplicon sequencing to characterize the MHC class I in the endangered loggerhead sea turtle (Caretta caretta) and to investigate their evolution at multiple relevant levels of organization. Results MHC class I genes revealed signatures of trans-species polymorphism across several reptile species. In the studied loggerhead turtle individuals, it results in the maintenance of two ancient allelic lineages. We also found that individuals carrying an intermediate number of MHC class I alleles are larger than those with either a low or high number of alleles. Conclusions Multiple modes of evolution seem to maintain MHC diversity in the loggerhead turtles, with relatively high polymorphism for an endangered species.
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Affiliation(s)
- Victor A Stiebens
- Department of Evolutionary Ecology of Marine Fishes, GEOMAR
- Helmholtz Center for Ocean Research, Kiel, 24105, Germany
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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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Feulner PGD, Chain FJJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Mundry M, Samonte IE, Stoll M, Milinski M, Reusch TBH, Bornberg-Bauer E. Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks. Mol Ecol 2012; 22:635-49. [PMID: 22747593 DOI: 10.1111/j.1365-294x.2012.05680.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the end of the Pleistocene, the three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to various freshwater habitats probably originating from ancestral marine populations. Standing genetic variation and the underlying genomic architecture both have been speculated to contribute to recent adaptive radiations of sticklebacks. Here, we expand on the current genomic resources of this fish by providing extensive genome-wide variation data from six individuals from a marine (North Sea) stickleback population. Using next-generation sequencing and a combination of paired-end and mate-pair libraries, we detected a wide size range of genetic variation. Among the six individuals, we found more than 7% of the genome is polymorphic, consisting of 2599111 SNPs, 233464 indels and structural variation (SV) (>50 bp) such as 1054 copy-number variable regions (deletions and duplications) and 48 inversions. Many of these polymorphisms affect gene and coding sequences. Based on SNP diversity, we determined outlier regions concordant with signatures expected under adaptive evolution. As some of these outliers overlap with pronounced regions of copy-number variation, we propose the consideration of such SV when analysing SNP data from re-sequencing approaches. We further discuss the value of this resource on genome-wide variation for further investigation upon the relative contribution of standing variation on the parallel evolution of sticklebacks and the importance of the genomic architecture in adaptive radiation.
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Affiliation(s)
- Philine G D Feulner
- Institute for Evolution and Biodiversity, Evolutionary Bioinformatics, Westfaelische Wilhelms University, Muenster, Germany.
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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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Eizaguirre C, Lenz TL, Kalbe M, Milinski M. Divergent selection on locally adapted major histocompatibility complex immune genes experimentally proven in the field. Ecol Lett 2012; 15:723-31. [PMID: 22583762 PMCID: PMC3440595 DOI: 10.1111/j.1461-0248.2012.01791.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 12/12/2011] [Accepted: 04/02/2012] [Indexed: 11/26/2022]
Abstract
Although crucial for the understanding of adaptive evolution, genetically resolved examples of local adaptation are rare. To maximize survival and reproduction in their local environment, hosts should resist their local parasites and pathogens. The major histocompatibility complex (MHC) with its key function in parasite resistance represents an ideal candidate to investigate parasite-mediated local adaptation. Using replicated field mesocosms, stocked with second-generation lab-bred three-spined stickleback hybrids of a lake and a river population, we show local adaptation of MHC genotypes to population-specific parasites, independently of the genetic background. Increased allele divergence of lake MHC genotypes allows lake fish to fight the broad range of lake parasites, whereas more specific river genotypes confer selective advantages against the less diverse river parasites. Hybrids with local MHC genotype gained more body weight and thus higher fitness than those with foreign MHC in either habitat, suggesting the evolutionary significance of locally adapted MHC genotypes.
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Affiliation(s)
- Christophe Eizaguirre
- Department of Evolutionary Ecology of Marine Fishes, GEOMAR
- Helmholtz Center for Ocean Research, Kiel, 24105, Germany.
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23
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Genotyping MHC classIIB in non-model species by reference strand-mediated conformational analysis (RSCA). CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9655-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Eizaguirre C, Lenz TL, Kalbe M, Milinski M. Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations. Nat Commun 2012; 3:621. [PMID: 22233631 PMCID: PMC3272583 DOI: 10.1038/ncomms1632] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 12/02/2011] [Indexed: 11/08/2022] Open
Abstract
The genes of the major histocompatibility complex are the most polymorphic genes in vertebrates, with more than 1,000 alleles described in human populations. How this polymorphism is maintained, however, remains an evolutionary puzzle. Major histocompatibility complex genes have a crucial function in the adaptive immune system by presenting parasite-derived antigens to T lymphocytes. Because of this function, varying parasite-mediated selection has been proposed as a major evolutionary force for maintaining major histocompatibility complex polymorphism. A necessary prerequisite of such a balancing selection process is rapid major histocompatibility complex allele frequency shifts resulting from emerging selection by a specific parasite. Here we show in six experimental populations of sticklebacks, each exposed to one of two different parasites, that only those major histocompatibility complex alleles providing resistance to the respective specific parasite increased in frequency in the next host generation. This result demonstrates experimentally that varying parasite selection causes rapid adaptive evolutionary changes, thus facilitating the maintenance of major histocompatibility complex polymorphism.
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Affiliation(s)
- Christophe Eizaguirre
- Leibniz Institute for Marine Sciences, Department of Evolutionary Ecology of Marine Fishes, Duesternbrooker Weg 20, 24105 Kiel, Germany.
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Promerová M, Babik W, Bryja J, Albrecht T, Stuglik M, Radwan J. Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing. Mol Ecol Resour 2011; 12:285-92. [PMID: 22018268 DOI: 10.1111/j.1755-0998.2011.03082.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Genes of the highly dynamic major histocompatibility complex (MHC) are directly linked to individual fitness and are of high interest in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high levels of polymorphism in the MHC region, making genotyping of MHC a challenging task. Here, we compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) analysis and 454 GS FLX Titanium pyrosequencing. According to our findings, the number of MHC variants (called alleles for simplicity) detected by CE-SSCP is significantly lower than detected by 454. To resolve discrepancies between the two methods, we cloned and Sanger sequenced a MHC class I amplicon for an individual with high number of alleles. We found a perfect congruence between cloning/Sanger sequencing results and 454. Thus, in case of multi-locus amplification, CE-SSCP considerably underestimates individual MHC diversity. However, numbers of alleles detected by both methods are significantly correlated, although the correlation is weak (r = 0.32). Thus, in systems with highly duplicated MHC, 454 provides more reliable information on individual diversity than CE-SSCP.
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Affiliation(s)
- Marta Promerová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 60365 Brno, Czech Republic.
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Strand TM, Höglund J. Genotyping of black grouse MHC class II B using reference Strand-Mediated Conformational Analysis (RSCA). BMC Res Notes 2011; 4:183. [PMID: 21672220 PMCID: PMC3141517 DOI: 10.1186/1756-0500-4-183] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 06/14/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is a cluster of genes involved in the vertebrate immune system and includes loci with an extraordinary number of alleles. Due to the complex evolution of MHC genes, alleles from different loci within the same MHC class can be very similar and therefore difficult to assign to separate loci. Consequently, single locus amplification of MHC genes is hard to carry out in species with recently duplicated genes in the same MHC class, and multiple MHC loci have to be genotyped simultaneously. Since amplified alleles have the same length, accurate genotyping is difficult. Reference Strand-Mediated Conformational Analysis (RSCA), which is increasingly used in studies of natural populations with multiple MHC genes, is a genotyping method capable to provide high resolution and accuracy in such cases. FINDINGS We adapted the RSCA method to genotype multiple MHC class II B (BLB) genes in black grouse (Tetrao tetrix), a non-model galliform bird species, using a 96-Capillary Array Electrophoresis, the MegaBACE™ 1000 DNA Analysing System (GE Healthcare). In this study we used fluorescently labelled reference strands from both black grouse and hazel grouse and observed good agreement between RSCA and cloning/sequencing since 71 alleles were observed by cloning/sequencing and 76 alleles by RSCA among the 24 individuals included in the comparison. At the individual level however, there was a trend towards more alleles scored with RSCA (1-6 per individual) than cloning/sequencing (1-4 per individual). In 63% of the pair-wise comparison, the identical allele was scored in RSCA as in cloning/sequencing. Nine out of 24 individuals had the same number of alleles in RSCA as in cloning/sequencing. Our RSCA protocol allows a faster RSCA genotyping than presented in many other RSCA studies. CONCLUSIONS In this study, we have developed the RSCA typing method further to work on a 96-Capillary Array Electrophoresis (MegaBACE™ 1000). Our RSCA protocol can be applied to fast and reliable screening of MHC class II B diversity of black grouse populations. This will facilitate future large-scale population studies of black grouse and other galliformes species with multiple inseparable MHC loci.
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Affiliation(s)
- Tanja M Strand
- Population Biology and Conservation Biology, Dept. of Ecology & Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Jacob Höglund
- Population Biology and Conservation Biology, Dept. of Ecology & Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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Cloutier A, Mills JA, Baker AJ. Characterization and locus-specific typing of MHC class I genes in the red-billed gull (Larus scopulinus) provides evidence for major, minor, and nonclassical loci. Immunogenetics 2011; 63:377-94. [PMID: 21327606 DOI: 10.1007/s00251-011-0516-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 01/28/2011] [Indexed: 12/23/2022]
Abstract
A major challenge facing studies of major histocompatibility complex (MHC) evolution in birds is the difficulty in genotyping alleles at individual loci, and the consequent inability to investigate sequence variation and selection pressures for each gene. In this study, four MHC class I loci were isolated from the red-billed gull (Larus scopulinus), representing both the first characterized MHCI genes within Charadriiformes (shorebirds, gulls, and allies) and the first full-length MHCI sequences described outside Galloanserae (gamebirds + waterfowl). Complete multilocus genotypes were obtained for 470 individuals using a combination of reference-strand conformation analysis and direct sequencing of gene-specific amplification products, and variation of peptide-binding region (PBR) exons was surveyed for all loci. Each gene is transcribed and has conserved sequence features characteristic of antigen-presenting MHCI molecules. However, higher allelic variation, a more even allele frequency distribution, and evidence of positive selection acting on a larger number of PBR residues suggest that only one locus (Lasc-UAA) functions as a major classical MHCI gene. Lasc-UBA, with more limited variation and PBR motifs that encompass a subset of Lasc-UAA diversity, was assigned a putative minor classical function, whereas the divergent and largely invariant binding-groove motifs of Lasc-UCA and -UDA are suggestive of nonclassical loci with specialized ligand-binding roles.
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Affiliation(s)
- Alison Cloutier
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
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Eizaguirre C, Lenz TL. Major histocompatibility complex polymorphism: dynamics and consequences of parasite-mediated local adaptation in fishes. JOURNAL OF FISH BIOLOGY 2010; 77:2023-2047. [PMID: 21133915 DOI: 10.1111/j.1095-8649.2010.02819.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Parasitism is a common form of life and represents a strong selective pressure for host organisms. In response to this evolutionary pressure, vertebrates have developed genetically coded defences such as the major histocompatibility complex (MHC). Mechanisms of parasite-mediated selection not only maintain outstanding polymorphism in these genes but have also been proposed to further promote host population divergence and ultimately speciation because it can drive evolution of local adaptation in which MHC genes play a crucial role. This review first highlights the dynamics and complexity of parasite-mediated selection in natural systems, which not only depends on dominating parasite strategies and on the taxonomic diversity of the parasite community but also includes the differences in parasite communities between habitats and niches, creating divergent selection on locally adapted populations. Then the different ways in which MHC genes potentially allow vertebrates to respond to these dynamics and to adapt locally are outlined. Finally, it is proposed that varying selection strength in time and space may lead to variation in the strength of precopulatory reproductive isolation which has evolved to maintain local adaptation.
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Affiliation(s)
- C Eizaguirre
- Leibniz Institute for Marine Sciences (IFM GEOMAR), Department of Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105, Kiel, Germany.
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Eizaguirre C, Lenz TL, Sommerfeld RD, Harrod C, Kalbe M, Milinski M. Parasite diversity, patterns of MHC II variation and olfactory based mate choice in diverging three-spined stickleback ecotypes. Evol Ecol 2010. [DOI: 10.1007/s10682-010-9424-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Canal D, Alcaide M, Anmarkrud JA, Potti J. Towards the simplification of MHC typing protocols: targeting classical MHC class II genes in a passerine, the pied flycatcher Ficedula hypoleuca. BMC Res Notes 2010; 3:236. [PMID: 20815923 PMCID: PMC2944132 DOI: 10.1186/1756-0500-3-236] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/05/2010] [Indexed: 11/13/2022] Open
Abstract
Background Major Histocompatibility Complex (MHC) has drawn the attention of evolutionary biologists due to its importance in crucial biological processes, such as sexual selection and immune response in jawed vertebrates. However, the characterization of classical MHC genes subjected to the effects of natural selection still remains elusive in many vertebrate groups. Here, we have tested the suitability of flanking intron sequences to guide the selective exploration of classical MHC genes driving the co-evolutionary dynamics between pathogens and their passerine (Aves, Order Passeriformes) hosts. Findings Intronic sequences flanking the usually polymorphic exon 2 were isolated from different species using primers sitting on conserved coding regions of MHC class II genes (β chain). Taking the pied flycatcher Ficedula hypoleuca as an example, we demonstrate that careful primer design can evade non-classical MHC gene and pseudogene amplification. At least four polymorphic and expressed loci were co-replicated using a single pair of primers in five non-related individuals (N = 28 alleles). The cross-amplification and preliminary inspection of similar MHC fragments in eight unrelated songbird taxa suggests that similar approaches can also be applied to other species. Conclusions Intron sequences flanking the usually polymorphic exon 2 may assist the specific investigation of classical MHC class II B genes in species characterized by extensive gene duplication and pseudogenization. Importantly, the evasion of non-classical MHC genes with a more specific function and non-functional pseudogenes may accelerate data collection and diminish lab costs. Comprehensive knowledge of gene structure, polymorphism and expression profiles may be useful not only for the selective examination of evolutionarily relevant genes but also to restrict chimera formation by minimizing the number of co-amplifying loci.
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Affiliation(s)
- David Canal
- Estación Biológica de Doñana - CSIC, Department of Evolutionary Ecology, Av, Américo Vespucio s/n, 41092 Seville, Spain.
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Alcaide M, López L, Tanferna A, Blas J, Sergio F, Hiraldo F. Simultaneous analysis of multiple PCR amplicons enhances capillary SSCP discrimination of MHC alleles. Electrophoresis 2010; 31:1353-6. [PMID: 20358545 DOI: 10.1002/elps.200900709] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Miguel Alcaide
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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Affiliation(s)
- W. BABIK
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30‐387 Kraków, Poland
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Lenz TL, Eizaguirre C, Scharsack JP, Kalbe M, Milinski M. Disentangling the role of MHC-dependent 'good genes' and 'compatible genes' in mate-choice decisions of three-spined sticklebacks Gasterosteus aculeatus under semi-natural conditions. JOURNAL OF FISH BIOLOGY 2009; 75:2122-2142. [PMID: 20738677 DOI: 10.1111/j.1095-8649.2009.02410.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
To investigate and disentangle the role of major histocompatibility complex (MHC)-based 'good genes' and 'compatible genes' in mate choice, three-spined sticklebacks Gasterosteus aculeatus with specific MHC IIB genotypes were allowed to reproduce in an outdoor enclosure system. Here, fish were protected from predators but encountered their natural parasites. Mate choice for an intermediate genetic distance between parental MHC genotypes was observed, which would result in intermediate diversity in the offspring, but no mate choice based on good genes was found under the current semi-natural conditions. Investigation of immunological variables revealed that the less-specific innate immune system was more active in individuals with a genetically more divergent MHC allele repertoire. This suggests the need to compensate for an MHC-diminished T-cell repertoire and potentially explains the observed mate choice for intermediate MHC genetic distance. The present findings support a general pattern of mate choice for intermediate MHC diversity (i.e. compatible genes). In addition, the potentially dynamic role of MHC good genes in mate choice under different parasite pressures is discussed in the light of present and previous results.
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Affiliation(s)
- T L Lenz
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Ecology, August-Thienemann-Str. 2, 24306 Plön, Germany.
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EIZAGUIRRE C, YEATES SE, LENZ TL, KALBE M, MILINSKI M. MHC-based mate choice combines good genes and maintenance of MHC polymorphism. Mol Ecol 2009; 18:3316-29. [DOI: 10.1111/j.1365-294x.2009.04243.x] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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