1
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Holmes IA, Durso AM, Myers CR, Hendry TA. Changes in capture availability due to infection can lead to detectable biases in population-level infectious disease parameters. PeerJ 2024; 12:e16910. [PMID: 38436008 PMCID: PMC10909344 DOI: 10.7717/peerj.16910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024] Open
Abstract
Correctly identifying the strength of selection that parasites impose on hosts is key to predicting epidemiological and evolutionary outcomes of host-parasite interactions. However, behavioral changes due to infection can alter the capture probability of infected hosts and thereby make selection difficult to estimate by standard sampling techniques. Mark-recapture approaches, which allow researchers to determine if some groups in a population are less likely to be captured than others, can be used to identify infection-driven capture biases. If a metric of interest directly compares infected and uninfected populations, calculated detection probabilities for both groups may be useful in identifying bias. Here, we use an individual-based simulation to test whether changes in capture rate due to infection can alter estimates of three key metrics: 1) reduction in the reproductive success of infected parents relative to uninfected parents, 2) the relative risk of infection for susceptible genotypes compared to resistant genotypes, and 3) changes in allele frequencies between generations. We explore the direction and underlying causes of the biases that emerge from these simulations. Finally, we argue that short series of mark-recapture sampling bouts, potentially implemented in under a week, can yield key data on detection bias due to infection while not adding a significantly higher burden to disease ecology studies.
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Affiliation(s)
- Iris A. Holmes
- Department of Microbiology, Cornell University, Ithaca, NY, United States
- Cornell Institute of Host Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States
| | - Andrew M. Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL, USA
| | - Christopher R. Myers
- Center for Advanced Computing & Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, United States
| | - Tory A. Hendry
- Department of Microbiology, Cornell University, Ithaca, NY, United States
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2
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Mellinger S, Stervander M, Lundberg M, Drews A, Westerdahl H. Improved haplotype resolution of highly duplicated MHC genes in a long-read genome assembly using MiSeq amplicons. PeerJ 2023; 11:e15480. [PMID: 37456901 PMCID: PMC10349553 DOI: 10.7717/peerj.15480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/08/2023] [Indexed: 07/18/2023] Open
Abstract
Long-read sequencing offers a great improvement in the assembly of complex genomic regions, such as the major histocompatibility complex (MHC) region, which can contain both tandemly duplicated MHC genes (paralogs) and high repeat content. The MHC genes have expanded in passerine birds, resulting in numerous MHC paralogs, with relatively high sequence similarity, making the assembly of the MHC region challenging even with long-read sequencing. In addition, MHC genes show rather high sequence divergence between alleles, making diploid-aware assemblers incorrectly classify haplotypes from the same locus as sequences originating from different genomic regions. Consequently, the number of MHC paralogs can easily be over- or underestimated in long-read assemblies. We therefore set out to verify the MHC diversity in an original and a haplotype-purged long-read assembly of one great reed warbler Acrocephalus arundinaceus individual (the focal individual) by using Illumina MiSeq amplicon sequencing. Single exons, representing MHC class I (MHC-I) and class IIB (MHC-IIB) alleles, were sequenced in the focal individual and mapped to the annotated MHC alleles in the original long-read genome assembly. Eighty-four percent of the annotated MHC-I alleles in the original long-read genome assembly were detected using 55% of the amplicon alleles and likewise, 78% of the annotated MHC-IIB alleles were detected using 61% of the amplicon alleles, indicating an incomplete annotation of MHC genes. In the haploid genome assembly, each MHC-IIB gene should be represented by one allele. The parental origin of the MHC-IIB amplicon alleles in the focal individual was determined by sequencing MHC-IIB in its parents. Two of five larger scaffolds, containing 6-19 MHC-IIB paralogs, had a maternal and paternal origin, respectively, as well as a high nucleotide similarity, which suggests that these scaffolds had been incorrectly assigned as belonging to different loci in the genome rather than as alternate haplotypes of the same locus. Therefore, the number of MHC-IIB paralogs was overestimated in the haploid genome assembly. Based on our findings we propose amplicon sequencing as a suitable complement to long-read sequencing for independent validation of the number of paralogs in general and for haplotype inference in multigene families in particular.
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Affiliation(s)
- Samantha Mellinger
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Martin Stervander
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
- Bird Group, Natural History Museum, Tring, Hertfordshire, United Kingdom
| | - Max Lundberg
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Anna Drews
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Helena Westerdahl
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
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3
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [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: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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4
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Petersen RM, Bergey CM, Roos C, Higham JP. Relationship between genome-wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate. Ecol Evol 2022; 12:e9346. [PMID: 36311412 PMCID: PMC9596323 DOI: 10.1002/ece3.9346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022] Open
Abstract
Although mate choice is expected to favor partners with advantageous genetic properties, the relative importance of genome‐wide characteristics, such as overall heterozygosity or kinship, versus specific loci, is unknown. To disentangle genome‐wide and locus‐specific targets of mate choice, we must first understand congruence in global and local variation within the same individual. This study compares genetic diversity, both absolute and relative to other individuals (i.e., complementarity), assessed across the genome to that found at the major histocompatibility complex (MHC), a hyper‐variable gene family integral to immune system function and implicated in mate choice across species. Using DNA from 22 captive olive baboons (Papio anubis), we conducted double digest restriction site‐associated DNA sequencing to estimate genome‐wide heterozygosity and kinship, and sequenced two class I and two class II MHC loci. We found that genome‐wide diversity was not associated with MHC diversity, and that diversity at class I MHC loci was not correlated with diversity at class II loci. Additionally, kinship was a significant predictor of the number of MHC alleles shared between dyads at class II loci. Our results provide further evidence of the strong selective pressures maintaining genetic diversity at the MHC in comparison to other randomly selected sites throughout the genome. Furthermore, our results indicate that class II MHC disassortative mate choice may mediate inbreeding avoidance in this population. Our study suggests that mate choice favoring genome‐wide genetic diversity is not always synonymous with mate choice favoring MHC diversity, and highlights the importance of controlling for kinship when investigating MHC‐associated mate choice.
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Affiliation(s)
- Rachel M. Petersen
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA,New York Consortium in Evolutionary PrimatologyNew YorkNew YorkUSA
| | - Christina M. Bergey
- Department of Genetics and the Human Genetics Institute of New JerseyRutgers UniversityPiscatawayNew JerseyUSA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - James P. Higham
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA,New York Consortium in Evolutionary PrimatologyNew YorkNew YorkUSA
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5
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Huang W, Dicks KL, Hadfield JD, Johnston SE, Ballingall KT, Pemberton JM. Contemporary selection on MHC genes in a free-living ruminant population. Ecol Lett 2022; 25:828-838. [PMID: 35050541 PMCID: PMC9306867 DOI: 10.1111/ele.13957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022]
Abstract
Genes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection is believed to be the main force maintaining MHC diversity. However, relatively few studies have demonstrated contemporary selection on MHC genes. Here, we examine associations between MHC variation and several fitness measurements including total fitness and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored between 1989 and 2012. In terms of total fitness, measured as lifetime breeding success of all individuals born, we found haplotypes named C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was associated with haplotype divergence while individual haplotypes (C, D and F) were associated with adult fitness components. Consistent with the increased male total fitness, the rarest haplotype D has increased in frequency throughout the study period more than expected under neutral expectations. Our results demonstrate contemporary natural selection is acting on MHC class II genes in Soay sheep and the mode of selection on specific fitness components can be different mode from selection on total fitness.
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Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Kara L Dicks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Royal Zoological Society of Scotland, Edinburgh, UK
| | - Jarrod D Hadfield
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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6
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Nandakumar M, Ishtiaq F. Genetic drift and bottleneck do not influence diversity in Toll-like receptor genes at a small spatial scale in a Himalayan passerine. Ecol Evol 2020; 10:12246-12263. [PMID: 33209285 PMCID: PMC7663051 DOI: 10.1002/ece3.6855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity is important for long-term viability of a population. Low genetic diversity reduces persistence and survival of populations and increases susceptibility to diseases. Comparisons of the neutral markers with functional loci such as immune genes [Toll-like receptors; TLR] can provide useful insights into evolutionary potential of a species and how the diversity of pathogens and selection pressures on their hosts are directly linked to their environment. In this study, we compare genetic diversity in neutral (eleven microsatellite loci) and adaptive (seven TLR loci) loci to determine genetic variation in a nonmigratory western Himalayan passerine, the black-throated tit (Aegithalos concinnus), distributed across an elevation gradient with varying degree of pathogen-mediated selection pressure. We further compare the diversity in TLR loci with a high-elevation sister species, the white-throated tit (Aegithalos niveogularis). Our results indicate a lack of population genetic structure in the black-throated tit and signatures of a past bottleneck. In contrast, we found high diversity in TLR loci and locus-specific (TLR7) signatures of pathogen-mediated selection, which was comparable to diversity in the white-throated tit. Levels of diversity at TLR5 locus corresponded very closely with neutral microsatellite variation. We found evidence of positive selection in TLR1LA, TLR5, and TLR7 loci highlighting the importance in pathogen recognition. Our finding demonstrates that reduction in neutral variation does not necessarily lead to reduction in functional genetic diversity and probably helps in revival of population in a widespread species.
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Affiliation(s)
- Mridula Nandakumar
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
- Present address:
Department of BiologyLund UniversityLundSweden
| | - Farah Ishtiaq
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
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7
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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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8
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Whittingham LA, Dunn PO, Freeman-Gallant CR, Taff CC, Johnson JA. Major histocompatibility complex variation and blood parasites in resident and migratory populations of the common yellowthroat. J Evol Biol 2018; 31:1544-1557. [DOI: 10.1111/jeb.13349] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/12/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Linda A. Whittingham
- Behavioral and Molecular Ecology Group; Department of Biological Sciences; University of Wisconsin-Milwaukee; Milwaukee WI USA
| | - Peter O. Dunn
- Behavioral and Molecular Ecology Group; Department of Biological Sciences; University of Wisconsin-Milwaukee; Milwaukee WI USA
| | | | - Conor C. Taff
- Cornell Laboratory of Ornithology; Cornell University; Ithaca NY USA
| | - Jeff A. Johnson
- Department of Biological Sciences; Institute of Applied Sciences; University of North Texas; Denton TX USA
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9
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Biedrzycka A, Bielański W, Ćmiel A, Solarz W, Zając T, Migalska M, Sebastian A, Westerdahl H, Radwan J. Blood parasites shape extreme major histocompatibility complex diversity in a migratory passerine. Mol Ecol 2018; 27:2594-2603. [PMID: 29654666 DOI: 10.1111/mec.14592] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 12/15/2022]
Abstract
Pathogens are one of the main forces driving the evolution and maintenance of the highly polymorphic genes of the vertebrate major histocompatibility complex (MHC). Although MHC proteins are crucial in pathogen recognition, it is still poorly understood how pathogen-mediated selection promotes and maintains MHC diversity, and especially so in host species with highly duplicated MHC genes. Sedge warblers (Acrocephalus schoenobaenus) have highly duplicated MHC genes, and using data from high-throughput MHC genotyping, we were able to investigate to what extent avian malaria parasites explain temporal MHC class I supertype fluctuations in a long-term study population. We investigated infection status and infection intensities of two different strains of Haemoproteus, that is avian malaria parasites that are known to have significant fitness consequences in sedge warblers. We found that prevalence of avian malaria in carriers of specific MHC class I supertypes was a significant predictor of their frequency changes between years. This finding suggests that avian malaria infections partly drive the temporal fluctuations of the MHC class I supertypes. Furthermore, we found that individuals with a large number of different supertypes had higher resistance to avian malaria, but there was no evidence for an optimal MHC class I diversity. Thus, the two studied malaria parasite strains appear to select for a high MHC class I supertype diversity. Such selection may explain the maintenance of the extremely high number of MHC class I gene copies in sedge warblers and possibly also in other passerines where avian malaria is a common disease.
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Affiliation(s)
| | - Wojciech Bielański
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | - Adam Ćmiel
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | - Wojciech Solarz
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | - Tadeusz Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
| | - Magdalena Migalska
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Alvaro Sebastian
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | | | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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10
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11
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Spatial distribution of microsatellite and MHC-DRB exon 2 gene variability in the Jamaican fruit bat (Artibeus jamaicensis) in Mexico. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2016.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Santos PSC, Courtiol A, Heidel AJ, Höner OP, Heckmann I, Nagy M, Mayer F, Platzer M, Voigt CC, Sommer S. MHC-dependent mate choice is linked to a trace-amine-associated receptor gene in a mammal. Sci Rep 2016; 6:38490. [PMID: 27941813 PMCID: PMC5150237 DOI: 10.1038/srep38490] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/11/2016] [Indexed: 01/28/2023] Open
Abstract
Major histocompatibility complex (MHC) genes play a pivotal role in vertebrate self/nonself recognition, parasite resistance and life history decisions. In evolutionary terms, the MHC’s exceptional diversity is likely maintained by sexual and pathogen-driven selection. Even though MHC-dependent mating preferences have been confirmed for many species, the sensory and genetic mechanisms underlying mate recognition remain cryptic. Since olfaction is crucial for social communication in vertebrates, variation in chemosensory receptor genes could explain MHC-dependent mating patterns. Here, we investigated whether female mate choice is based on MHC alleles and linked to variation in chemosensory trace amine-associated receptors (TAARs) in the greater sac-winged bat (Saccopteryx bilineata). We sequenced several MHC and TAAR genes and related their variation to mating and paternity data. We found strong evidence for MHC class I-dependent female choice for genetically diverse and dissimilar males. We also detected a significant interaction between mate choice and the female TAAR3 genotype, with TAAR3-heterozygous females being more likely to choose MHC-diverse males. These results suggest that TAARs and olfactory cues may be key mediators in mammalian MHC-dependent mate choice. Our study may help identify the ligands involved in the chemical communication between potential mates.
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Affiliation(s)
- Pablo S C Santos
- Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Alexandre Courtiol
- Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), 14195 Berlin, Germany
| | - Andrew J Heidel
- Leibniz Institute on Age - Fritz Lipmann Institute, Jena, Germany
| | - Oliver P Höner
- Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany
| | - Ilja Heckmann
- Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany
| | - Martina Nagy
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany
| | - Matthias Platzer
- Leibniz Institute on Age - Fritz Lipmann Institute, Jena, Germany
| | - Christian C Voigt
- Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany
| | - Simone Sommer
- Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin, Germany.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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13
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Biedrzycka A, Sebastian A, Migalska M, Westerdahl H, Radwan J. Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird. Mol Ecol Resour 2016; 17:642-655. [DOI: 10.1111/1755-0998.12612] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 02/10/2016] [Accepted: 08/23/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Aleksandra Biedrzycka
- Institute of Nature Conservation; Polish Academy of Sciences; Al. Mickiewicza 33 31-120 Kraków Poland
| | - Alvaro Sebastian
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznań Poland
| | - Magdalena Migalska
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznań Poland
| | - Helena Westerdahl
- Department of Biology; Lund University; Ecology Building, Sölvegatan 37 223 62 Lund Sweden
| | - Jacek Radwan
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznań Poland
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14
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MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion. Immunogenetics 2016; 69:101-111. [PMID: 27717988 DOI: 10.1007/s00251-016-0953-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/26/2016] [Indexed: 12/23/2022]
Abstract
The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influenced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signatures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes.
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15
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Biedrzycka A, Kloch A. Development of novel associations between MHC alleles and susceptibility to parasitic infections in an isolated population of an endangered mammal. INFECTION GENETICS AND EVOLUTION 2016; 44:210-217. [PMID: 27423515 DOI: 10.1016/j.meegid.2016.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 10/21/2022]
Abstract
The role of pathogens in dynamics of endangered species is not fully understood, and the effect of infection often interacts with other processes affecting those species, such as fragmentation and isolation or loss of genetic variation. Small, isolated populations are prone to losing functional alleles due to demographic processes and genetic drift, which may diminish their ability to resist infection if immune genes are affected. Demographic processes may also alter the selective pressure exerted by a parasite, as they influence the rate of parasite transmission between individuals. In the present paper we studied changes in parasite infection levels and genetic variability in an isolated population of spotted suslik (Spermophillus suslicus). Over a three-year period (approx. three generations), when the population size remained relatively stable, we observed a considerable increase in parasite prevalence and infection intensity, followed by the development of novel associations between MHC DRB alleles and parasite burden. Contrary to expectations, the change in MHC allele frequency over time was not consistent with the effect of the allele - for instance, Spsu-DRB*07, associated with higher intensity of infection with a nematode Capillaria sp., increased in frequency from 11.8 to 20.2%. Yet, we found no signatures of selection in the studied loci. Our results show that an isolated, stable population may experience a sudden increase in parasitic infections, resulting in a development of novel associations between MHC alleles and parasite susceptibility/resistance, even though no signatures of selection can be found.
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Affiliation(s)
- Aleksandra Biedrzycka
- Institute of Nature Conservation, Polish Academy of Sciences, al. A. Mickiewicza 33, 31-120 Kraków, Poland.
| | - Agnieszka Kloch
- Department of Ecology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland.
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Knafler GJ, Ortiz-Catedral L, Jackson B, Varsani A, Grueber CE, Robertson BC, Jamieson IG. Comparison of beak and feather disease virus prevalence and immunity-associated genetic diversity over time in an island population of red-crowned parakeets. Arch Virol 2015; 161:811-20. [PMID: 26699786 DOI: 10.1007/s00705-015-2717-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 12/03/2015] [Indexed: 11/30/2022]
Abstract
Pathogen outbreaks in the wild can contribute to a population's extinction risk. Concern over the effects of pathogen outbreaks in wildlife is amplified in small, threatened populations, where degradation of genetic diversity may hinder natural selection for enhanced immunocompetence. Beak and feather disease virus (BFDV) was detected for the first time in an island population of red-crowned parakeets (Cyanoramphus novaezelandiae) in 2008 on Little Barrier Island (Hauturu-o-Toi) of New Zealand. By 2013, the prevalence of the viral infection had significantly decreased within the population. We tested whether the population of red-crowned parakeets showed a selective response to BFDV, using neutral microsatellite and two immunity-associated genetic markers, the major histocompatibility complex (MHC) and Toll-like receptors (TLRs). We found evidence for selection at viral-associated TLR3; however, the ability of TLR3 to elicit an immune response in the presence of BFDV warrants confirmation. Alternatively, because red-crowned parakeet populations are prone to fluctuations in size, the decrease in BFDV prevalence over time may be attributed to the Little Barrier Island population dropping below the density threshold for viral maintenance. Our results highlight that natural processes such as adaptation for enhanced immunocompetence and/or density fluctuations are efficient mechanisms for reducing pathogen prevalence in a threatened, isolated population.
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Affiliation(s)
- Gabrielle J Knafler
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
| | - Luis Ortiz-Catedral
- Ecology and Conservation Group, Institute of Natural and Mathematical Sciences, Massey University, Private Bag 102-904, Auckland, New Zealand
| | - Bethany Jackson
- College of Veterinary Medicine, Murdoch University, Perth, WA, Australia
| | - Arvind Varsani
- Centre for Integrative Ecology, Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA
| | - Catherine E Grueber
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW, Australia
- San Diego Zoo Global, San Diego, USA
| | - Bruce C Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Ian G Jamieson
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
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Villanea FA, Safi KN, Busch JW. A General Model of Negative Frequency Dependent Selection Explains Global Patterns of Human ABO Polymorphism. PLoS One 2015; 10:e0125003. [PMID: 25946124 PMCID: PMC4422588 DOI: 10.1371/journal.pone.0125003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/19/2015] [Indexed: 11/18/2022] Open
Abstract
The ABO locus in humans is characterized by elevated heterozygosity and very similar allele frequencies among populations scattered across the globe. Using knowledge of ABO protein function, we generated a simple model of asymmetric negative frequency dependent selection and genetic drift to explain the maintenance of ABO polymorphism and its loss in human populations. In our models, regardless of the strength of selection, models with large effective population sizes result in ABO allele frequencies that closely match those observed in most continental populations. Populations must be moderately small to fall out of equilibrium and lose either the A or B allele (N(e) ≤ 50) and much smaller (N(e) ≤ 25) for the complete loss of diversity, which nearly always involved the fixation of the O allele. A pattern of low heterozygosity at the ABO locus where loss of polymorphism occurs in our model is consistent with small populations, such as Native American populations. This study provides a general evolutionary model to explain the observed global patterns of polymorphism at the ABO locus and the pattern of allele loss in small populations. Moreover, these results inform the range of population sizes associated with the recent human colonization of the Americas.
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Affiliation(s)
- Fernando A. Villanea
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington, 99164, United States of America
| | - Kristin N. Safi
- Department of Anthropology, Washington State University, PO Box 644910, Pullman, Washington, 99164, United States of America
| | - Jeremiah W. Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington, 99164, United States of America
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Whittingham LA, Freeman-Gallant CR, Taff CC, Dunn PO. Different ornaments signal male health and MHC variation in two populations of a warbler. Mol Ecol 2015; 24:1584-95. [PMID: 25728470 DOI: 10.1111/mec.13130] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 12/12/2022]
Abstract
Male traits that signal health and vigour are used by females to choose better quality mates, but in some cases the male trait selected by females differs among populations. Multiple male traits can be maintained through female mate choice if both traits are equally honest indicators of male quality, but tests of this prediction are rare. By choosing males based on such traits, females could gain direct benefits from males (assistance with parental care), but when females choose extra-pair mates based on these traits, females gain only male sperm, and potentially indirect genetic benefits for their offspring. In common yellowthroats (Geothylpis trichas), female choice of extra-pair mates targets two different plumage ornaments: the black mask in a Wisconsin population and the yellow bib in a New York population. Previously, we found that the black mask in Wisconsin is related to greater major histocompatibility complex (MHC) class II variation, which in turn signals better survival and disease resistance. In this study, we examined the signalling function of the yellow bib in New York to test whether it signals the same aspects of male quality as the black mask in Wisconsin. As predicted, we found that the yellow bib in New York is most closely associated with MHC variation, which also signals survival and resistance to blood parasites. Thus, the ornament preferred by females differs between the two populations, but the different ornaments signal similar aspects of male health and genetic quality, specifically information regarding MHC variation and potential indirect genetic benefits to females.
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Affiliation(s)
- Linda A Whittingham
- Department of Biological Sciences, Behavioral and Molecular Ecology Group, University of Wisconsin-Milwaukee, Milwaukee, WI, 53201, USA
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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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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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Serieys LEK, Lea A, Pollinger JP, Riley SPD, Wayne RK. Disease and freeways drive genetic change in urban bobcat populations. Evol Appl 2014; 8:75-92. [PMID: 25667604 PMCID: PMC4310583 DOI: 10.1111/eva.12226] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/20/2014] [Indexed: 01/04/2023] Open
Abstract
Urbanization profoundly impacts animal populations by causing isolation, increased susceptibility to disease, and exposure to toxicants. Genetic effects include reduced effective population size, increased population substructure, and decreased adaptive potential. We investigated the influence that urbanization and a disease epizootic had on the population genetics of bobcats (Lynx rufus) distributed across a highly fragmented urban landscape. We genotyped more than 300 bobcats, sampled from 1996 to 2012, for variation at nine neutral and seven immune gene-linked microsatellite loci. We found that two freeways are significant barriers to gene flow. Further, a 3-year disease epizootic, associated with secondary anticoagulant rodenticide exposure, caused a population bottleneck that led to significant genetic differentiation between pre- and post-disease populations that was greater than that between populations separated by major freeways for >60 years. However, balancing selection acted on immune-linked loci during the epizootic, maintaining variation at functional regions. Conservation assessments need to assay loci that are potentially under selection to better preserve the adaptive potential of populations at the urban–wildland interface. Further, interconnected regions that contain appropriate habitat for wildlife will be critical to the long-term viability of animal populations in urban landscapes.
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Affiliation(s)
- Laurel E K Serieys
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, CA, USA
| | - Amanda Lea
- Department of Biology, Duke University Durham, NC, USA
| | - John P Pollinger
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, CA, USA
| | - Seth P D Riley
- Santa Monica Mountains National Recreation Area, National Park Service Thousand Oaks, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, CA, USA
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Preen secretions encode information on MHC similarity in certain sex-dyads in a monogamous seabird. Sci Rep 2014; 4:6920. [PMID: 25370306 PMCID: PMC4220275 DOI: 10.1038/srep06920] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/13/2014] [Indexed: 12/21/2022] Open
Abstract
Animals are known to select mates to maximize the genetic diversity of their offspring in order to achieve immunity against a broader range of pathogens. Although several bird species preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC), it remains unknown whether they can use olfactory cues to assess MHC similarity with potential partners. Here we combined gas chromatography data with genetic similarity indices based on MHC to test whether similarity in preen secretion chemicals correlated with MHC relatedness in the black-legged kittiwake (Rissa tridactyla), a species that preferentially mates with genetically dissimilar partners. We found that similarity in preen secretion chemicals was positively correlated with MHC relatedness in male-male and male-female dyads. This study provides the first evidence that preen secretion chemicals can encode information on MHC relatedness and suggests that odor-based mechanisms of MHC-related mate choice may occur in birds.
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Cutrera AP, Zenuto RR, Lacey EA. Interpopulation differences in parasite load and variable selective pressures on MHC genes inCtenomys talarum. J Mammal 2014. [DOI: 10.1644/13-mamm-a-120] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Role of selection versus neutral processes determining genetic variation in a small mammal along a climatic gradient in southern Africa. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9731-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Huchard E, Baniel A, Schliehe-Diecks S, Kappeler PM. MHC-disassortative mate choice and inbreeding avoidance in a solitary primate. Mol Ecol 2013; 22:4071-86. [DOI: 10.1111/mec.12349] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 04/03/2013] [Accepted: 04/09/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Elise Huchard
- Behavioral Ecology and Sociobiology Unit; German Primate Center; Kellnerweg 4 Göttingen Germany
- Courant Research Centre Evolution of Social Behaviour; University of Göttingen; Kellnerweg 6 Göttingen Germany
| | - Alice Baniel
- Behavioral Ecology and Sociobiology Unit; German Primate Center; Kellnerweg 4 Göttingen Germany
| | - Susanne Schliehe-Diecks
- Behavioral Ecology and Sociobiology Unit; German Primate Center; Kellnerweg 4 Göttingen Germany
- Courant Research Centre Evolution of Social Behaviour; University of Göttingen; Kellnerweg 6 Göttingen Germany
| | - Peter M. Kappeler
- Behavioral Ecology and Sociobiology Unit; German Primate Center; Kellnerweg 4 Göttingen Germany
- Courant Research Centre Evolution of Social Behaviour; University of Göttingen; Kellnerweg 6 Göttingen Germany
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Aguilar JRD, Schut E, Merino S, Martínez J, Komdeur J, Westerdahl H. MHC class II B diversity in blue tits: a preliminary study. Ecol Evol 2013; 3:1878-89. [PMID: 23919136 PMCID: PMC3728931 DOI: 10.1002/ece3.598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/17/2013] [Indexed: 12/18/2022] Open
Abstract
In this study, we partly characterize major histocompatibility complex (MHC) class II B in the blue tit (Cyanistes caeruleus). A total of 22 individuals from three different European locations: Spain, The Netherlands, and Sweden were screened for MHC allelic diversity. The MHC genes were investigated using both PCR-based methods and unamplified genomic DNA with restriction fragment length polymorphism (RFLP) and southern blots. A total of 13 different exon 2 sequences were obtained independently from DNA and/or RNA, thus confirming gene transcription and likely functionality of the genes. Nine out of 13 alleles were found in more than one country, and two alleles appeared in all countries. Positive selection was detected in the region coding for the peptide binding region (PBR). A maximum of three alleles per individual was detected by sequencing and the RFLP pattern consisted of 4-7 fragments, indicating a minimum number of 2-4 loci per individual. A phylogenetic analysis, demonstrated that the blue tit sequences are divergent compared to sequences from other passerines resembling a different MHC lineage than those possessed by most passerines studied to date.
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Affiliation(s)
- Juan Rivero-de Aguilar
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC)J. Gutiérrez Abascal 2, E-28006, Madrid, Spain
| | - Elske Schut
- Behavioural Ecology and Self-Organization, The University of GroningenPO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Santiago Merino
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC)J. Gutiérrez Abascal 2, E-28006, Madrid, Spain
| | - Javier Martínez
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de AlcaláAlcalá de Henares, E-28871, Madrid, Spain
| | - Jan Komdeur
- Behavioural Ecology and Self-Organization, The University of GroningenPO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Ecology Building, Lund UniversitySölvegatan 37, SE-22362, Lund, Sweden
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Pavey SA, Sevellec M, Adam W, Normandeau E, Lamaze FC, Gagnaire PA, Filteau M, Hebert FO, Maaroufi H, Bernatchez L. Nonparallelism in MHCIIβ diversity accompanies nonparallelism in pathogen infection of lake whitefish (Coregonus clupeaformis) species pairs as revealed by next-generation sequencing. Mol Ecol 2013; 22:3833-49. [DOI: 10.1111/mec.12358] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/03/2013] [Accepted: 04/08/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Scott A. Pavey
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
| | - Maelle Sevellec
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
| | - William Adam
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
| | - Eric Normandeau
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
| | - Fabien C. Lamaze
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
| | - Pierre-Alexandre Gagnaire
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
- Institut des Sciences de l'Evolution - Montpellier (ISEM); Universite Montpellier II; Place Eugene Bataillon 34095 Montpellier Cedex France
| | - Marie Filteau
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
| | - Francois Olivier Hebert
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
| | - Halim Maaroufi
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
- Plate-forme de Bio-informatique and Institut de Biologie Intégrative et des Systèmes; Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
| | - Louis Bernatchez
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugene-Marchand Québec Québec Canada G1V 0A6
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References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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McMullan M, van Oosterhout C. Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families. PLoS One 2012; 7:e42119. [PMID: 22900006 PMCID: PMC3416836 DOI: 10.1371/journal.pone.0042119] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/02/2012] [Indexed: 01/12/2023] Open
Abstract
The co-evolutionary arms race between host immune genes and parasite virulence genes is known as Red Queen dynamics. Temporal fluctuations in allele frequencies, or the ‘turnover’ of alleles at immune genes, are concordant with predictions of the Red Queen hypothesis. Such observations are often taken as evidence of host-parasite co-evolution. Here, we use computer simulations of the Major Histocompatibility Complex (MHC) of guppies (Poecilia reticulata) to study the turnover rate of alleles (temporal genetic differentiation, G'ST). Temporal fluctuations in MHC allele frequencies can be ≥≤order of magnitude larger than changes observed at neutral loci. Although such large fluctuations in the MHC are consistent with Red Queen dynamics, simulations show that other demographic and population genetic processes can account for this observation, these include: (1) overdominant selection, (2) fluctuating population size within a metapopulation, and (3) the number of novel MHC alleles introduced by immigrants when there are multiple duplicated genes. Synergy between these forces combined with migration rate and the effective population size can drive the rapid turnover in MHC alleles. We posit that rapid allelic turnover is an inherent property of highly polymorphic multigene families and that it cannot be taken as evidence of Red Queen dynamics. Furthermore, combining temporal samples in spatial FST outlier analysis may obscure the signal of selection.
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Affiliation(s)
- Mark McMullan
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
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Marsden CD, Woodroffe R, Mills MGL, McNutt JW, Creel S, Groom R, Emmanuel M, Cleaveland S, Kat P, Rasmussen GSA, Ginsberg J, Lines R, André JM, Begg C, Wayne RK, Mable BK. Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus). Mol Ecol 2012; 21:1379-93. [PMID: 22320891 DOI: 10.1111/j.1365-294x.2012.05477.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e) < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.
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Affiliation(s)
- Clare D Marsden
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, UK.
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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: 198] [Impact Index Per Article: 16.5] [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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Biedrzycka A, Kloch A, Buczek M, Radwan J. Major histocompatibility complex DRB genes and blood parasite loads in fragmented populations of the spotted suslik Spermophilus suslicus. Mamm Biol 2011. [DOI: 10.1016/j.mambio.2011.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Westerdahl H, Asghar M, Hasselquist D, Bensch S. Quantitative disease resistance: to better understand parasite-mediated selection on major histocompatibility complex. Proc Biol Sci 2011; 279:577-84. [PMID: 21733902 DOI: 10.1098/rspb.2011.0917] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We outline a descriptive framework of how candidate alleles of the immune system associate with infectious diseases in natural populations of animals. Three kinds of alleles can be separated when both prevalence of infection and infection intensity are measured--qualitative disease resistance, quantitative disease resistance and susceptibility alleles. Our descriptive framework demonstrates why alleles for quantitative resistance and susceptibility cannot be separated based on prevalence data alone, but are distinguishable on infection intensity. We then present a case study to evaluate a previous finding of a positive association between prevalence of a severe avian malaria infection (GRW2, Plasmodium ashfordi) and a major histocompatibility complex (MHC) class I allele (B4b) in great reed warblers Acrocephalus arundinaceus. Using the same dataset, we find that individuals with allele B4b have lower GRW2 infection intensities than individuals without this allele. Therefore, allele B4b provides quantitative resistance rather than increasing susceptibility to infection. This implies that birds carrying B4b can mount an immune response that suppresses the acute-phase GRW2 infection, while birds without this allele cannot and may die. We argue that it is important to determine whether MHC alleles related to infections are advantageous (quantitative and qualitative resistance) or disadvantageous (susceptibility) to obtain a more complete picture of pathogen-mediated balancing selection.
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Affiliation(s)
- Helena Westerdahl
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Ecology Building, 223 62 Lund, Sweden.
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34
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Evans ML, Dionne M, Miller KM, Bernatchez L. Mate choice for major histocompatibility complex genetic divergence as a bet-hedging strategy in the Atlantic salmon (Salmo salar). Proc Biol Sci 2011; 279:379-86. [PMID: 21697172 DOI: 10.1098/rspb.2011.0909] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Major histocompatibility complex (MHC)-dependent mating preferences have been observed across vertebrate taxa and these preferences are expected to promote offspring disease resistance and ultimately, viability. However, little empirical evidence linking MHC-dependent mate choice and fitness is available, particularly in wild populations. Here, we explore the adaptive potential of previously observed patterns of MHC-dependent mate choice in a wild population of Atlantic salmon (Salmo salar) in Québec, Canada, by examining the relationship between MHC genetic variation and adult reproductive success and offspring survival over 3 years of study. While Atlantic salmon choose their mates in order to increase MHC diversity in offspring, adult reproductive success was in fact maximized between pairs exhibiting an intermediate level of MHC dissimilarity. Moreover, patterns of offspring survival between years 0+ and 1+, and 1+ and 2+ and population genetic structure at the MHC locus relative to microsatellite loci indicate that strong temporal variation in selection is likely to be operating on the MHC. We interpret MHC-dependent mate choice for diversity as a likely bet-hedging strategy that maximizes parental fitness in the face of temporally variable and unpredictable natural selection pressures.
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Affiliation(s)
- Melissa L Evans
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Université Laval, Québec, Canada.
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Bollmer JL, Hull JM, Ernest HB, Sarasola JH, Parker PG. Reduced MHC and neutral variation in the Galápagos hawk, an island endemic. BMC Evol Biol 2011; 11:143. [PMID: 21612651 PMCID: PMC3118149 DOI: 10.1186/1471-2148-11-143] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 05/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genes at the major histocompatibility complex (MHC) are known for high levels of polymorphism maintained by balancing selection. In small or bottlenecked populations, however, genetic drift may be strong enough to overwhelm the effect of balancing selection, resulting in reduced MHC variability. In this study we investigated MHC evolution in two recently diverged bird species: the endemic Galápagos hawk (Buteo galapagoensis), which occurs in small, isolated island populations, and its widespread mainland relative, the Swainson's hawk (B. swainsoni). RESULTS We amplified at least two MHC class II B gene copies in each species. We recovered only three different sequences from 32 Galápagos hawks, while we amplified 20 unique sequences in 20 Swainson's hawks. Most of the sequences clustered into two groups in a phylogenetic network, with one group likely representing pseudogenes or nonclassical loci. Neutral genetic diversity at 17 microsatellite loci was also reduced in the Galápagos hawk compared to the Swainson's hawk. CONCLUSIONS The corresponding loss in neutral diversity suggests that the reduced variability present at Galápagos hawk MHC class II B genes compared to the Swainson's hawk is primarily due to a founder event followed by ongoing genetic drift in small populations. However, purifying selection could also explain the low number of MHC alleles present. This lack of variation at genes involved in the adaptive immune response could be cause for concern should novel diseases reach the archipelago.
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Affiliation(s)
- Jennifer L Bollmer
- Department of Biology, University of Missouri-St. Louis, One University Boulevard, St. Louis, MO 63121, USA
- Department of Biological Sciences, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, WI 53201, USA
| | - Joshua M Hull
- Wildlife and Ecology Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA
- Department of Animal Science, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Holly B Ernest
- Wildlife and Ecology Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - José H Sarasola
- Department of Evolutionary Ecology, Estación Biológica de Doñana, Avda. Américo Vespucio, 41092 Sevilla, Spain
| | - Patricia G Parker
- Department of Biology, University of Missouri-St. Louis, One University Boulevard, St. Louis, MO 63121, USA
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Campos JL, Bellocq JGD, Schaschl H, Suchentrunk F. MHC class II DQA gene variation across cohorts of brown hares (Lepus europaeus) from eastern Austria: Testing for different selection hypotheses. Mamm Biol 2011. [DOI: 10.1016/j.mambio.2010.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Loiseau C, Zoorob R, Robert A, Chastel O, Julliard R, Sorci G. Plasmodium relictum infection and MHC diversity in the house sparrow (Passer domesticus). Proc Biol Sci 2011; 278:1264-72. [PMID: 20943698 PMCID: PMC3049082 DOI: 10.1098/rspb.2010.1968] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 09/22/2010] [Indexed: 01/22/2023] Open
Abstract
Antagonistic coevolution between hosts and parasites has been proposed as a mechanism maintaining genetic diversity in both host and parasite populations. In particular, the high level of genetic diversity usually observed at the major histocompatibility complex (MHC) is generally thought to be maintained by parasite-driven selection. Among the possible ways through which parasites can maintain MHC diversity, diversifying selection has received relatively less attention. This hypothesis is based on the idea that parasites exert spatially variable selection pressures because of heterogeneity in parasite genetic structure, abundance or virulence. Variable selection pressures should select for different host allelic lineages resulting in population-specific associations between MHC alleles and risk of infection. In this study, we took advantage of a large survey of avian malaria in 13 populations of the house sparrow (Passer domesticus) to test this hypothesis. We found that (i) several MHC alleles were either associated with increased or decreased risk to be infected with Plasmodium relictum, (ii) the effects were population specific, and (iii) some alleles had antagonistic effects across populations. Overall, these results support the hypothesis that diversifying selection in space can maintain MHC variation and suggest a pattern of local adaptation where MHC alleles are selected at the local host population level.
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Affiliation(s)
- Claire Loiseau
- Laboratoire Parasitologie Evolutive, Université Pierre et Marie Curie, CNRS UMR 7103, 7, quai St Bernard, Case 237, 75252 Paris Cedex 05, France
| | - Rima Zoorob
- Laboratoire de Génétique Moléculaire et Intégration des Fonctions Cellulaires, CNRS FRE 2937, 7 rue Guy Mocquet, 94801 Villejuif Cedex, France
| | - Alexandre Robert
- Laboratoire Conservation des Espèces, Restauration et Suivi des Populations, Muséum National d'Histoire Naturelle, UMR 5173 CNRS-MNHN-UPMC 55 rue Buffon, 75005 Paris, France
| | - Olivier Chastel
- Centre d'Etudes Biologique de Chizé, CNRS UPR 1934, 79360 Beauvoir-sur-Niort, France
| | - Romain Julliard
- Laboratoire Conservation des Espèces, Restauration et Suivi des Populations, Muséum National d'Histoire Naturelle, UMR 5173 CNRS-MNHN-UPMC 55 rue Buffon, 75005 Paris, France
| | - Gabriele Sorci
- BioGéoSciences, Université de Bourgogne, CNRS UMR 5561, 6 Boulevard Gabriel, 21000 Dijon, France
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Cutrera AP, Zenuto RR, Lacey EA. MHC variation, multiple simultaneous infections and physiological condition in the subterranean rodent Ctenomys talarum. INFECTION GENETICS AND EVOLUTION 2011; 11:1023-36. [PMID: 21497205 DOI: 10.1016/j.meegid.2011.03.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 02/28/2011] [Accepted: 03/24/2011] [Indexed: 01/15/2023]
Abstract
Parasites and pathogens can play a significant role in shaping the genetic diversity of host populations, particularly at genes associated with host immune response. To explore this relationship in a natural population of vertebrates, we characterized Major Histocompatibility Complex (MHC) variation in the subterranean rodent Ctenomys talarum (the talas tuco-tuco) as a function of parasite load and ability to mount an adaptive immune response against a novel antigen. Specifically, we quantified genotypic diversity at the MHC class II DRB locus in relation to (1) natural variation in infection by multiple genera of parasites (potential agents of selection on MHC genes) and (2) antibody production in response to injection with sheep red blood cells (a measure of immunocompetence). Data were analyzed using co-inertia multivariate statistics, with epidemiological proxies for individual condition (hematocrit, leukocyte profile, body weight) and risk of parasite exposure (season of capture, sex). A significant excess of DRB heterozygotes was evident in the study population. Co-inertia analyses revealed significant associations between specific DRB alleles and both parasite load and intensity of humoral immune response against sheep red blood cells. The presence of specific DRB aminoacid sequences appeared to be more strongly associated with parasite load and response to a novel antigen than was heterozygosity at the DRB locus. These data suggest a role for parasite-driven balancing selection in maintaining MHC variation in natural populations of C. talarum. At the same time, these findings underscore the importance of using diverse parameters to study interactions among physiological conditions, immunocompetence, and MHC diversity in free-living animals that are confronted with multiple simultaneous immune challenges.
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Affiliation(s)
- Ana Paula Cutrera
- Laboratorio de Ecofisiología, Departamento de Biología, Universidad Nacional de Mar del Plata, CONICET, CC 1245, Mar del Plata, Argentina.
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Contrasting responses to selection in class I and class IIα major histocompatibility-linked markers in salmon. Heredity (Edinb) 2011; 107:143-54. [PMID: 21266985 DOI: 10.1038/hdy.2010.177] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Comparison of levels and patterns of genetic variation in natural populations either across loci or against neutral expectation can yield insight into locus-specific differences in the strength and direction of evolutionary forces. We used both approaches to test the hypotheses on patterns of selection on major histocompatibility (MH)-linked markers. We performed temporal analyses of class I and class IIα MH-linked markers and eight microsatellite loci in two Atlantic salmon populations in Ireland on two temporal scales: over six decades and 9 years in the rivers Burrishoole and Delphi, respectively. We also compared contemporary Burrishoole and Delphi samples with nearby populations for the same loci. On comparing patterns of temporal and spatial differentiation among classes of loci, the class IIα MH-linked marker was consistently identified as an outlier compared with patterns at the other microsatellite loci or neutral expectation. We found higher levels of temporal and spatial heterogeneity in heterozygosity (but not in allelic richness) for the class IIα MH-linked marker compared with microsatellites. Tests on both within- and among-population differentiation are consistent with directional selection acting on the class IIα-linked marker in both temporal and spatial comparisons, but only in temporal comparisons for the class I-linked marker. Our results indicate a complex pattern of selection on MH-linked markers in natural populations of Atlantic salmon. These findings highlight the importance of considering selection on MH-linked markers when using these markers for management and conservation purposes.
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40
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Cammen K, Hoffman JI, Knapp LA, Harwood J, Amos W. Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus). Mol Ecol 2010; 20:740-52. [PMID: 21199032 DOI: 10.1111/j.1365-294x.2010.04975.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pathogen-driven balancing selection maintains high genetic diversity in many vertebrates, particularly in the major histocompatibility complex (MHC) immune system gene family, which is often associated with disease susceptibility. In large natural populations where subpopulations face different pathogen pressures, the MHC should show greater genetic differentiation within a species than neutral markers. We examined genetic diversity at the MHC-DQB locus and nine putatively neutral microsatellite markers in grey seals (Halichoerus grypus) from eight United Kingdom (UK) colonies, the Faeroe Islands and Sable Island, Canada. Five DQB alleles were identified in grey seals, which varied in prevalence across the grey seal range. Among the seal colonies, significant differences in DQB allele and haplotype frequencies and in average DQB heterozygosity were observed. Additionally, the DQB gene exhibited greater differentiation among colonies compared with neutral markers, yet a weaker pattern of isolation by distance (IBD). After correcting for the underlying IBD pattern, subpopulations breeding in similar habitats were more similar to one another in DQB allele frequencies than populations breeding in different habitats, but the same did not hold true for microsatellites, suggesting that habitat-specific pathogen pressure influences MHC evolution. Overall, the data are consistent with selection at MHC-DQB loci in grey seals with both varying selective pressures and geographic population structure appearing to influence the DQB genetic composition of breeding colonies.
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Affiliation(s)
- K Cammen
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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41
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McCairns RJS, Bourget S, Bernatchez L. Putative causes and consequences of MHC variation within and between locally adapted stickleback demes. Mol Ecol 2010; 20:486-502. [PMID: 21134013 DOI: 10.1111/j.1365-294x.2010.04950.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genes of the major histocompatibility complex (MHC) have been a source of considerable research interest, owing in large part to the growing body of evidence that they may be subject to both natural and sexual selection. However, much remains to be learned about the dynamics of MHC genes in subdivided populations, particularly those characterized by divergent ecological pressures. In this study, we attempt to disentangle the relative roles of both parasite-mediated selection and MHC-mediated mate choice in an open estuarine system inhabited by two parapatric, adaptively divergent threespine stickleback (Gasterosteus aculeatus) demes. We sequenced the putative peptide-binding region (PBR) of an estimated four Class IIβ loci from 127 individuals, identifying 329 sequence variants (276 translated amino acid sequences). Demes differed significantly both in the frequency of MHC alleles and in the communities of helminth parasites infecting resident sticklebacks. Strong signatures of natural selection were inferred from analyses of codon substitutions, particularly in the derived (freshwater) rather than the ancestral (marine) deme. Relationships between parasite load and MHC diversity were indicative of balancing selection, but only within the freshwater deme. Signals of MHC-mediated mate choice were weak and differed significantly between demes. Moreover, MHC-mediated mate choice was significantly influenced by environmental salinity and appeared of secondary importance to tendencies towards assortative mating. We discuss the implications of these findings in respect to ecological adaptation and the potential demographic consequences of possible outcomes of MHC-mediated mate choice.
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42
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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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Garamszegi LZ, Nunn CL. Parasite-mediated evolution of the functional part of the MHC in primates. J Evol Biol 2010; 24:184-95. [PMID: 21091566 DOI: 10.1111/j.1420-9101.2010.02156.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The major histocompatibility complex (MHC) is a key model of genetic polymorphism, but the mechanisms underlying its extreme variability are debated. Most hypotheses for MHC diversity focus on pathogen-driven selection and predict that MHC polymorphism evolves under the pressure of a diverse parasite fauna. Several studies reported that certain alleles offer protection against certain parasites, yet it remains unclear whether variation in parasite pressure more generally covaries with allelic diversity and rates of molecular evolution of MHC across species. We tested this prediction in a comparative study of 41 primate species. We characterized polymorphism of the exon 2 of DRB region of the MHC class II. Our phylogenetic analyses controlled for the potential effects of neutral mutation rate, population size, geographic origin and body mass and revealed that nematode species richness associates positively with nonsynonymous nucleotide substitution rate at the functional part of the molecule. We failed to find evidence for allelic diversity being strongly related to parasite species richness. Continental distribution was a strong predictor of both allelic diversity and substitution rate, with higher values in Malagasy and Neotropical primates. These results indicate that parasite pressure can influence the different estimates of MHC polymorphism, whereas geography plays an independent role in the natural history of MHC.
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Affiliation(s)
- L Z Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Seville, Spain.
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44
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Ejsmond MJ, Babik W, Radwan J. MHC allele frequency distributions under parasite-driven selection: A simulation model. BMC Evol Biol 2010; 10:332. [PMID: 20979635 PMCID: PMC2978226 DOI: 10.1186/1471-2148-10-332] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 10/27/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The extreme polymorphism that is observed in major histocompatibility complex (MHC) genes, which code for proteins involved in recognition of non-self oligopeptides, is thought to result from a pressure exerted by parasites because parasite antigens are more likely to be recognized by MHC heterozygotes (heterozygote advantage) and/or by rare MHC alleles (negative frequency-dependent selection). The Ewens-Watterson test (EW) is often used to detect selection acting on MHC genes over the recent history of a population. EW is based on the expectation that allele frequencies under balancing selection should be more even than under neutrality. We used computer simulations to investigate whether this expectation holds for selection exerted by parasites on host MHC genes under conditions of heterozygote advantage and negative frequency-dependent selection acting either simultaneously or separately. RESULTS In agreement with simple models of symmetrical overdominance, we found that heterozygote advantage acting alone in populations does, indeed, result in more even allele frequency distributions than expected under neutrality, and this is easily detectable by EW. However, under negative frequency-dependent selection, or under the joint action of negative frequency-dependent selection and heterozygote advantage, distributions of allele frequencies were less predictable: the majority of distributions were indistinguishable from neutral expectations, while the remaining runs resulted in either more even or more skewed distributions than under neutrality. CONCLUSIONS Our results indicate that, as long as negative frequency-dependent selection is an important force maintaining MHC variation, the EW test has limited utility in detecting selection acting on these genes.
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Affiliation(s)
- Maciej Jan Ejsmond
- Institute of Environmental Sciences, Jagiellonian University, ul, Gronostajowa 7, 30-387 Kraków, Poland.
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Worley K, Collet J, Spurgin LG, Cornwallis C, Pizzari T, Richardson DS. MHC heterozygosity and survival in red junglefowl. Mol Ecol 2010; 19:3064-75. [PMID: 20618904 DOI: 10.1111/j.1365-294x.2010.04724.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genes of the major histocompatibility complex (MHC) form a vital part of the vertebrate immune system and play a major role in pathogen resistance. The extremely high levels of polymorphism observed at the MHC are hypothesised to be driven by pathogen-mediated selection. Although the exact nature of selection remains unclear, three main hypotheses have been put forward; heterozygote advantage, negative frequency-dependence and fluctuating selection. Here, we report the effects of MHC genotype on survival in a cohort of semi-natural red junglefowl (Gallus gallus) that suffered severe mortality as a result of an outbreak of the disease coccidiosis. The cohort was followed from hatching until 250 days of age, approximately the age of sexual maturity in this species, during which time over 80% of the birds died. We show that on average birds with MHC heterozygote genotypes survived infection longer than homozygotes and that this effect was independent of genome-wide heterozygosity, estimated across microsatellite loci. This MHC effect appeared to be caused by a single susceptible haplotype (CD_c) the effect of which was masked in all heterozygote genotypes by other dominant haplotypes. The CD_c homozygous genotype had lower survival than all other genotypes, but CD_c heterozygous genotypes had survival probabilities equal to the most resistant homozygote genotype. Importantly, no heterozygotes conferred greater resistance than the most resistant homozygote genotype, indicating that the observed survival advantage of MHC heterozygotes was the product of dominant, rather than overdominant processes. This pattern and effect of MHC diversity in our population could reflect the processes ongoing in similarly small, fragmented natural populations.
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Affiliation(s)
- Kirsty Worley
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
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46
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Are there Ubiquitous Parasite-driven Major Histocompatibility Complex Selection Mechanisms in Gray Mouse Lemurs? INT J PRIMATOL 2010. [DOI: 10.1007/s10764-010-9411-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Fraser BA, Ramnarine IW, Neff BD. Temporal variation at the MHC class IIb in wild populations of the guppy (Poecilia reticulata). Evolution 2010; 64:2086-96. [PMID: 20148955 DOI: 10.1111/j.1558-5646.2010.00965.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Understanding genetic diversity in natural populations is a fundamental objective of evolutionary biology. The immune genes of the major histocompatibility complex (MHC) are excellent candidates to study such diversity because they are highly polymorphic in populations. Although balancing selection may be responsible for maintaining diversity at these functionally important loci, temporal variation in selection pressure has rarely been examined. We examine temporal variation in MHC class IIB diversity in nine guppy (Poecilia reticulata) populations over two years. We found that five of the populations changed significantly more at the MHC than at neutral (microsatellite) loci as measured by F(ST), which suggests that the change at the MHC was due to selection and not neutral processes. Additionally, pairwise population differentiation measures at the MHC were higher in 2007 than in 2006, with the signature of selection changing from homogenizing to diversifying selection or neutral evolution. Interestingly, within the populations the magnitude of the change at the MHC between years was related to the change in the proportion of individuals infected by a common parasite, indicating a link between genetic structure and the parasite. Our data thereby implicate temporal variation in selective pressure as an important mechanism maintaining diversity at the MHC in wild populations.
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Affiliation(s)
- Bonnie A Fraser
- Department of Biology, Florida State University, Tallahassee, Florida 32306, USA.
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CUTRERA ANAPAULA, LACEY EILEENA, MORA MATÍASS, LESSA ENRIQUEP. Effects of contrasting demographic histories on selection at major histocompatibility complex loci in two sympatric species of tuco-tucos (Rodentia: Ctenomyidae). Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01358.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Spurgin LG, Richardson DS. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc Biol Sci 2010; 277:979-88. [PMID: 20071384 DOI: 10.1098/rspb.2009.2084] [Citation(s) in RCA: 508] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Major histocompatibility complex (MHC) genes have been put forward as a model for studying how genetic diversity is maintained in wild populations. Pathogen-mediated selection (PMS) is believed to generate the extraordinary levels of MHC diversity observed. However, establishing the relative importance of the three proposed mechanisms of PMS (heterozygote advantage, rare-allele advantage and fluctuating selection) has proved extremely difficult. Studies have attempted to differentiate between mechanisms of PMS using two approaches: (i) comparing MHC diversity with that expected under neutrality and (ii) relating MHC diversity to pathogen regime. Here, we show that in many cases the same predictions arise from the different mechanisms under these approaches, and that most studies that have inferred one mechanism of selection have not fully considered the alternative explanations. We argue that, while it may be possible to demonstrate that particular mechanisms of PMS are occurring, resolving their relative importance within a system is probably impossible. A more realistic target is to continue to demonstrate when and where the different mechanisms of PMS occur, with the aim of determining their relative importance across systems. We put forward what we believe to be the most promising approaches that will allow us to progress towards achieving this.
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Affiliation(s)
- Lewis G Spurgin
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich, UK
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