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Heimeier D, Garland EC, Eichenberger F, Garrigue C, Vella A, Baker CS, Carroll EL. A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Mol Ecol Resour 2024; 24:e13955. [PMID: 38520161 DOI: 10.1111/1755-0998.13955] [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: 05/19/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 03/25/2024]
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
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Affiliation(s)
- Dorothea Heimeier
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
| | - Ellen C Garland
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Franca Eichenberger
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Claire Garrigue
- UMR ENTROPIE, (IRD, Université de La Réunion, Université de la Nouvelle-Calédonie, IFREMER, CNRS, Laboratoire d'Excellence-CORAIL), Nouméa, New Caledonia
- Opération Cétacés, Nouméa, New Caledonia
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, Malta
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Corvallis, Oregon, USA
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
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2
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Garaud L, Nusbaumer D, Marques da Cunha L, de Guttry C, Ançay L, Atherton A, Lasne E, Wedekind C. Parental kinship coefficient but not paternal coloration predicts early offspring growth in lake char. Heredity (Edinb) 2024; 132:247-256. [PMID: 38480957 DOI: 10.1038/s41437-024-00678-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 05/08/2024] Open
Abstract
The 'good genes' hypotheses of sexual selection predict that females prefer males with strong ornaments because they are in good health and vigor and can afford the costs of the ornaments. A key assumption of this concept is that male health and vigor are useful predictors of genetic quality and hence offspring performance. We tested this prediction in wild-caught lake char (Salvelinus umbla) whose breeding coloration is known to reveal aspects of male health. We first reanalyzed results from sperm competition trials in which embryos of known parenthood had been raised singly in either a stress- or non-stress environment. Paternal coloration did not correlate with any measures of offspring performance. However, offspring growth was reduced with higher kinship coefficients between the parents. To test the robustness of these first observations, we collected a new sample of wild males and females, used their gametes in a full-factorial in vitro breeding experiment, and singly raised about 3000 embryos in either a stress- or non-stress environment (stress induced by microbes). Again, paternal coloration did not predict offspring performance, while offspring growth was reduced with higher kinship between the parents. We conclude that, in lake char, the genetic benefits of mate choice would be strongest if females could recognize and avoid genetically related males, while male breeding colors may be more relevant in intra-sexual selection.
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Affiliation(s)
- Laura Garaud
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - David Nusbaumer
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Christian de Guttry
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Environmental Bioinformatic Group, Lausanne, Switzerland
| | - Laurie Ançay
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Audrey Atherton
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emilien Lasne
- Université Savoie Mont Blanc, INRAE, UMR CARRTEL, Station d'Hydrobiologie Lacustre, Thonon Cedex, France
- UMR DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Claus Wedekind
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland.
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3
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Ferreira D, San‐Jose LM, Roulin A, Gaigher A, Fumagalli L. Limited associations between MHC diversity and reproductive success in a bird species with biparental care. Ecol Evol 2024; 14:e10950. [PMID: 38384825 PMCID: PMC10879840 DOI: 10.1002/ece3.10950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 02/23/2024] Open
Abstract
The selective pressure from pathogens on individuals can have direct consequences on reproduction. Genes from the major histocompatibility complex (MHC) are central to the vertebrate adaptive immune system and pathogen resistance. In species with biparental care, each sex has distinct reproductive roles and levels of investment, and due to a trade-off with immunity, one can expect different selective regimes acting upon the MHC of each parent. Here, we addressed whether couples combine each other's variation at MHC loci to increase their breeding success. Specifically, we used a 23-year dataset from a barn owl population (Tyto alba) to understand how MHC class Iα and IIβ functional divergence and supertypes of each parent were associated with clutch size and fledging success. We did not detect associations between MHC diversity and supertypes with the clutch size or with the fledging success. In addition, to understand the relative contribution from the MHC of the genetic parents and the social parents, we analyzed the fledging success using only a cross-fostered dataset. We found several associations of weak-to-moderate effect sizes between the father's MHC and fledging success: (i) lower MHC-Iα divergence in the genetic father increases fledging success, which might improve paternal care during incubation, and (ii) one and two MHC-IIβ DAB2 supertypes in the social father decrease and increase, respectively, fledging success, which may affect the paternal care after hatching. Furthermore, fledging success increased when both parents did not carry MHC-IIβ DAB1 supertype 2, which could suggest conditional effects of this supertype. Although our study relied on a substantial dataset, we showed that the associations between MHC diversity and reproductive success remain scarce and of complex interpretation in the barn owl. Moreover, our results highlighted the need to incorporate more than one proxy of reproductive success and several MHC classes to capture more complex associations.
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Affiliation(s)
- Diana Ferreira
- Laboratory for Conservation Biology, Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - Luis M. San‐Jose
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRSUniversité Toulouse III Paul Sabatier, IRDToulouseFrance
| | - Alexandre Roulin
- Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic ResourcesUniversity of PortoVairãoPortugal
- Research Unit for Evolutionary Immunogenomics, Department of BiologyUniversity of HamburgHamburgGermany
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne‐GenevaLausanne University Hospital and University of LausanneLausanneSwitzerland
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4
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Liu S, Wei S, Sun Y, Xu G, Zhang S, Li J. Molecular Characteristics, Functional Definitions, and Regulatory Mechanisms for Cross-Presentation Mediated by the Major Histocompatibility Complex: A Comprehensive Review. Int J Mol Sci 2023; 25:196. [PMID: 38203367 PMCID: PMC10778590 DOI: 10.3390/ijms25010196] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
The major histocompatibility complexes of vertebrates play a key role in the immune response. Antigen-presenting cells are loaded on MHC I molecules, which mainly present endogenous antigens; when MHC I presents exogenous antigens, this is called cross-presentation. The discovery of cross-presentation provides an important theoretical basis for the study of exogenous antigens. Cross-presentation is a complex process in which MHC I molecules present antigens to the cell surface to activate CD8+ T lymphocytes. The process of cross-representation includes many components, and this article briefly outlines the origins and development of MHC molecules, gene structures, functions, and their classical presentation pathways. The cross-presentation pathways of MHC I molecules, the cell lines that support cross-presentation, and the mechanisms of MHC I molecular transporting are all reviewed. After more than 40 years of research, the specific mechanism of cross-presentation is still unclear. In this paper, we summarize cross-presentation and anticipate the research and development prospects for cross-presentation.
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Affiliation(s)
| | | | | | | | - Shidong Zhang
- Engineering Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Animal Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.L.); (S.W.); (Y.S.); (G.X.)
| | - Jianxi Li
- Engineering Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, Lanzhou Institute of Animal Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (S.L.); (S.W.); (Y.S.); (G.X.)
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5
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Mahdjoub H, Khelifa R, Roy J, Sbilordo SH, Zeender V, Perdigón Ferreira J, Gourgoulianni N, Lüpold S. Interplay between male quality and male-female compatibility across episodes of sexual selection. SCIENCE ADVANCES 2023; 9:eadf5559. [PMID: 37774022 PMCID: PMC10541500 DOI: 10.1126/sciadv.adf5559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
The processes underlying mate choice profoundly influence the dynamics of sexual selection and the evolution of male sexual traits. Consistent preference for certain phenotypes may erode genetic variation in populations through directional selection, whereas divergent preferences (e.g., genetically compatible mates) provide one mechanism to maintain such variation. However, the relative contributions of these processes across episodes of selection remain unknown. Using Drosophila melanogaster, we followed the fate of male genotypes, previously scored for their overall reproductive value and their compatibility with different female genotypes, across pre- and postmating episodes of selection. When pairs of competitor males differed in their intrinsic quality and their compatibility with the female, both factors influenced outcomes from mating success to paternity but to a varying degree between stages. These results add further dimensions to our understanding of how the interactions between genotypes and forms of selection shape reproductive outcomes and ultimately reproductive trait evolution.
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Affiliation(s)
- Hayat Mahdjoub
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Biology Department, Concordia University, 7141 Sherbrooke St. W., Montreal QC H4B 1R6, Canada
| | - Rassim Khelifa
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Biology Department, Concordia University, 7141 Sherbrooke St. W., Montreal QC H4B 1R6, Canada
| | - Jeannine Roy
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Sonja H. Sbilordo
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Valérian Zeender
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jhoniel Perdigón Ferreira
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Natalia Gourgoulianni
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Stefan Lüpold
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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6
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Przesmycka K, Herdegen-Radwan M, Phillips KP, Mohammed RS, Radwan J. The quest for good genes: Epigamic traits, fitness, MHC and multilocus heterozygosity in the guppy. Mol Ecol 2023; 32:5055-5070. [PMID: 37492990 DOI: 10.1111/mec.17083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023]
Abstract
The 'good genes' hypothesis for the evolution of male secondary sexual traits poses that female preferences for such traits are driven by indirect genetic benefits. However, support for the hypothesis remains ambiguous, and, in particular, the genetic basis for the benefits has rarely been investigated. Here, we use seminatural populations of Trinidadian guppies to investigate whether sexually selected traits (orange, black and iridescent colouration, gonopodium length and body size) predict fitness measured as the number of grandoffspring, a metric that integrates across fitness components and sexes. Furthermore, we tested whether two potential sources of genetic benefits-major histocompatibility complex (MHC) genotypes and multilocus heterozygosity (MLH)-are significant predictors of fitness and of the size of sexually selected traits. We found a significant, nonlinear effect of the area of black pigmentation and male body size on the number of grandoffspring, suggesting stabilizing selection on black area, and nonlinear selection favouring small body size. MLH was heritable (h2 = 0.14) and significantly predicted the number of grandoffspring, indicating the potential for genetic benefits based on heterozygosity. We also found support for local heterozygosity effects, which may reflect a noneven distribution of genetic load across the genome. MHC genotype was not significantly associated with any tested fitness component, or with the load of Gyrodactylus parasites. Neither MHC nor MLH was significant predictor of sexually selected traits. Overall, our results highlight the role of heterozygosity in determining fitness, but do not provide support for male sexually selected traits being indicators of genetic quality.
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Affiliation(s)
- Karolina Przesmycka
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | | | - Karl P Phillips
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Canadian Rivers Institute, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Ryan S Mohammed
- Department of Biology, Auburn University, Auburn, Alabama, USA
| | - Jacek Radwan
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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7
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Auer KE, Primus J, Istel S, Dahlhoff M, Rülicke T. Mate genetic similarity affects mating behaviour but not maternal investment in mice. Sci Rep 2023; 13:10536. [PMID: 37386286 PMCID: PMC10310752 DOI: 10.1038/s41598-023-37547-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/23/2023] [Indexed: 07/01/2023] Open
Abstract
Maternal investment can affect the survival and development of offspring. Here we experimentally investigated in mice, whether females alter implantation rates and pup survival after embryo transfer depending on the genetic similarity with their vasectomised mating partner. We selected the MHC genotype and genetic background of males and paired females either with males that shared the same MHC haplotype and genetic background (CBA/J inbred males, isogenic group), that shared half of the MHC haplotype and genetic background (B6CBAF1 hybrid males, semi-isogenic group), or that had a different MHC haplotype and genetic background (C57BL/6N inbred males, allogenic group). We performed 304 pairings, resulting in 81 vaginal plugs, which confirmed mating. Plug rates were significantly higher in the semi-isogenic group (36.9%) compared to the isogenic group (19.5%), but not the allogenic group (26%). We found no difference in the number of implantation sites, the number of born or surviving pups until weaning, or litter weight or sex ratio between groups. Even though we found a mating bias, we found no difference in maternal investment under laboratory conditions. At least under pathogen-free conditions our study does not provide any evidence for differential maternal investment when females could increase offspring genetic diversity or heterozygosity.
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Affiliation(s)
- Kerstin E Auer
- Institute of in vivo and in vitro Models, University of Veterinary Medicine Vienna, Vienna, Austria.
| | - Jasmin Primus
- Institute of in vivo and in vitro Models, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sonja Istel
- Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Maik Dahlhoff
- Institute of in vivo and in vitro Models, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Rülicke
- Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
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8
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Nelson-Flower MJ, Grieves LA, Reid JM, Germain RR, Lazic S, Taylor SS, MacDougall-Shackleton EA, Arcese P. Immune genotypes, immune responses, and survival in a wild bird population. Mol Ecol 2023. [PMID: 36919652 DOI: 10.1111/mec.16923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 02/18/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
Individuals vary in their immune genotype, inbreeding coefficient f, immune responses, survival to adulthood, and adult longevity. However, whether immune genes predict survival or longevity, whether such relationships are mediated through immune responses, and how f affects immune genotype remain unclear. We use a wild song sparrow (Melospiza melodia) population in which survival to adulthood, adult longevity, and f were measured precisely, and in which immune responses have previously been assessed. We investigate four toll-like receptor (TLR) and the major histocompatibility complex (MHC) class IIB exon 2 genes. We test whether immune genes predict fitness (survival to adulthood or adult longevity); whether immune genes predict immune response; whether immune response predicts fitness and whether fitness, immune responses, or immune genotypes are correlated with f. We find that survival to adulthood is not associated with immune gene variation, but adult longevity is decreased by high MHC allele diversity (especially in birds that were relatively outbred), and by the presence of a specific MHC supertype. Immune responses were affected by specific immune genotypes. Survival to adulthood and adult longevity were not predicted by immune response, implying caution in the use of immune response as a predictor for fitness. We also found no relationship between f and immune genotype. This finding indicates that immune gene associations with longevity and immune response are not artefacts of f, and suggests that pathogen-mediated selection at functional loci can slow the loss of genetic variation arising from genetic drift and small population size.
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Affiliation(s)
- Martha J Nelson-Flower
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology, Langara College, Vancouver, British Columbia, Canada
| | - Leanne A Grieves
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jane M Reid
- Centre for Biodiversity Dynamics, Institut for Biologi, NTNU, Trondheim, Norway
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Ryan R Germain
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Kobenhavn, Denmark
| | - Savo Lazic
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, Louisiana, USA
| | | | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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9
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Dodge TO, Farquharson KA, Ford C, Cavanagh L, Schubert K, Schumer M, Belov K, Hogg CJ. Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights. Mol Ecol Resour 2023. [PMID: 36872490 DOI: 10.1111/1755-0998.13780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
Genomics can play important roles in biodiversity conservation, especially for Extinct-in-the-Wild species where genetic factors greatly influence risk of total extinction and probability of successful reintroductions. The Christmas Island blue-tailed skink (Cryptoblepharus egeriae) and Lister's gecko (Lepidodactylus listeri) are two endemic reptile species that went extinct in the wild shortly after the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand individuals; however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long-read and Hi-C sequencing to generate highly contiguous reference genomes for both reptiles, including the XY chromosome pair in the skink. We then analyse patterns of genetic diversity to infer ancient demography and more recent histories of inbreeding. We observe high genome-wide heterozygosity in the skink (0.007 heterozygous sites per base-pair) and gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the blue-tailed skink reference genome falls within long (>1 Mb) runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci. In contrast, we detect a single ROH in Lister's gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in these species' histories and implications for management. We show how reference genomes can contribute evolutionary and conservation insights, and we provide resources for future population-level and comparative genomic studies in reptiles.
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Affiliation(s)
- Tristram O Dodge
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
- Department of Biology, Stanford University, Stanford, California, USA
- Australian-American Fulbright Commission, Deakin, Australian Capital Territory, Australia
| | - Katherine A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Claire Ford
- Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Lisa Cavanagh
- Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | | | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
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10
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Rekdal SL, Anmarkrud JA, Lifjeld JT, Johnsen A. Do female bluethroats without extra-pair offspring have more MHC-compatible social mates? Behav Ecol Sociobiol 2023. [DOI: 10.1007/s00265-023-03311-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Abstract
Genes of the major histocompatibility complex (MHC) are crucial for adaptive immunity in jawed vertebrates, and theory predicts that there should be mate choice for optimizing MHC constitution in the offspring. In a previous study, we demonstrated a non-random female choice of extra-pair males in the bluethroat (Luscinia svecica), yielding offspring that was closer to an intermediate MHC class II (MHCII) allele count than their within-pair halfsiblings. The present study tests whether social pairs with only within-pair young (WPY) in their brood, in the same study population, had a combined MHC-constitution closer to a presumed intermediate optimum, than social pairs with extra-pair young (EPY), with a corresponding pattern in their offspring. As expected, we found that WPY from pure WPY-broods were more MHC-optimal than WPY from mixed broods, but only in broods of young (second year) males. Correspondingly, there was a tendency for social pairs with only WPY in their brood to be more MHC-compatible than social pairs with EPY in their brood, when the male was young. Older bluethroat males have considerably larger testes than young males, and their higher sperm competitiveness could help them secure paternity in their own brood, also when they are not MHC-compatible. In other words, in the sexual conflict over paternity, females may be more likely to realise their preference for a MHC-compatible mate when paired to a young male. As a possible fitness indicator, immune responsiveness to an injected antigen (PHA) was elevated for offspring closer to “the golden mean” in MHCII allele count.
Significance statement
This study contributes to our understanding of MHC-based mate choice in extra-pair mating systems, by showing that female bluethroats (Luscinia svecica) with an MHCII-compatible social mate tend to have no extra-pair young in their brood, but only when the social male is young. This elucidates a possible sexual conflict, in which older social males are able to override female preferences and prevent other males from gaining paternity in their brood through higher sperm production. Studying systems in which extra-pair paternity occurs offers an insight into the genetic benefits of mate choice, as extra-pair males, in contrast to social males, generally contribute only sperm. Further, the strict and thorough genotyping scheme applied in this study enabled us to demonstrate a preference for “the golden mean” in MHC-diversity in a species with one of the highest MHC class II-diversity known to date.
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11
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Lam DK, Frantz AC, Burke T, Geffen E, Sin SYW. Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal. Evolution 2023; 77:221-238. [PMID: 36626810 DOI: 10.1093/evolut/qpac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 10/03/2022] [Accepted: 11/04/2022] [Indexed: 01/12/2023]
Abstract
The major histocompatibility complex (MHC) has been intensively studied for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (Meles meles) covering most of their geographic range. By comparing variation of microsatellite and diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g., immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely distributed wild mammal.
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Affiliation(s)
- Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg, Luxembourg
| | - Terry Burke
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
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12
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Fieder M, Huber S. Facial attractiveness is only weakly linked to genome-wide heterozygosity. Front Psychol 2023; 14:1009962. [PMID: 37151335 PMCID: PMC10157054 DOI: 10.3389/fpsyg.2023.1009962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction It has been frequently suggested that overall genomic heterozygosity and, particularly, heterozygosity of loci on the so-called major histocompatibility complex (MHC), which is responsible for the recognition of foreign substances/ pathogens and the recognition of self and non-self, is associated with better health and better resistance to infections and parasites. It has further been speculated that such a potentially beneficial heterozygosity can be detected through body odor and facial attractiveness. Methods On the basis of genome wide SNP data (713,014 SNPs) of participants from the Wisconsin Longitudinal Study, we therefore investigated whether homozygosity either on the MHC (measured as inbreeding coefficient) or genome-wide (measured as runs of homozygosity and inbreeding coefficient) is associated with rated facial attractiveness. Results Although we found that the genome-wide average length of homozygous segments and the genome-wide inbreeding coefficient are significantly negatively associated with some measures of facial attractiveness, if corrected for multiple testing, any significant association was no longer formally significant after correction. In addition, the variance in facial attractiveness explained by the genome wide homozygosity is very low (<0.15%). We did not find any significant association between the inbreeding coefficient on the MHC and facial attractiveness. Discussion We only find a weak association of genome- wide heterozygosity and facial attractiveness.
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Affiliation(s)
- Martin Fieder
- Department of Evolutionary Anthropology and Network of Human Evolution and Archeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Religion and Transformation in Contemporary Society, University of Vienna, Vienna, Austria
- *Correspondence: Martin Fieder,
| | - Susanne Huber
- Department of Evolutionary Anthropology and Network of Human Evolution and Archeological Sciences (HEAS), University of Vienna, Vienna, Austria
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13
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Dearborn DC, Warren S, Hailer F. Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species. Mol Ecol 2022; 31:6390-6406. [PMID: 36208104 PMCID: PMC9729452 DOI: 10.1111/mec.16726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analysed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future studies should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.
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Affiliation(s)
- Donald C Dearborn
- Biology Department, Bates College, 44 Campus Ave, Lewiston, Maine, USA,Roux Institute, Northeastern University, Fore St, Portland, Maine, USA,Co-corresponding authors: and
| | - Sophie Warren
- Biology Department, Bates College, 44 Campus Ave, Lewiston, Maine, USA,Present address: Department of Health Policy, London School of Economics and Political Science, Houghton Street, London WC2A 2AE, UK
| | - Frank Hailer
- Organisms and Environment, School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK,Co-corresponding authors: and
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14
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Major Histocompatibility Complex (MHC) Diversity of the Reintroduction Populations of Endangered Przewalski's Horse. Genes (Basel) 2022; 13:genes13050928. [PMID: 35627313 PMCID: PMC9140943 DOI: 10.3390/genes13050928] [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: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 12/07/2022] Open
Abstract
Major histocompatibility complex (MHC) genes are the most polymorphic in vertebrates and the high variability in many MHC genes is thought to play a crucial role in pathogen recognition. The MHC class II locus DQA polymorphism was analyzed in the endangered Przewalski’s horse, Equus przewalskii, a species that has been extinct in the wild and all the current living individuals descend from 12 founders. We used the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) to detect the polymorphism within the MHC DQA in 31 Przewalski’s horses from two reintroduced populations. Consequently, only seven alleles were identified, with only four presenting in each population. In comparison with other mammals, the Przewalski’s horse demonstrated less MHC variation. The nucleotide genetic distance of the seven ELA-DQA alleles was between 0.012 and 0.161. The Poisson corrected amino acid genetic distance of the founded alleles was 0.01–0.334. The allele and genotype frequencies of both reintroduced populations of Przewalski’s horse deviated from the Hardy–Weinberg equilibrium. Specific MHC DQA alleles may have been lost during the extreme bottleneck event that this species underwent throughout history. We suggest the necessity to detect the genetic background of individuals prior to performing the reintroduction project.
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15
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Mancilla-Morales MD, Velarde E, Contreras-Rodríguez A, Gómez-Lunar Z, Rosas-Rodríguez JA, Heras J, Soñanez-Organis JG, Ruiz EA. Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes). Genes (Basel) 2022; 13:genes13050917. [PMID: 35627302 PMCID: PMC9140796 DOI: 10.3390/genes13050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/16/2022] Open
Abstract
The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull MHC class II (MHCIIB) and compare these loci with other Charadriiformes. Fifty-nine MHCIIB haplotypes were recovered from sixty-eight Heermann’s Gulls by cloning, of them, twelve were identified as putative true alleles, forty-five as unique alleles, and two as pseudogenes. Intra and interspecific relationships indicated at least two loci in Heermann’s Gull MHCIIB and trans-species polymorphism among Charadriiformes (coinciding with the documented evidence of two ancient avian MHCIIB lineages, except in the Charadriidae family). Additionally, sites under diversifying selection revealed a better match with peptide-binding sites inferred in birds than those described in humans. Despite the negative anthropogenic activity reported on Isla Rasa, Heermann’s Gull showed MHCIIB variability consistent with population expansion, possibly due to a sudden growth following conservation efforts. Duplication must play an essential role in shaping Charadriiformes MHCIIB variability, buffering selective pressures through balancing selection. These findings suggest that MHC copy number and protected islands can contribute to seabird conservation.
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Affiliation(s)
- Misael Daniel Mancilla-Morales
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
| | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Hidalgo 617, Colonia Río Jamapa, Boca del Rio, Veracruz CP 94290, Mexico;
| | - Araceli Contreras-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico; (A.C.-R.); (Z.G.-L.)
| | - Zulema Gómez-Lunar
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico; (A.C.-R.); (Z.G.-L.)
| | - Jesús A. Rosas-Rodríguez
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Lázaro Cárdenas del Río No. 100, Francisco Villa, Navojoa CP 85880, Mexico;
| | - Joseph Heras
- Departament of Biology, California State University, San Bernardino, 5500 University Parkway, San Bernardino, CA 92407, USA;
| | - José G. Soñanez-Organis
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Lázaro Cárdenas del Río No. 100, Francisco Villa, Navojoa CP 85880, Mexico;
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
| | - Enrico A. Ruiz
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
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16
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Pineaux M, Merkling T, Danchin E, Hatch SA, Leclaire S, Blanchard P. MHC-II distance between parents predicts sex allocation decisions in a genetically monogamous bird. Behav Ecol 2021. [DOI: 10.1093/beheco/arab130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Theory predicts that parental heritable characteristics should shape sex allocation decisions when their effects on reproduction or survival are offspring sex-dependent. Numerous studies have questioned to what extent characteristics displayed by one of the parents matched theoretical expectations. This contrasts with the handful of studies that investigated whether compatibility between parents could also trigger selective pressures for sex allocation adjustments. We studied the genetically monogamous black-legged kittiwake (Rissa tridactyla), where previous data revealed that female chicks suffered higher fitness costs from low diversity at genes of the major histocompatibility complex (MHC) than male chicks. We predicted, and found in our dataset, that MHC-similar parents, producing low MHC-diverse offspring, should avoid the production of females. The relation between MHC-distance between parents (i.e. the functional distinctness of their MHC alleles) and offspring sex was not linear, such that MHC-dissimilar parents also overproduced sons. Overall, our results suggest that the genetically monogamous black-legged kittiwake parents flexibly adapt their reproduction and circumvent the costs of suboptimal pairing by manipulating offspring sex.
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Affiliation(s)
- Maxime Pineaux
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bât. 4R1, 31062 Toulouse cedex 9, France
| | - Thomas Merkling
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bât. 4R1, 31062 Toulouse cedex 9, France
| | - Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bât. 4R1, 31062 Toulouse cedex 9, France
| | - Scott A Hatch
- Institute for Seabird Research and Conservation, 12850 Mountain Place, Anchorage, AK 99516, USA
| | - Sarah Leclaire
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bât. 4R1, 31062 Toulouse cedex 9, France
| | - Pierrick Blanchard
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bât. 4R1, 31062 Toulouse cedex 9, France
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17
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Riley JL, Stow A, Bolton PE, Dennison S, Byrne RW, Whiting MJ. Sperm Storage in a Family-Living Lizard, the Tree Skink (Egernia striolata). J Hered 2021; 112:526-534. [PMID: 34409996 DOI: 10.1093/jhered/esab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/16/2021] [Indexed: 11/14/2022] Open
Abstract
The ability to produce viable offspring without recently mating, either through sperm storage or parthenogenesis, can provide fitness advantages under a suite of challenging ecological scenarios. Using genetic analysis, we demonstrate that 3 wild-caught female Tree Skinks (Egernia striolata) reproduced in captivity with no access to males for over a year, and that this is best explained by sperm storage. To the best of our knowledge, this is the first time female sperm storage has been documented in any monogamous family-living reptile, including social Australian egerniine skinks (from the subfamily Egerniinae). Furthermore, by using paternal reconstruction of genotypes we show that captive-born offspring produced by the same females in the preceding year, presumably without sperm storage, were sired by different males. We qualitatively compared aspects of these females' mates and offspring between years. The parents of each litter were unrelated, but paternal and offspring genotypes from litters resulting from stored sperm were more heterozygous than those inferred to be from recent matings. Family-living egerniine skinks generally have low rates of multiple paternity, yet our study suggests that female sperm storage, potentially from outside social partners, offers the real possibility of benefits. Possible benefits include increasing genetic compatibility of mates and avoiding inbreeding depression via cryptic female choice. Sperm storage in Tree Skinks, a family-living lizard with a monogamous mating system, suggests that females may bet-hedge through extra-pair copulation with more heterozygous males, reinforcing the idea that females could have more control on reproductive outcomes than previously thought.
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Affiliation(s)
- Julia L Riley
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.,Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Adam Stow
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Peri E Bolton
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.,Department of Biology, East Carolina University, Greenville, NC
| | - Siobhan Dennison
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Richard W Byrne
- School of Psychology and Neuroscience, University of St. Andrews, St. Andrews, Fife, UK
| | - Martin J Whiting
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
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18
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Grieves LA, Gloor GB, Bernards MA, MacDougall-Shackleton EA. Preen gland microbiota covary with major histocompatibility complex genotype in a songbird. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210936. [PMID: 34754501 PMCID: PMC8493191 DOI: 10.1098/rsos.210936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/13/2021] [Indexed: 05/30/2023]
Abstract
Pathogen-mediated selection at the major histocompatibility complex (MHC) is thought to promote MHC-based mate choice in vertebrates. Mounting evidence implicates odour in conveying MHC genotype, but the underlying mechanisms remain uncertain. MHC effects on odour may be mediated by odour-producing symbiotic microbes whose community structure is shaped by MHC genotype. In birds, preen oil is a primary source of body odour and similarity at MHC predicts similarity in preen oil composition. Hypothesizing that this relationship is mediated by symbiotic microbes, we characterized MHC genotype, preen gland microbial communities and preen oil chemistry of song sparrows (Melospiza melodia). Consistent with the microbial mediation hypothesis, pairwise similarity at MHC predicted similarity in preen gland microbiota. Counter to this hypothesis, overall microbial similarity did not predict chemical similarity of preen oil. However, permutation testing identified a maximally predictive set of microbial taxa that best reflect MHC genotype, and another set of taxa that best predict preen oil chemical composition. The relative strengths of relationships between MHC and microbes, microbes and preen oil, and MHC and preen oil suggest that MHC may affect host odour both directly and indirectly. Thus, birds may assess MHC genotypes based on both host-associated and microbially mediated odours.
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Affiliation(s)
- L. A. Grieves
- Department of Biology, University of Western Ontario, London, ON, Canada N6A 5B7
| | - G. B. Gloor
- Department of Biochemistry, University of Western Ontario, London, ON, Canada N6A 5C1
| | - M. A. Bernards
- Department of Biology, University of Western Ontario, London, ON, Canada N6A 5B7
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19
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Minias P, Drzewińska-Chańko J, Włodarczyk R. Evolution of innate and adaptive immune genes in a non-model waterbird, the common tern. INFECTION GENETICS AND EVOLUTION 2021; 95:105069. [PMID: 34487864 DOI: 10.1016/j.meegid.2021.105069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Toll-like receptors (TLRs) and the Major Histocompatibility Complex (MHC) are the key pathogen-recognition genes of vertebrate immune system and they have a crucial role in the initiation of innate and adaptive immune response, respectively. Recent advancements in sequencing technology sparked research on highly duplicated MHC genes in non-model species, but TLR variation in natural vertebrate populations has remained little studied and comparisons of polymorphism across both TLRs and MHC are scarce. Here, we aimed to compare variation across innate (four TLR loci) and adaptive (MHC class I and class II) immune genes in a non-model avian species, the common tern Sterna hirundo. We detected relatively high allelic richness at TLR genes (9-48 alleles per locus), which was similar to or even higher than the estimated per locus allelic richness at the MHC (24-30 alleles at class I and 13-16 alleles at class II under uniform sample sizes). Despite this, the total number of MHC alleles across all duplicated loci (four class I and three class II) was much higher and MHC alleles showed greater sequence divergence than TLRs. Positive selection targeted relatively more sites at the MHC than TLRs, but the strength of selection (dN/dS ratios) at TLRs was higher when compared to MHC class I. There were also differences in the signature of positive selection and recombination (gene conversion) between MHC class I and II (stronger signature at class II), suggesting that mechanisms maintaining variation at the MHC may vary between both classes. Our study indicates that allelic richness of both innate and adaptive immune receptors may be maintained at relatively high levels in viable avian populations and we recommend a transition from the traditional gene-specific to multi-gene approach in studying molecular evolution of vertebrate immune system.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland.
| | - Joanna Drzewińska-Chańko
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
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20
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Auld HL, Jacobson DP, Rhodes AC, Banks MA. Differences in Mate Pairings of Hatchery- and Natural-Origin Coho Salmon Inferred from Offspring Genotypes. Integr Org Biol 2021; 3:obab020. [PMID: 34409260 PMCID: PMC8363981 DOI: 10.1093/iob/obab020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 05/20/2021] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
Captive breeding can affect how sexual selection acts on subsequent generations. One context where this is important is in fish hatcheries. In many salmon hatcheries, spawning is controlled artificially and offspring are reared in captivity before release into the wild. While previous studies have suggested that hatchery- and natural-origin fish may make different mate choice decisions, it remains to be determined how hatchery fish may be making different mate choice decisions compared with natural-origin fish at a genetic level. Using genotyping-by-sequencing, we identify single-nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery- and natural-origin coho salmon (Oncorhynchus kisutch). In both natural-origin and hatchery mate pairs, we observed more SNPs with negative assortment than positive assortment. However, only 3% of the negative assortment SNPs were shared between the two mating groups, and 1% of the positive assortment SNPs were shared between the two mating groups, indicating divergence in mating cues between wild and hatchery-raised salmon. These findings shed light on mate choice in general and may have important implications in the conservation management of species as well as for improving other captive breeding scenarios. There remains much to discover about mate choice in salmon and research described here reflects our intent to test the potential of ongoing advances in population genomics to develop new hatchery practices that may improve the performance of hatchery offspring, lessening the differences and thus potential impacts upon wild stocks.
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Affiliation(s)
- H L Auld
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - D P Jacobson
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - A C Rhodes
- Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - M A Banks
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
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21
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Undin M, Lockhart PJ, Hills SFK, Armstrong DP, Castro I. Mixed Mating in a Multi-Origin Population Suggests High Potential for Genetic Rescue in North Island Brown Kiwi, Apteryx mantelli. FRONTIERS IN CONSERVATION SCIENCE 2021. [DOI: 10.3389/fcosc.2021.702128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reinforcement translocations are increasingly utilised in conservation with the goal of achieving genetic rescue. However, concerns regarding undesirable results, such as genetic homogenisation or replacement, are widespread. One factor influencing translocation outcomes is the rate at which the resident and the introduced individuals interbreed. Consequently, post-release mate choice is a key behaviour to consider in conservation planning. Here we studied mating, and its consequences for genomic admixture, in the North Island brown kiwi Apteryx mantelli population on Ponui Island which was founded by two translocation events over 50 years ago. The two source populations used are now recognised as belonging to two separate management units between which birds differ in size and are genetically differentiated. We examined the correlation between male and female morphometrics for 17 known pairs and quantified the relatedness of 20 pairs from this admixed population. In addition, we compared the genetic similarity and makeup of 106 Ponui Island birds, including 23 known pairs, to birds representing the source populations for the original translocations. We found no evidence for size-assortative mating. On the contrary, genomic SNP data suggested that kiwi of one feather did not flock together, meaning that mate choice resulted in pairing between individuals that were less related than expected by random chance. Furthermore, the birds in the current Ponui Island population were found to fall along a gradient of genomic composition consistent with non-clustered representation of the two parental genomes. These findings indicate potential for successful genetic rescue in future Apteryx reinforcement translocations, a potential that is currently under utilised due to restrictive translocation policies. In light of our findings, we suggest that reconsideration of these policies could render great benefits for the future diversity of this iconic genus in New Zealand.
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22
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Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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23
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Vekemans X, Castric V, Hipperson H, Müller NA, Westerdahl H, Cronk Q. Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility. Mol Ecol 2021; 30:6072-6086. [PMID: 34137092 PMCID: PMC9290700 DOI: 10.1111/mec.16020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 11/27/2022]
Abstract
Whole‐genome sequencing of non‐model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data‐handling. Three such regions are the major histocompatibility complex (MHC), sex‐determining regions (SDRs) and the plant self‐incompatibility locus (S‐locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short‐read sequences against multiple alternative references improves genotyping comprehensiveness at the S‐locus thereby contributing to more accurate assessments of allelic frequencies. Long‐read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S‐locus haplotypes. These advances are adding value to short‐read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.
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Affiliation(s)
| | | | - Helen Hipperson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Helena Westerdahl
- Molecular Ecology and Evolution Laboratory, Department of Biology, Lund University, Lund, Sweden
| | - Quentin Cronk
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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24
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Winternitz JC, Schubert N, Nichols HJ. Let’s keep alternative hypotheses on the table: a response to comments on Schubert et al. Behav Ecol 2021. [DOI: 10.1093/beheco/arab039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jamie C Winternitz
- Department of Animal Behavior, Bielefeld University, Konsequenz, Bielefeld, Germany
| | - Nadine Schubert
- Department of Animal Behavior, Bielefeld University, Konsequenz, Bielefeld, Germany
| | - Hazel J Nichols
- Department of Animal Behavior, Bielefeld University, Konsequenz, Bielefeld, Germany
- Department of Biosciences, Swansea University, Singleton Park, Swansea, Wales, UK
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25
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Huang W, Pilkington JG, Pemberton JM. Patterns of MHC-dependent sexual selection in a free-living population of sheep. Mol Ecol 2021; 30:6733-6742. [PMID: 33960549 DOI: 10.1111/mec.15938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/18/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
The MHC is one of the most polymorphic gene clusters in vertebrates and play an essential role in adaptive immunity. Apart from pathogen-mediated selection, sexual selection can also contribute to the maintenance of MHC diversity. MHC-dependent sexual selection could occur via several mechanisms but at present there is no consensus as to which of these mechanisms are involved and their importance. Previous studies have often suffered from limited genetic and behavioural data and small sample size, and were rarely able to examine all the mechanisms together, determine whether signatures of MHC-based non-random mating are independent of genomic effects or differentiate whether MHC-dependent sexual selection takes place at the pre- or post-copulatory stage. In this study, we use Monte Carlo simulation to investigate evidence for non-random MHC-dependent mating patterns by all three mechanisms in a free-living population of Soay sheep. Using 1710 sheep diplotyped at the MHC class IIa region and genome-wide SNPs, together with field observations of consorts, we found sexual selection against a particular haplotype in males at the pre-copulatory stage and sexual selection against female MHC heterozygosity during the rut. We also found MHC-dependent disassortative mating at the post-copulatory stage, along with strong evidence of inbreeding avoidance at both stages. However, results from generalized linear mixed models suggest that the pattern of MHC-dependent disassortative mating could be a by-product of inbreeding avoidance. Our results therefore suggest that while multiple apparent mechanisms of non-random mating with respect to the MHC may occur, some of them have alternative explanations.
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Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology,School of Biological Science, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology,School of Biological Science, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology,School of Biological Science, University of Edinburgh, Edinburgh, UK
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26
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O'Dea RE, Lagisz M, Jennions MD, Koricheva J, Noble DWA, Parker TH, Gurevitch J, Page MJ, Stewart G, Moher D, Nakagawa S. Preferred reporting items for systematic reviews and meta-analyses in ecology and evolutionary biology: a PRISMA extension. Biol Rev Camb Philos Soc 2021; 96:1695-1722. [PMID: 33960637 PMCID: PMC8518748 DOI: 10.1111/brv.12721] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta-analytic methods to understand ecological and evolutionary phenomena. Meta-analyses can resolve long-standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta-analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta-analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta-analysis should be trusted - and to be able to build upon the review - authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by 'reporting quality'. To assess perceptions and standards of reporting quality of systematic reviews and meta-analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta-analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (~16%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta-analysis community in ecology and evolutionary biology: PRISMA-EcoEvo (version 1.0). PRISMA-EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta-analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA-EcoEvo guideline both in the planning and writing stages of a systematic review and meta-analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA-EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta-analyses.
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Affiliation(s)
- Rose E O'Dea
- Evolution & Ecology Research Centre and School of Biological and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre and School of Biological and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Michael D Jennions
- Research School of Biology, Australian National University, 46 Sullivans Creek Road, Canberra, 2600, Australia
| | - Julia Koricheva
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, U.K
| | - Daniel W A Noble
- Evolution & Ecology Research Centre and School of Biological and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,Research School of Biology, Australian National University, 46 Sullivans Creek Road, Canberra, 2600, Australia
| | - Timothy H Parker
- Department of Biology, Whitman College, Walla Walla, WA, 99362, U.S.A
| | - Jessica Gurevitch
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794-5245, U.S.A
| | - Matthew J Page
- School of Public Health and Preventative Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Gavin Stewart
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - David Moher
- Centre for Journalology, Clinical Epidemiology Program, Ottawa Hospital Research Institute, General Campus, 501 Smyth Road, Room L1288, Ottawa, ON, K1H 8L6, Canada
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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27
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Davies CS, Taylor MI, Hammers M, Burke T, Komdeur J, Dugdale HL, Richardson DS. Contemporary evolution of the innate immune receptor gene TLR3 in an isolated vertebrate population. Mol Ecol 2021; 30:2528-2542. [PMID: 33949028 DOI: 10.1111/mec.15914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/15/2022]
Abstract
Understanding where genetic variation exists, and how it influences fitness within populations is important from an evolutionary and conservation perspective. Signatures of past selection suggest that pathogen-mediated balancing selection is a key driver of immunogenetic variation, but studies tracking contemporary evolution are needed to help resolve the evolutionary forces and mechanism at play. Previous work in a bottlenecked population of Seychelles warblers (Acrocephalus sechellensis) show that functional variation has been maintained at the viral-sensing Toll-like receptor 3 (TLR3) gene, including one nonsynonymous SNP, resulting in two alleles. Here, we characterise evolution at this TLR3 locus over a 25-year period within the original remnant population of the Seychelles warbler, and in four other derived, populations. Results show a significant and consistent temporal decline in the frequency of the TLR3C allele in the original population, and that similar declines in the TLR3C allele frequency occurred in all the derived populations. Individuals (of both sexes) with the TLR3CC genotype had lower survival, and males - but not females - that carry the TLR3C allele had significantly lower lifetime reproductive success than those with only the TLR3A allele. These results indicate that positive selection on the TLR3A allele, caused by an as yet unknown agent, is driving TLR3 evolution in the Seychelles warbler. No evidence of heterozygote advantage was detected. However, whether the positive selection observed is part of a longer-term pattern of balancing selection (through fluctuating selection or rare-allele advantage) cannot be resolved without tracking the TLR3C allele over an extended time period.
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Affiliation(s)
- Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK
| | - Martijn Hammers
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.,Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, UK.,Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles
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28
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Minias P, Janiszewska A, Pikus E, Zadworny T, Anderwald D. MHC Reflects Fine-Scale Habitat Structure in White-Tailed Eagles, Haliaeetus albicilla. J Hered 2021; 112:335-345. [PMID: 33942876 DOI: 10.1093/jhered/esab026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/26/2021] [Indexed: 11/12/2022] Open
Abstract
The major histocompatibility complex (MHC) genes code for key immune receptors responsible for recognition of intra- and extracellular pathogens (MHC class I and class II, respectively). It was hypothesized that MHC polymorphism can be maintained via fluctuating selection resulting from between-habitat variation in pathogen regimes. We examined associations between MHC class I and class II genes and habitat structure in an apex avian predator, the white-tailed eagle, Haliaeetus albicilla. We genotyped MHC class I and class II genes in ca. 150 white-tailed eagle chicks from nearly 100 nesting territories distributed across 3 distinct populations in Poland. Habitat structure was quantified at the level of foraging territories and directly at the nest sites. We found strong support for associations of habitat traits with diversity and allelic composition at the MHC class II. Forest area within territory and forest productivity were identified as the major habitat predictors of MHC class II polymorphism, whereas other habitat traits (distance to nearest open water, grassland, and water area within territory or understory presence) showed fewer associations with class II alleles. In contrast, there was little support for associations between MHC class I genes and habitat structure. All significant associations were apparent at the within-population level rather than between populations. Our results suggest that extracellular (rather than intracellular) pathogens may exert much stronger selective pressure on the white-tailed eagle. Associations of habitat structure with MHC class II may reflect fluctuating (balancing) selection, which maintains MHC diversity within populations.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha, Łódź, Poland
| | - Aleksandra Janiszewska
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha, Łódź, Poland
| | - Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha, Łódź, Poland
| | - Tomasz Zadworny
- Regional Directorate of Environmental Protection in Łódź, Traugutta, Łódź, Poland
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29
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Ivy-Israel NMD, Moore CE, Schwartz TS, Steury TD, Zohdy S, Newbolt CH, Ditchkoff SS. Association between sexually selected traits and allelic distance in two unlinked MHC II loci in white-tailed deer (Odocoileus virginianus). Evol Ecol 2021. [DOI: 10.1007/s10682-021-10108-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Huang W, Pemberton JM. Within-trio tests provide little support for post-copulatory selection on major histocompatibility complex haplotypes in a free-living population. Proc Biol Sci 2021; 288:20202862. [PMID: 33622127 PMCID: PMC7934901 DOI: 10.1098/rspb.2020.2862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/27/2021] [Indexed: 11/12/2022] Open
Abstract
Sexual selection has been proposed as a force that could help maintain the diversity of major histocompatibility complex (MHC) genes in vertebrates. Potential selective mechanisms can be divided into pre-copulatory and post-copulatory, and in both cases, the evidence for occurrence is mixed, especially in natural populations. In this study, we used a large number of parent-offspring trios that were diplotyped for MHC class II genes in a wild population of Soay sheep (Ovis aries) to examine whether there was within-trio post-copulatory selection on MHC class II genes at both the haplotype and diplotype levels. We found there was transmission ratio distortion of one of the eight MHC class II haplotypes (E) which was transmitted less than expected by fathers, and transmission ratio distortion of another haplotype (A) which was transmitted more than expected by chance to male offspring. However, in both cases, these deviations were not significant after correction for multiple tests. In addition, we did not find any evidence of post-copulatory selection at the diplotype level. These results imply that, given known parents, there is no strong post-copulatory selection on MHC class II genes in this population.
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Affiliation(s)
- W. Huang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - J. M. Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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31
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Grueber CE, Peel E, Wright B, Hogg CJ, Belov K. A Tasmanian devil breeding program to support wild recovery. Reprod Fertil Dev 2020; 31:1296-1304. [PMID: 32172782 DOI: 10.1071/rd18152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/01/2018] [Indexed: 01/03/2023] Open
Abstract
Tasmanian devils are threatened in the wild by devil facial tumour disease: a transmissible cancer with a high fatality rate. In response, the Save the Tasmanian Devil Program (STDP) established an 'insurance population' to enable the preservation of genetic diversity and natural behaviours of devils. This breeding program includes a range of institutions and facilities, from zoo-based intensive enclosures to larger, more natural environments, and a strategic approach has been required to capture and maintain genetic diversity, natural behaviours and to ensure reproductive success. Laboratory-based research, particularly genetics, in tandem with adaptive management has helped the STDP reach its goals, and has directly contributed to the conservation of the species in the wild. Here we review this work and show that the Tasmanian devil breeding program is a powerful example of how genetic research can be used to understand and improve reproductive success in a threatened species.
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Affiliation(s)
- C E Grueber
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - E Peel
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - B Wright
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - C J Hogg
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
| | - K Belov
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW 2006, Australia
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32
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Croy I, Ritschel G, Kreßner-Kiel D, Schäfer L, Hummel T, Havlíček J, Sauter J, Ehninger G, Schmidt AH. Marriage does not relate to major histocompatibility complex: a genetic analysis based on 3691 couples. Proc Biol Sci 2020; 287:20201800. [PMID: 33023409 DOI: 10.1098/rspb.2020.1800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Optimization of chances for healthy offspring is thought to be one of the factors driving mate choice and compatibility of the major histocompatibility complex (MHC) is assumed to determine the offspring's fitness. While humans have been claimed to be able to perceive information of MHC compatibility via the olfactory channel, it remains unknown whether humans use such information for mate choice. By investigation of 3691 married couples, we observed that the high polymorphism of MHC leads to a low chance for homozygous offspring. MHC similarity between couples did not differ from chance, we hence observed no MHC effect in married couples. Hormonal contraception at the time of relationship initiation had no significant effect towards enhanced similarity. A low variety of alleles within a postcode area led to a higher likelihood of homozygous offspring. Based on this data, we conclude that there is no pattern of MHC dis-assortative mating in a genetically diverse Western society. We discuss the question of olfactory mate preference, in-group mating bias and the high polymorphism as potential explanations.
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Affiliation(s)
- Ilona Croy
- Department of Psychotherapy and Psychosomatic Medicine, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Gerhard Ritschel
- Department of Psychotherapy and Psychosomatic Medicine, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Denise Kreßner-Kiel
- Department of Psychotherapy and Psychosomatic Medicine, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Laura Schäfer
- Department of Psychotherapy and Psychosomatic Medicine, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Thomas Hummel
- Interdisciplinary Center 'Smell & Taste', Department of Otorhinolaryngology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Jan Havlíček
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | | | - Alexander H Schmidt
- DKMS gemeinnützige GmbH, Tübingen, Germany.,DKMS Life Science Laboratory GmbH, Dresden, Germany
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33
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Farquharson KA, Hogg CJ, Belov K, Grueber CE. Deciphering genetic mate choice: Not so simple in group-housed conservation breeding programs. Evol Appl 2020; 13:2179-2189. [PMID: 33005217 PMCID: PMC7513713 DOI: 10.1111/eva.12981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 02/19/2020] [Accepted: 03/30/2020] [Indexed: 11/28/2022] Open
Abstract
Incorporating mate choice into conservation breeding programs can improve reproduction and the retention of natural behaviors. However, different types of genetic-based mate choice can have varied consequences for genetic diversity management. As a result, it is important to examine mechanisms of mate choice in captivity to assess its costs and benefits. Most research in this area has focused on experimental pairing trials; however, this resource-intensive approach is not always feasible in captive settings and can interfere with other management constraints. We used generalized linear mixed models and permutation approaches to investigate overall breeding success in group-housed Tasmanian devils at three nonmutually exclusive mate choice hypotheses: (a) advantage of heterozygous individuals, (b) advantage of dissimilar mates, and (c) optimum genetic distance, using both 1,948 genome-wide SNPs and 12 MHC-linked microsatellites. The managed devil insurance population is the largest such breeding program in Australia and is known to have high variance in reproductive success. We found that nongenetic factors such as age were the best predictors of breeding success in a competitive breeding scenario, with younger females and older males being more successful. We found no evidence of mate choice under the hypotheses tested. Mate choice varies among species and across environments, so we advocate for more studies in realistic captive management contexts as experimental or wild studies may not apply. Conservation managers must weigh up the need to wait for adequate sample sizes to detect mate choice with the risk that genetic changes may occur during this time in captivity. Our study shows that examining and integrating mate choice into the captive management of species housed in realistic, semi-natural group-based contexts may be more difficult than previously considered.
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Affiliation(s)
- Katherine A Farquharson
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Katherine Belov
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia
- San Diego Zoo Global San Diego USA
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34
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DeAngelis RS, Hofmann HA. Neural and molecular mechanisms underlying female mate choice decisions in vertebrates. ACTA ACUST UNITED AC 2020; 223:223/17/jeb207324. [PMID: 32895328 DOI: 10.1242/jeb.207324] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Female mate choice is a dynamic process that allows individuals to selectively mate with those of the opposite sex that display a preferred set of traits. Because in many species males compete with each other for fertilization opportunities, female mate choice can be a powerful agent of sexual selection, often resulting in highly conspicuous traits in males. Although the evolutionary causes and consequences of the ornamentation and behaviors displayed by males to attract mates have been well studied, embarrassingly little is known about the proximate neural mechanisms through which female choice occurs. In vertebrates, female mate choice is inherently a social behavior, and although much remains to be discovered about this process, recent evidence suggests the neural substrates and circuits underlying other fundamental social behaviors (such as pair bonding, aggression and parental care) are likely similarly recruited during mate choice. Notably, female mate choice is not static, as social and ecological environments can shape the brain and, consequently, behavior in specific ways. In this Review, we discuss how social and/or ecological influences mediate female choice and how this occurs within the brain. We then discuss our current understanding of the neural substrates underlying female mate choice, with a specific focus on those that also play a role in regulating other social behaviors. Finally, we propose several promising avenues for future research by highlighting novel model systems and new methodological approaches, which together will transform our understanding of the causes and consequences of female mate choice.
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Affiliation(s)
- Ross S DeAngelis
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA
| | - Hans A Hofmann
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA .,Institute for Neuroscience, The University of Texas, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
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35
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Jokiniemi A, Magris M, Ritari J, Kuusipalo L, Lundgren T, Partanen J, Kekäläinen J. Post-copulatory genetic matchmaking: HLA-dependent effects of cervical mucus on human sperm function. Proc Biol Sci 2020; 287:20201682. [PMID: 32811307 PMCID: PMC7482290 DOI: 10.1098/rspb.2020.1682] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Several studies have demonstrated that women show pre-copulatory mating preferences for human leucocyte antigen (HLA)-dissimilar men. A fascinating, yet unexplored, possibility is that the ultimate mating bias towards HLA-dissimilar partners could occur after copulation, at the gamete level. Here, we explored this possibility by investigating whether the selection towards HLA-dissimilar partners occurs in the cervical mucus. After combining sperm and cervical mucus from multiple males and females (full factorial design), we found that sperm performance (swimming velocity, hyperactivation, and viability) was strongly influenced by the male–female combination. This indicates that sperm fertilization capability may be dependent on the compatibility between cervical mucus (female) and sperm (male). We also found that sperm viability was associated with partners' HLA dissimilarity, indicating that cervical mucus may selectively facilitate later gamete fusion between immunogenetically compatible partners. Together, these results provide novel insights into the female-mediated sperm selection (cryptic female choice) in humans and indicate that processes occurring after copulation may contribute to the mating bias towards HLA-dissimilar partners. Finally, by showing that sperm performance in cervical mucus is influenced by partners' genetic compatibility, the present findings may promote a deeper understanding of infertility.
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Affiliation(s)
- Annalaura Jokiniemi
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Martina Magris
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Jarmo Ritari
- Finnish Red Cross Blood Service, Research and Development, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Liisa Kuusipalo
- North Karelia Central Hospital, Tikkamäentie 16, 80210 Joensuu, Finland
| | - Tuulia Lundgren
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Research and Development, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Jukka Kekäläinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
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36
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Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus). BMC Genet 2020; 21:83. [PMID: 32727360 PMCID: PMC7392685 DOI: 10.1186/s12863-020-00889-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type II genes into two subregions (IIa, IIb). Recombination rates are reportedly high between these subregions, and a lack of linkage has been documented in domestic ruminants. However, no study has yet examined the degree of linkage between these subregions in a wild ruminant. The white-tailed deer (Odocoileus virginianus), a popular ruminant of the Cervidae family, is habitually plagued by pathogens in its natural environment (e.g. Haemonchus contortus, Elaeophora). Due to the association between MHC haplotypes and disease susceptibility, a deeper understanding of MHC polymorphism and linkage between MHC genes can further aid in this species' successful management. We sequenced MHC-DRB exon 2 (IIa) and MHC-DOB exon 2 (IIb) on the MiSeq platform from an enclosed white-tailed deer population located in Alabama. RESULTS We identified 12 new MHC-DRB alleles, and resampled 7 alleles, which along with other published alleles brings the total number of documented alleles in white-tailed deer to 30 for MHC-DRB exon 2. The first examination of MHC-DOB in white-tailed deer found significantly less polymorphism (11 alleles), as was expected of a non-classical MHC gene. While MHC-DRB was found to be under positive, diversifying selection, MHC-DOB was found to be under purifying selection for white-tailed deer. We found no significant linkage disequilibrium between MHC-DRB and MHC-DOB, suggesting that these loci are unlikely to be closely linked. CONCLUSIONS Overall, this study identified 12 new MHC-DRB exon 2 alleles and characterized a new, non-classical, MHC II gene (MHC-DOB) for white-tailed deer. We also found a lack of significant linkage between these two loci, which supports previous findings of a chromosomal inversion within the MHC type II gene region in ruminants, and suggests that white-tailed deer may have a recombination hotspot between these MHC regions similar to that found for Bos taurus.
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Stervander M, Dierickx EG, Thorley J, Brooke MDL, Westerdahl H. High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice. Mol Ecol 2020; 29:3578-3592. [PMID: 32416000 DOI: 10.1111/mec.15471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/14/2020] [Accepted: 05/04/2020] [Indexed: 12/30/2022]
Abstract
Small population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity and its effects on mate choice and survival in the Critically Endangered Raso lark Alauda razae, a species restricted to the 7 km2 islet of Raso, Cape Verde, since ~1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC-I genotype/diversity on mate choice or survival. However, we demonstrate that MHC-I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by cosegregation of multiple haplotypes comprising 2-8 linked MHC-I loci. Within-locus homozygosity is high, contributing to low population-wide diversity. Conversely, each individual had comparably many alleles, 6-16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within-individual MHC-I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species' adaptive potential.
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Affiliation(s)
- Martin Stervander
- Department of Biology, Lund University, Lund, Sweden.,Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Elisa G Dierickx
- Department of Zoology, University of Cambridge, Cambridge, UK.,Fauna & Flora International, Cambridge, UK
| | - Jack Thorley
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - M de L Brooke
- Department of Zoology, University of Cambridge, Cambridge, UK
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Zhu Y, Grueber C, Li Y, He M, Hu L, He K, Liu H, Zhang H, Wu H. MHC-associated Baylisascaris schroederi load informs the giant panda reintroduction program. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2020; 12:113-120. [PMID: 32528846 PMCID: PMC7283101 DOI: 10.1016/j.ijppaw.2020.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 12/27/2022]
Abstract
Reintroducing captive giant pandas (Ailuropoda melanoleuca) to the wild is the ultimate goal of their ex situ conservation. Choosing higher fitness candidates to train prior to release is the first step in the giant panda reintroduction program. Disease resistance is one important index of individual fitness and presumed to be related to variation at major histocompatibility complex genes (MHC). Here, we used seven polymorphic functional MHC genes (Aime-C, Aime-I, Aime-L, Aime-DQA1, Aime-DQA2, Aime-DQB1 and Aime-DRB3) and estimate their relationship with Baylisascaris schroederi (Ascarididae) infection in giant panda. We found that DQA1 heterozygous pandas were less frequently infected than homozygotes. The presence of one MHC genotype and one MHC allele were also associated with B. schroederi infection: Aime-C*0203 and Aime-L*08 were both associated with B. schroederi resistance. Our results indicate that both heterozygosity and certain MHC variants are important for panda disease resistance, and should therefore be considered in future reintroduction programs for this species alongside conventional selection criteria (such as physical condition and pedigree-based information). MHC heterozygous pandas were less frequently infected by Baylisascaris schroederi than homozygotes. Presence of Aime-C*0203 and Aime-L*08 are associated with Baylisascaris schroederi resistance. MHC types are important for panda parasite resistance.
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Affiliation(s)
- Ying Zhu
- Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China.,Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Catherine Grueber
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Yudong Li
- Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Ming He
- China Conservation and Research Center for the Giant Panda, Dujiangyan, Sichuan, China
| | - Lan Hu
- China Conservation and Research Center for the Giant Panda, Dujiangyan, Sichuan, China
| | - Ke He
- College of Animal Sciences & Technology, Zhejiang A & F University, Hangzhou, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hemin Zhang
- China Conservation and Research Center for the Giant Panda, Dujiangyan, Sichuan, China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, Dujiangyan, Sichuan, China
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Havlíček J, Winternitz J, Roberts SC. Major histocompatibility complex-associated odour preferences and human mate choice: near and far horizons. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190260. [PMID: 32306884 PMCID: PMC7209936 DOI: 10.1098/rstb.2019.0260] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2019] [Indexed: 12/11/2022] Open
Abstract
The major histocompatibility complex (MHC) is a core part of the adaptive immune system. As in other vertebrate taxa, it may also affect human chemical communication via odour-based mate preferences, with greater attraction towards MHC-dissimilar partners. However, despite some well-known findings, the available evidence is equivocal and made complicated by varied approaches to quantifying human mate choice. To address this, we here conduct comprehensive meta-analyses focusing on studies assessing: (i) genomic mate selection, (ii) relationship satisfaction, (iii) odour preference, and (iv) all studies combined. Analysis of genomic studies reveals no association between MHC-dissimilarity and mate choice in actual couples; however, MHC effects appear to be independent of the genomic background. The effect of MHC-dissimilarity on relationship satisfaction was not significant, and we found evidence for publication bias in studies on this area. There was also no significant association between MHC-dissimilarity and odour preferences. Finally, combining effect sizes from all genomic, relationship satisfaction, odour preference and previous mate choice studies into an overall estimate showed no overall significant effect of MHC-similarity on human mate selection. Based on these findings, we make a set of recommendations for future studies, focusing both on aspects that should be implemented immediately and those that lurk on the far horizon. We need larger samples with greater geographical and cultural diversity that control for genome-wide similarity. We also need more focus on mechanisms of MHC-associated odour preferences and on MHC-associated pregnancy loss. This article is part of the Theo Murphy meeting issue 'Olfactory communication in humans'.
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Affiliation(s)
- Jan Havlíček
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 42 Prague 2, Czech Republic
| | - Jamie Winternitz
- Department of Animal Behaviour, Bielefeld University, Bielefeld 33615, Germany
| | - S. Craig Roberts
- Division of Psychology, University of Stirling, Stirling FK9 4LA, UK
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40
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Jaworska J, Jaworski Z, Tobolski D, Siemieniuch M, Janowski T, Górecka-Bruzda A. Selection of reproductive partners in semi-feral horses (Equus caballus) is not influenced by major histocompatibility complex (MHC): A field study. Appl Anim Behav Sci 2020. [DOI: 10.1016/j.applanim.2020.104973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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41
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Roberts SC, Havlíček J, Schaal B. Human olfactory communication: current challenges and future prospects. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190258. [PMID: 32306869 DOI: 10.1098/rstb.2019.0258] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Although anthropologists frequently report the centrality of odours in the daily lives and cultural beliefs of many small-scale communities, Western scholars have historically considered the sense of smell as minimally involved in human communication. Here, we suggest that the origin and persistence of this latter view might be a consequence of the fact that most research is conducted on participants from Western societies who, collectively, were rather old (adults), deodorized and desensitized (ODD) to various aspects of olfactory perception. The view is rapidly changing, however, and this themed issue provides a timely overview of the current state-of-the-art on human chemocommunication. Based on evolutionary models of communication, the papers cover both general mechanisms of odour production by 'senders' and odour perception by 'receivers'. Focus on specific functional contexts includes reciprocal impact of odours between infants and mothers, the role of odour in mate choice and how odours communicate emotion and disease. Finally, a position paper outlines pitfalls and opportunities for the future, against the context of the replication crisis in psychology. We believe a more nuanced view of human chemical communication is within our grasp if we can continue to develop inter-disciplinary insights and expand research activities beyond ODD people. This article is part of the Theo Murphy meeting issue 'Olfactory communication in humans'.
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Affiliation(s)
- S Craig Roberts
- Division of Psychology, University of Stirling, Stirling FK9 4LA, UK
| | - Jan Havlíček
- Faculty of Science, Charles University, Viničná 7, 128 42 Prague 2, Czech Republic
| | - Benoist Schaal
- Developmental Ethology and Cognitive Psychology Laboratory, Centre for Taste, Smell and Feeding Behaviour Science, UMR 6265 CNRS-Université de Bourgogne-Inra-AgroSup, Dijon, France
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42
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Sawada A, Ando H, Takagi M. Evaluating the existence and benefit of major histocompatibility complex-based mate choice in an isolated owl population. J Evol Biol 2020; 33:762-772. [PMID: 32281698 DOI: 10.1111/jeb.13629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/16/2020] [Accepted: 04/01/2020] [Indexed: 11/28/2022]
Abstract
How mate preferences evolve in the first place has been a major conundrum for sexual selection. Some hypotheses explaining this assume fitness benefit derived from subsequent generations. Major histocompatibility complex (MHC)-based mate choice is a representative example of the mate choice that is associated with such trans-generational mechanisms. To provide evidences for fitness benefit of MHC-based mate choice, previous studies assessed the association between own MHC genotype and own fitness components. However, the association between MHC-based mate choice in the parental generation and fitness components in the resultant offspring generation has only rarely been measured in wild populations. Focusing on the isolated population of the monogamous Ryukyu Scops Owl (Otus elegans interpositus) on Minami-daito Island, Japan, we found evidence of MHC-based mate choice. However, we found no evidence of MHC-based mate choice increasing own reproductive success or offspring survival. This is a rare case study that directly examines the existence of the trans-generational indirect benefit of MHC-based mate choice for genetic compatibility from trans-generational data in a wild bird population. By investigating the fitness benefits of mate choice, this study serves to facilitate our understanding of the evolution of MHC-based mate choice.
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Affiliation(s)
- Akira Sawada
- Department of Natural History Science, Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Haruko Ando
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masaoki Takagi
- Department of Natural History Science, Graduate School of Science, Hokkaido University, Sapporo, Japan
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43
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Radwan J, Babik W, Kaufman J, Lenz TL, Winternitz J. Advances in the Evolutionary Understanding of MHC Polymorphism. Trends Genet 2020; 36:298-311. [DOI: 10.1016/j.tig.2020.01.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/26/2022]
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44
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Dandine-Roulland C, Laurent R, Dall'Ara I, Toupance B, Chaix R. Genomic evidence for MHC disassortative mating in humans. Proc Biol Sci 2020; 286:20182664. [PMID: 30890093 DOI: 10.1098/rspb.2018.2664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Although pervasive in many animal species, the evidence for major histocompatibility complex (MHC) disassortative mating in humans remains inconsistent across studies. Here, to revisit this issue, we analyse dense genotype data for 883 European and Middle Eastern couples. To distinguish MHC-specific effects from socio-cultural confounders, the pattern of relatedness between spouses in the MHC region is compared to the rest of the genome. Couples from Israel exhibit no significant pattern of relatedness across the MHC region, whereas across the genome, they are more similar than random pairs of individuals, which may reflect social homogamy and/or cousin marriages. On the other hand, couples from The Netherlands and more generally from Northern Europe are significantly more MHC-dissimilar than random pairs of individuals, and this pattern of dissimilarity is extreme when compared with the rest of the genome. Our findings support the hypothesis that the MHC influences mate choice in humans in a context-dependent way: MHC-driven preferences may exist in all populations but, in some populations, social constraints over mate choice may reduce the ability of individuals to rely on such biological cues when choosing their mates.
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Affiliation(s)
- Claire Dandine-Roulland
- Eco-Anthropologie, UMR 7206, CNRS, MNHN, Université Paris Diderot , Sorbonne Paris Cité, Paris , France
| | - Romain Laurent
- Eco-Anthropologie, UMR 7206, CNRS, MNHN, Université Paris Diderot , Sorbonne Paris Cité, Paris , France
| | - Irene Dall'Ara
- Eco-Anthropologie, UMR 7206, CNRS, MNHN, Université Paris Diderot , Sorbonne Paris Cité, Paris , France
| | - Bruno Toupance
- Eco-Anthropologie, UMR 7206, CNRS, MNHN, Université Paris Diderot , Sorbonne Paris Cité, Paris , France
| | - Raphaëlle Chaix
- Eco-Anthropologie, UMR 7206, CNRS, MNHN, Université Paris Diderot , Sorbonne Paris Cité, Paris , France
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45
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Silveira L, Garner SR, Neff BD. Similarity at the major histocompatibility complex class II does not influence mating patterns in bluegill (Lepomis macrochirus). Behav Ecol Sociobiol 2020. [DOI: 10.1007/s00265-020-2822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Bentkowski P, Radwan J. Mating preferences can drive expansion or contraction of major histocompatibility complex gene family. Proc Biol Sci 2020; 287:20192706. [PMID: 32097586 DOI: 10.1098/rspb.2019.2706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Major histocompatibility complex (MHC)-based mating rules can evolve as a way to avoid inbreeding or to increase offspring immune competence. While the role of mating preference in shaping the MHC diversity in vertebrates has been acknowledged, its impact on individual MHC diversity has not been considered. Here, we use computer simulations to investigate how simple mating rules favouring MHC-dissimilar partners affect the evolution of the number of MHC variants in individual genomes, accompanying selection for resistance to parasites. We showed that the effect of such preferences could sometimes be dramatic. If preferences are aimed at avoiding identical alleles, the equilibrium number of MHC alleles is much smaller than under random mating. However, if the mating rule minimizes the ratio of shared to different alleles in partners, MHC number is higher than under random mating. Additionally, our simulations revealed that a negative correlation between the numbers of MHC variants in mated individuals can arise from simple rules of MHC-disassortative mating. Our results reveal unexpected potential of MHC-based mating preferences to drive MHC gene family expansions or contractions and highlight the need to study the mechanistic basis of such preferences, which is currently poorly understood.
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Affiliation(s)
- Piotr Bentkowski
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań 61-614, Poland
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań 61-614, Poland
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47
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Gaigher A, Burri R, San-Jose LM, Roulin A, Fumagalli L. Lack of statistical power as a major limitation in understanding MHC-mediated immunocompetence in wild vertebrate populations. Mol Ecol 2019; 28:5115-5132. [PMID: 31614047 DOI: 10.1111/mec.15276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 01/09/2023]
Abstract
Disentangling the sources of variation in developing an effective immune response against pathogens is of major interest to immunoecology and evolutionary biology. To date, the link between immunocompetence and genetic variation at the major histocompatibility complex (MHC) has received little attention in wild animals, despite the key role of MHC genes in activating the adaptive immune system. Although several studies point to a link between MHC and immunocompetence, negative findings have also been reported. Such disparate findings suggest that limited statistical power might be affecting studies on this topic, owing to insufficient sample sizes and/or a generally small effect of MHC on the immunocompetence of wild vertebrates. To clarify this issue, we investigated the link between MHC variation and seven immunocompetence proxies in a large sample of barn owls and estimated the effect sizes and statistical power of this and published studies on this topic. We found that MHC poorly explained variation in immunocompetence of barn owls, with small-to-moderate associations between MHC and immunocompetence in owls (effect size: .1 ≥ r ≤ .3) similar to other vertebrates studied to date. Such small-to-moderate effects were largely associated with insufficient power, which was only sufficient (>0.8) to detect moderate-to-large effect sizes (r ≥ .3). Thus, studies linking MHC variation with immunocompetence in wild populations are underpowered to detect MHC effects, which are likely to be of generally small magnitude. Larger sample sizes (>200) will be required to achieve sufficient power in future studies aiming to robustly test for a link between MHC variation and immunocompetence.
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Affiliation(s)
- Arnaud Gaigher
- Department of Ecology and Evolution, Laboratory for Conservation Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland.,CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Reto Burri
- Department of Population Ecology, Institute of Ecology & Evolution, Friedrich Schiller University Jena, Jena, Germany
| | - Luis M San-Jose
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland.,Laboratoire Évolution & Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Alexandre Roulin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Luca Fumagalli
- Department of Ecology and Evolution, Laboratory for Conservation Biology, Biophore, University of Lausanne, Lausanne, Switzerland
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48
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Rekdal SL, Anmarkrud JA, Lifjeld JT, Johnsen A. Extra‐pair mating in a passerine bird with highly duplicated major histocompatibility complex class II: Preference for the golden mean. Mol Ecol 2019; 28:5133-5144. [DOI: 10.1111/mec.15273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/30/2019] [Accepted: 10/14/2019] [Indexed: 12/26/2022]
Affiliation(s)
| | | | | | - Arild Johnsen
- Natural History Museum University of Oslo Oslo Norway
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49
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Nelson-Flower MJ, Germain RR, MacDougall-Shackleton EA, Taylor SS, Arcese P. Purifying Selection in the Toll-Like Receptors of Song Sparrows Melospiza melodia. J Hered 2019; 109:501-509. [PMID: 29893971 DOI: 10.1093/jhered/esy027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/08/2018] [Indexed: 01/22/2023] Open
Abstract
Variation in immune gene sequences is known to influence resistance to infectious diseases and parasites, and hence survival and mate choice, across animal taxa. Toll-like receptors (TLRs) comprise one essential gene family in the vertebrate innate immune system and recognize evolutionarily conserved structures from all major microorganism classes. However, the causes and consequences of TLR variation in passerine birds remain largely unexplored. We examined 7 TLR genes in song sparrows (Melospiza melodia), a species that is studied across North America. We then examined sequences from 4 unduplicated TLRs (TLR1LB, TLR3, TLR4, and TLR15) from birds in 2 parts of the species' range (N = 27, N = 6), tested for evidence of selection, and conducted pilot analyses of the role of TLR heterozygosity in survival. We identified 45 SNPs: 19 caused changes in amino acid sequences and 2 of these were likely deleterious. We found no evidence of codon-level episodic positive selection but detected purifying selection at codons in all TLRs. Contrary to expectations we found no strong correlation between heterozygosity at TLRs and inbreeding coefficient f (estimate ± standard error [SE] = -0.68 ± 0.37, Radj2 = 0.08, F1,25 = 3.38, P = 0.08). In addition, pilot analyses revealed no relationship between TLR heterozygosity and survival (β ± SE: 0.09 ± 2.00, P = 0.96), possibly due to small sample size. Further analyses of genetic diversity in TLRs are likely to advance understanding of the effects of innate immune gene diversity on the fitness and persistence of wild populations.
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Affiliation(s)
- Martha J Nelson-Flower
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Sabrina S Taylor
- The School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
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50
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O'Connor EA, Westerdahl H, Burri R, Edwards SV. Avian MHC Evolution in the Era of Genomics: Phase 1.0. Cells 2019; 8:E1152. [PMID: 31561531 PMCID: PMC6829271 DOI: 10.3390/cells8101152] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.
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Affiliation(s)
| | | | - Reto Burri
- Department of Population Ecology, Institute of Ecology & Evolution, Friedrich Schiller University Jena, 07737 Jena, Germany.
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
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