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Budi T, Kumnan N, Singchat W, Chalermwong P, Thong T, Wongloet W, Faniriharisoa Maxime Toky R, Pathomvanich P, Panthum T, Wattanadilokchatkun P, Farhan Ahmad S, Tanglertpaibul N, Vangnai K, Chaiyes A, Yokthongwattana C, Sinthuvanich C, Han K, Muangmai N, Koga A, Nunome M, Sawatdichaikul O, Duengkae P, Matsuda Y, Srikulnath K. Weak purifying selection in allelic diversity of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand. Gene 2024; 923:148587. [PMID: 38768877 DOI: 10.1016/j.gene.2024.148587] [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: 01/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
High levels of purine and uric acid, which are associated with health issues such as gout and cardiovascular disease, are found in the meat of fast-growing broiler chickens, which raises concerns about the quality of chicken meat and the health of the consumers who consume it. High genetic homogeneity and uniformity, particularly in genes involved in the synthesis of inosine monophosphate (IMP) and subsequent process of purine synthesis, which are associated with the meat quality, are exhibited in commercial broiler chickens owing to intensive inbreeding programs. Adenosine succinate lyase (ADSL) is a key enzyme involved in de novo purine biosynthetic pathway and its genetic polymorphisms affect IMP metabolism and purine content. In this study, we investigated the polymorphism of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand, using metabarcoding and genetic diversity analyses. Five alleles with 73 single nucleotide polymorphisms in exon 2, including missense and silent mutations, which may act on the synthesis efficiency of IMP and purine. Their protein structures revealed changes in amino acid composition that may affect ADSL enzyme activity. Weak purifying selection in these ADSL alleles was observed in the chicken population studied, implying that the variants have minor fitness impacts and a greater probability of fixation of beneficial mutations than strong purifying selection. A potential selective sweep was observed in Mae Hong Son chickens, whose purine content was lower than that in other breeds. This suggests a potential correlation between variations of the ADSL gene and reduced purine content and an impact of ADSL expression on the quality of chicken meat. However, further studies are required to validate its potential availability as a genetic marker for selecting useful traits that are beneficial to human health and well-being.
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Affiliation(s)
- Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Rajaonarison Faniriharisoa Maxime Toky
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Prangyapawn Pathomvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nivit Tanglertpaibul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kanithaporn Vangnai
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Aingorn Chaiyes
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi 11120, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Chomdao Sinthuvanich
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea; Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Republic of Korea
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Mitsuo Nunome
- Department of Zoology, Faculty of Science, Okayama University of Science, Ridai-cho 1-1, Kita-ku, Okayama City, Okayama 700-0005, Japan
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand.
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2
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Różańska-Wróbel J, Migalska M, Urbanowicz A, Grzybek M, Rego ROM, Bajer A, Dwuznik-Szarek D, Alsarraf M, Behnke-Borowczyk J, Behnke JM, Radwan J. Interplay between vertebrate adaptive immunity and bacterial infectivity genes: Bank vole MHC versus Borrelia afzelii OspC. Mol Ecol 2024:e17534. [PMID: 39314079 DOI: 10.1111/mec.17534] [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: 05/16/2024] [Revised: 08/12/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024]
Abstract
Coevolution of parasites with their hosts may lead to balancing selection on genes involved in determining the specificity of host-parasite interactions, but examples of such specific interactions in wild vertebrates are scarce. Here, we investigated whether the polymorphic outer surface protein C (OspC), used by the Lyme disease agent, Borrelia afzelii, to manipulate vertebrate host innate immunity, interacts with polymorphic major histocompatibility genes (MHC), while concurrently eliciting a strong antibody response, in one of its main hosts in Europe, the bank vole. We found signals of balancing selection acting on OspC, resulting in little differentiation in OspC variant frequencies between years. Neither MHC alleles nor their inferred functional groupings (supertypes) significantly predicted the specificity of infection with strains carrying different OspC variants. However, we found that MHC alleles, but not supertypes, significantly predicted the level of IgG antibodies against two common OspC variants among seropositive individuals. Our results thus indicate that MHC alleles differ in their ability to induce antibody responses against specific OspC variants, which may contribute to selection of OspC polymorphism by the vole immune system.
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Affiliation(s)
- Joanna Różańska-Wróbel
- Evolutionary Biology Group, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Magdalena Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Anna Urbanowicz
- Laboratory of Protein Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Maciej Grzybek
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdańsk, Gdynia, Poland
| | - Ryan O M Rego
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Anna Bajer
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dorota Dwuznik-Szarek
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Mohammed Alsarraf
- Department of Eco-Epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jolanta Behnke-Borowczyk
- Department of Forest Phytopathology, Faculty of Forestry, Poznań University of Life Sciences, Poznań, Poland
| | - Jerzy M Behnke
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | - Jacek Radwan
- Evolutionary Biology Group, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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3
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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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4
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Babik W, Marszałek M, Dudek K, Antunes B, Palomar G, Zając B, Taugbøl A, Pabijan M. Limited evidence for genetic differentiation or adaptation in two amphibian species across replicated rural-urban gradients. Evol Appl 2024; 17:e13700. [PMID: 38832082 PMCID: PMC11146147 DOI: 10.1111/eva.13700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Urbanization leads to complex environmental changes and poses multiple challenges to organisms. Amphibians are highly susceptible to the effects of urbanization, with land use conversion, habitat destruction, and degradation ranked as the most significant threats. Consequently, amphibians are declining in urban areas, in both population numbers and abundance, however, the effect of urbanization on population genetic parameters remains unclear. Here, we studied the genomic response to urbanization in two widespread European species, the common toad Bufo bufo (26 localities, 480 individuals), and the smooth newt Lissotriton vulgaris (30 localities, 516 individuals) in three geographic regions: southern and northern Poland and southern Norway. We assessed genome-wide SNP variation using RADseq (ca. 42 and 552 thousand SNPs in toads and newts, respectively) and adaptively relevant major histocompatibility complex (MHC) class I and II genes. The results linked most of the genetic differentiation in both marker types to regional (latitudinal) effects, which also correspond to historical biogeography. Further, we did not find any association between genetic differentiation and level of urbanization at local scales for either species. However, urban smooth newts, but not toads, have lower levels of within-population genome-wide diversity, suggesting higher susceptibility to the negative effects of urbanization. A decreasing level of genetic diversity linked to increasing urbanization was also found for MHC II in smooth newts, while the relationship between MHC class I diversity and urbanization differed between geographic regions. We did not find any effects of urbanization on MHC diversity in the toad populations. Although two genetic environment association analyses of genome-wide data, LFMM and BayPass, revealed numerous (219 in B. bufo and 7040 in L. vulgaris) SNPs statistically associated with urbanization, we found a marked lack of repeatability between geographic regions, suggesting a complex and multifaceted response to natural selection elicited by life in the city.
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Affiliation(s)
- W. Babik
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - M. Marszałek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - K. Dudek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - B. Antunes
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - G. Palomar
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
- Department of Genetics, Physiology and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
| | - B. Zając
- Faculty of Biology, Institute of Zoology and Biomedical ResearchJagiellonian UniversityKrakówPoland
| | - A. Taugbøl
- Norwegian Institute for Nature ResearchLillehammerNorway
| | - M. Pabijan
- Faculty of Biology, Institute of Zoology and Biomedical ResearchJagiellonian UniversityKrakówPoland
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5
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Megía-Palma R, Palomar G, Martínez J, Antunes B, Dudek K, Žagar A, Serén N, Carretero MA, Babik W, Merino S. Lizard host abundances and climatic factors explain phylogenetic diversity and prevalence of blood parasites on an oceanic island. Mol Ecol 2024; 33:e17276. [PMID: 38243603 DOI: 10.1111/mec.17276] [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: 05/22/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
Host abundance might favour the maintenance of a high phylogenetic diversity of some parasites via rapid transmission rates. Blood parasites of insular lizards represent a good model to test this hypothesis because these parasites can be particularly prevalent in islands and host lizards highly abundant. We applied deep amplicon sequencing and analysed environmental predictors of blood parasite prevalence and phylogenetic diversity in the endemic lizard Gallotia galloti across 24 localities on Tenerife, an island in the Canary archipelago that has experienced increasing warming and drought in recent years. Parasite prevalence assessed by microscopy was over 94%, and a higher proportion of infected lizards was found in warmer and drier locations. A total of 33 different 18s rRNA parasite haplotypes were identified, and the phylogenetic analyses indicated that they belong to two genera of Adeleorina (Apicomplexa: Coccidia), with Karyolysus as the dominant genus. The most important predictor of between-locality variation in parasite phylogenetic diversity was the abundance of lizard hosts. We conclude that a combination of climatic and host demographic factors associated with an insular syndrome may be favouring a rapid transmission of blood parasites among lizards on Tenerife, which may favour the maintenance of a high phylogenetic diversity of parasites.
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Affiliation(s)
- Rodrigo Megía-Palma
- Universidad de Alcalá (UAH), Department of Biomedicine and Biotechnology, Parasitology Unit, Alcalá de Henares, Spain
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Gemma Palomar
- Universidad de Alcalá (UAH), Department of Biomedicine and Biotechnology, Parasitology Unit, Alcalá de Henares, Spain
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Department of Genetics, Physiology, and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid, Madrid, Spain
| | - Javier Martínez
- Universidad de Alcalá (UAH), Department of Biomedicine and Biotechnology, Parasitology Unit, Alcalá de Henares, Spain
| | - Bernardo Antunes
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Anamarija Žagar
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- NIB, National Institute of Biology, Ljubljana, Slovenia
| | - Nina Serén
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Miguel A Carretero
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Santiago Merino
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
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6
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Migalska M, Węglarczyk K, Dudek K, Homa J. Evolutionary trade-offs constraining the MHC gene expansion: beyond simple TCR depletion model. Front Immunol 2024; 14:1240723. [PMID: 38259496 PMCID: PMC10801004 DOI: 10.3389/fimmu.2023.1240723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
The immune system is as much shaped by the pressure of pathogens as it is by evolutionary trade-offs that constrain its structure and function. A perfect example comes from the major histocompatibility complex (MHC), molecules that initiate adaptive immune response by presentation of foreign antigens to T cells. The remarkable, population-level polymorphism of MHC genes is assumed to result mainly from a co-evolutionary arms race between hosts and pathogens, while the limited, within-individual number of functional MHC loci is thought to be the consequence of an evolutionary trade-off between enhanced pathogen recognition and excessive T cell depletion during negative selection in the thymus. Certain mathematical models and infection studies suggest that an intermediate individual MHC diversity would thus be optimal. A recent, more direct test of this hypothesis has shown that the effects of MHC diversity on T-cell receptor (TCR) repertoires may differ between MHC classes, supporting the depletion model only for MHC class I. Here, we used the bank vole (Myodes=Cletronomys glareolus), a rodent species with variable numbers of expressed MHC genes, to test how an individual MHC diversity influences the proportions and TCR repertoires of responding T cell subsets. We found a non-linear relationship between MHC diversity and T cell proportions (with intermediate MHC numbers coinciding with the largest T cell proportions), perhaps reflecting an optimality effect of balanced positive and negative thymic selection. The association was strongest for the relationship between MHC class I and splenic CD8+ T cells. The CD8+ TCR richness alone was unaffected by MHC class I diversity, suggesting that MHC class I expansion may be limited by decreasing T cell counts, rather than by direct depletion of TCR richness. In contrast, CD4+ TCR richness was positively correlated with MHC class II diversity, arguing against a universal TCR depletion. It also suggests that different evolutionary forces or trade-offs may limit the within-individual expansion of the MHC class II loci.
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Affiliation(s)
- Magdalena Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Kazimierz Węglarczyk
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Joanna Homa
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Krakow, Poland
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7
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Roved J. MHCtools 1.5: Analysis of MHC Sequencing Data in R. Methods Mol Biol 2024; 2809:275-295. [PMID: 38907904 DOI: 10.1007/978-1-0716-3874-3_18] [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] [Indexed: 06/24/2024]
Abstract
The genes of the major histocompatibility complex (MHC) play a vital role in the vertebrate immune system and have attracted considerable interest in evolutionary biology. While the MHC has been characterized in detail in humans (human leukocyte antigen, HLA) and in model organisms such as the mouse, studies in non-model organisms often lack prior knowledge about structure, genetic variability, and evolutionary properties of this locus. MHC genotyping in non-model species commonly relies on PCR-based amplicon sequencing, and while several published protocols facilitate generation of MHC sequence data, there is a lack of transparent and standardized tools for downstream data analysis.Here, I present the R package MHCtools version 1.5, which contains 15 tools that (i) assist accurate MHC genotyping from high-throughput amplicon sequencing data, and provide standardized methods to analyze (ii) MHC diversity, (iii) MHC supertypes, and (iv) MHC haplotypes.I hope that MHCtools will be helpful in future studies of the MHC in non-model species and that it may help to advance our understanding of the important roles of the MHC in ecology and evolution.
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Affiliation(s)
- Jacob Roved
- Section for Molecular Ecology and Evolution, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
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8
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Cortazar-Chinarro M, Richter-Boix A, Rödin-Mörch P, Halvarsson P, Logue JB, Laurila A, Höglund J. Association between the skin microbiome and MHC class II diversity in an amphibian. Mol Ecol 2024; 33:e17198. [PMID: 37933583 DOI: 10.1111/mec.17198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.
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Affiliation(s)
- M Cortazar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- MEMEG/Department of Biology, Lund University, Lund, Sweden
- Department of Earth Ocean and Atmospheric Sciences, Faculty of Science 2020-2207, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Richter-Boix
- Department of Political and Social Science, Pompeu Fabra University, Barcelona, Spain
| | - P Rödin-Mörch
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - P Halvarsson
- Parasitology/Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J B Logue
- Aquatic Ecology/Department of Biology, Lund University, Lund, Sweden
- SLU University Library, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - J Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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9
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Sebastian A, Migalska M, Gaczorek T. AmpliSAS and AmpliHLA: Web Server and Local Tools for MHC Typing of Non-model Species and Human Using NGS Data. Methods Mol Biol 2024; 2809:37-66. [PMID: 38907889 DOI: 10.1007/978-1-0716-3874-3_3] [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] [Indexed: 06/24/2024]
Abstract
AmpliSAS and AmpliHLA are tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human specific version; it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Both tools are available in AmpliSAT web-server as well as scripts for local/server installation. Here we describe the installation and deployment of AmpliSAS and AmpliHLA Perl scripts and dependencies on a local or a server computer. We will show how to run them in the command line using as examples four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.
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Affiliation(s)
| | - Magdalena Migalska
- Genomics and Experimental Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland.
| | - Tomasz Gaczorek
- Genomics and Experimental Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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10
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Napolitano C, Sacristán I, Acuña F, Aguilar E, García S, López-Jara MJ, Cabello J, Hidalgo-Hermoso E, Poulin E, Grueber CE. Assessing micro-macroparasite selective pressures and anthropogenic disturbance as drivers of immune gene diversity in a Neotropical wild cat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:166289. [PMID: 37591403 DOI: 10.1016/j.scitotenv.2023.166289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
Anthropogenic environmental change is reducing available habitat for wild species, providing novel selection pressures such as infectious diseases and causing species to interact in new ways. The potential for emerging infectious diseases and zoonoses at the interface between humans, domestic animals, and wild species is a key global concern. In vertebrates, diversity at the major histocompatibility complex MHC is critical to disease resilience, and its study in wild populations provides insights into eco-evolutionary dynamics that human activities alter. In natural populations, variation at MHC loci is partly maintained by balancing selection, driven by pathogenic selective pressures. We hypothesize that MHC genetic diversity differs between guigna populations inhabiting human-dominated landscapes (higher pathogen pressures) versus more natural habitats (lower pathogen pressures). We predict that MHC diversity in guignas would be highest in human-dominated landscapes compared with continuous forest habitats. We also expected to find higher MHC diversity in guignas infected with micro and macro parasites (higher parasite load) versus non infected guignas. We characterized for the first time the genetic diversity at three MHC class I and II exons in 128 wild guignas (Leopardus guigna) across their distribution range in Chile (32-46° S) and Argentina, representing landscapes with varying levels of human disturbance. We integrated MHC sequence diversity with multiple measures of anthropogenic disturbance and both micro and macro parasite infection data. We also assessed signatures of positive selection acting on MHC genes. We found significantly higher MHC class I diversity in guignas inhabiting landscapes where houses were present, and with lower percentage of vegetation cover, and also in animals with more severe cardiorespiratory helminth infection (richness and intensity) and micro-macroparasite co-infection. This comprehensive, landscape-level assessment further enhances our knowledge on the evolutionary dynamics and adaptive potential of vertebrates in the face of emerging infectious disease threats and increasing anthropogenic impacts.
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Affiliation(s)
- Constanza Napolitano
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile; Institute of Ecology and Biodiversity (IEB), Concepción, Chile; Cape Horn International Center (CHIC), Puerto Williams, Chile.
| | - Irene Sacristán
- Universidad Andres Bello, Santiago, Chile; Animal Health Research Centre, National Institute for Agricultural and Food Research and Technology (INIA), Centro Superior de Investigaciones Científicas (CSIC), Valdeolmos, Madrid, Spain
| | - Francisca Acuña
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Emilio Aguilar
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Sebastián García
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María José López-Jara
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Javier Cabello
- Chiloé Silvestre Center for the Conservation of Biodiversity, Ancud, Chile
| | | | - Elie Poulin
- Institute of Ecology and Biodiversity (IEB), Concepción, Chile; Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems and Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
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11
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Minias P, Podlaszczuk P, Indykiewicz P, Ledwoń M, Nowakowski J, Chyb A, Janiszewski T. Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull. Heredity (Edinb) 2023; 131:282-291. [PMID: 37553491 PMCID: PMC10539538 DOI: 10.1038/s41437-023-00645-2] [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: 05/04/2023] [Revised: 07/15/2023] [Accepted: 07/30/2023] [Indexed: 08/10/2023] Open
Abstract
Immunogenetic variation in natural vertebrate populations is expected to respond to spatial and temporal fluctuations in pathogen assemblages. While spatial heterogeneity in pathogen-driven selection enhances local immunogenetic adaptations and population divergence, different immune genes may yield contrasting responses to the environment. Here, we investigated population differentiation at the key pathogen recognition genes of the innate and adaptive immune system in a colonial bird species, the black-headed gull Chroicocephalus ridibundus. We assessed genetic variation at three toll-like receptor (TLR) genes (innate immunity) and the major histocompatibility complex (MHC) class I and II genes (adaptive immunity) in gulls from seven colonies scattered across Poland. As expected, we found much greater polymorphism at the MHC than TLRs. Population differentiation at the MHC class II, but not MHC-I, was significantly stronger than at neutral microsatellite loci, suggesting local adaptation. This could reflect spatial variation in the composition of extracellular parasite communities (e.g., helminths), possibly driven by sharp differences in habitat structure between colonies. Despite contrasting patterns of population differentiation, both MHC classes showed similar regimes of diversifying selection. Some significant population differentiation was also observed at TLRs, suggesting that innate immune receptors may respond to fine-scale spatial variation in pathogen pressure, although this pattern could have been enhanced by drift. Our results suggested that local adaptation at the pathogen recognition immune genes can be maintained at relatively small or moderate spatial scales in species with high dispersal potential and they highlighted the complexity of immunogenetic responses of animals to heterogeneous environments.
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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.
| | - Patrycja Podlaszczuk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Piotr Indykiewicz
- Department of Biology and Animal Environment, Faculty of Animal Breeding and Biology, Bydgoszcz University of Science and Technology, Mazowiecka 28, 85-084, Bydgoszcz, Poland
| | - Mateusz Ledwoń
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
| | - Jacek Nowakowski
- Department of Ecology and Environmental Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-727, Olsztyn, Poland
| | - Amelia Chyb
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Tomasz Janiszewski
- 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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12
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Zhang J, Wang S, Xu C, Wang S, Du J, Niu M, Yang J, Li Y. Pathogenic selection promotes adaptive immune variations against serious bottlenecks in early invasions of bullfrogs. iScience 2023; 26:107316. [PMID: 37539025 PMCID: PMC10393753 DOI: 10.1016/j.isci.2023.107316] [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: 04/08/2023] [Revised: 05/22/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Adaptive genetic variations are key for understanding evolutionary processes influencing invasions. However, we have limited knowledge on how adaptive genetic diversity in invasive species responds to new pathogenic environments. Here, we compared variations in immune major histocompatibility complex (MHC) class-II β gene and neutral loci in relation to pathogenic chytrid fungus (Batrachochytrium dendrobatidis, Bd) infection across invasive and native populations of American bullfrog between China and United States (US). Chinese invasive populations show a 60% reduction in neutral cytb variations relative to US native populations, and there were similar MHC variation and functional diversity between them. One MHC allele private to China was under recent positive selection and associated with decreased Bd infection, partly explaining the lower Bd prevalence for Chinese populations than for native US populations. These results suggest that pathogen-mediated selection favors adaptive MHC variations and functional diversity maintenance against serious bottlenecks during the early invasions (within 15 generations) of bullfrogs.
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Affiliation(s)
- Jiaqi Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
- University of Chinese Academy of Sciences Beijing 100049, China
| | - Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
| | - Chunxia Xu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
- University of Chinese Academy of Sciences Beijing 100049, China
| | - Siqi Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
- University of Chinese Academy of Sciences Beijing 100049, China
| | - Jiacong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Meiling Niu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Jiaxue Yang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, Beijing 100101, China
- University of Chinese Academy of Sciences Beijing 100049, China
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
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13
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Chaves PB, Strier KB, Di Fiore A. Paternity data reveal high MHC diversity among sires in a polygynandrous, egalitarian primate. Proc Biol Sci 2023; 290:20231035. [PMID: 37528707 PMCID: PMC10394425 DOI: 10.1098/rspb.2023.1035] [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: 05/10/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023] Open
Abstract
Evidence from human and nonhuman primates suggests that females avoid breeding with close kin and may choose mates based on MHC diversity, which can improve offspring survival. In despotic societies, female mate choice may be hindered by male sexual coercion, but in egalitarian societies, females may be less constrained. Among northern muriquis-an egalitarian, polygynandrous primate with male philopatry-analyses of new data on paternity and variation at microsatellite and MHC loci, combined with behavioural and life-history data, revealed that sires showed higher MHC diversity than expected by chance and were never close kin of dams, consistent with predictions of female mate choice and close inbreeding avoidance. However, females did not differentially reproduce with males who were more distantly related to them or more dissimilar at the MHC than expected by chance, nor with those who had more MHC alleles distinct from their own. The lack of male dominance may permit females to identify and reproduce preferentially with non-offspring males and with males who are more diverse at the MHC. Nonetheless, the absence of disassortative mating at the MHC and neutral loci suggests that female mate choice may be limited by other factors impacting male fertilization success.
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Affiliation(s)
- Paulo B. Chaves
- Department of Anthropology, New York University, New York, USA
- Department of Anthropology and the Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, USA
| | - Karen B. Strier
- Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA
| | - Anthony Di Fiore
- Department of Anthropology and the Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, USA
- Tiputini Biodiversity Station, College of Biological and Environmental Sciences, Universidad San Francisco de Quito, Cumbayá, Ecuador
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14
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Liu P, Li G, Zhao N, Song X, Wang J, Shi X, Wang B, Zhang L, Dong L, Li Q, Liu Q, Lu L. Neutral Forces and Balancing Selection Interplay to Shape the Major Histocompatibility Complex Spatial Patterns in the Striped Hamster in Inner Mongolia: Suggestive of Broad-Scale Local Adaptation. Genes (Basel) 2023; 14:1500. [PMID: 37510404 PMCID: PMC10379431 DOI: 10.3390/genes14071500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) plays a key role in the adaptive immune response to pathogens due to its extraordinary polymorphism. However, the spatial patterns of MHC variation in the striped hamster remain unclear, particularly regarding the relative contribution of the balancing selection in shaping MHC spatial variation and diversity compared to neutral forces. METHODS In this study, we investigated the immunogenic variation of the striped hamster in four wild populations in Inner Mongolia which experience a heterogeneous parasitic burden. Our goal was to identify local adaptation by comparing the genetic structure at the MHC with that at seven microsatellite loci, taking into account neutral processes. RESULTS We observed significant variation in parasite pressure among sites, with parasite burden showing a correlation with temperature and precipitation. Molecular analysis revealed a similar co-structure between MHC and microsatellite loci. We observed lower genetic differentiation at MHC loci compared to microsatellite loci, and no correlation was found between the two. CONCLUSIONS Overall, these results suggest a complex interplay between neutral evolutionary forces and balancing selection in shaping the spatial patterns of MHC variation. Local adaptation was not detected on a small scale but may be applicable on a larger scale.
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Affiliation(s)
- Pengbo Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Guichang Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ning Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiuping Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xinfei Shi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Bin Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Public Health School, Jiamusi University, Jiamusi 154007, China
| | - Lu Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Li Dong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Qingduo Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Liang Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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15
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Winternitz J, Chakarov N, Rinaud T, Ottensmann M, Krüger O. High functional allelic diversity and copy number in both MHC classes in the common buzzard. BMC Ecol Evol 2023; 23:24. [PMID: 37355591 PMCID: PMC10290333 DOI: 10.1186/s12862-023-02135-9] [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: 11/11/2021] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC), which encodes molecules that recognize various pathogens and parasites and initiates the adaptive immune response in vertebrates, is renowned for its exceptional polymorphism and is a model of adaptive gene evolution. In birds, the number of MHC genes and sequence diversity varies greatly among taxa, believed due to evolutionary history and differential selection pressures. Earlier characterization studies and recent comparative studies suggest that non-passerine species have relatively few MHC gene copies compared to passerines. Additionally, comparative studies that have looked at partial MHC sequences have speculated that non-passerines have opposite patterns of selection on MHC class I (MHC-I) and class II (MHC-II) loci than passerines: namely, greater sequence diversity and signals of selection on MHC-II than MHC-I. However, new sequencing technology is revealing much greater MHC variation than previously expected while also facilitating full sequence variant detection directly from genomic data. Our study aims to take advantage of high-throughput sequencing methods to fully characterize both classes and domains of MHC of a non-passerine bird of prey, the common buzzard (Buteo buteo), to test predictions of MHC variation and differential selection on MHC classes. RESULTS Using genetic, genomic, and transcriptomic high-throughput sequencing data, we established common buzzards have at least three loci that produce functional alleles at both MHC classes. In total, we characterize 91 alleles from 113 common buzzard chicks for MHC-I exon 3 and 41 alleles from 125 chicks for MHC-IIB exon 2. Among these alleles, we found greater sequence polymorphism and stronger diversifying selection at MHC-IIB exon 2 than MHC-I exon 3, suggesting differential selection pressures on MHC classes. However, upon further investigation of the entire peptide-binding groove by including genomic data from MHC-I exon 2 and MHC-IIA exon 2, this turned out to be false. MHC-I exon 2 was as polymorphic as MHC-IIB exon 2 and MHC-IIA exon 2 was essentially invariant. Thus, comparisons between MHC-I and MHC-II that included both domains of the peptide-binding groove showed no differences in polymorphism nor diversifying selection between the classes. Nevertheless, selection analysis indicates balancing selection has been acting on common buzzard MHC and phylogenetic inference revealed that trans-species polymorphism is present between common buzzards and species separated for over 33 million years for class I and class II. CONCLUSIONS We characterize and confirm the functionality of unexpectedly high copy number and allelic diversity in both MHC classes of a bird of prey. While balancing selection is acting on both classes, there is no evidence of differential selection pressure on MHC classes in common buzzards and this result may hold more generally once more data for understudied MHC exons becomes available.
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Affiliation(s)
- Jamie Winternitz
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
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16
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Gaigher A, Rota A, Neves F, Muñoz-Mérida A, Blasco-Aróstegui J, Almeida T, Veríssimo A. Extensive MHC class IIβ diversity across multiple loci in the small-spotted catshark (Scyliorhinus canicula). Sci Rep 2023; 13:3837. [PMID: 36882519 PMCID: PMC9992475 DOI: 10.1038/s41598-023-30876-6] [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: 12/20/2022] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
The major histocompatibility complex (MHC) is a multigene family responsible for pathogen detection, and initiation of adaptive immune responses. Duplication, natural selection, recombination, and their resulting high functional genetic diversity spread across several duplicated loci are the main hallmarks of the MHC. Although these features were described in several jawed vertebrate lineages, a detailed MHC IIβ characterization at the population level is still lacking for chondrichthyans (chimaeras, rays and sharks), i.e. the most basal lineage to possess an MHC-based adaptive immune system. We used the small-spotted catshark (Scyliorhinus canicula, Carcharhiniformes) as a case-study species to characterize MHC IIβ diversity using complementary molecular tools, including publicly available genome and transcriptome datasets, and a newly developed high-throughput Illumina sequencing protocol. We identified three MHC IIβ loci within the same genomic region, all of which are expressed in different tissues. Genetic screening of the exon 2 in 41 individuals of S. canicula from a single population revealed high levels of sequence diversity, evidence for positive selection, and footprints of recombination. Moreover, the results also suggest the presence of copy number variation in MHC IIβ genes. Thus, the small-spotted catshark exhibits characteristics of functional MHC IIβ genes typically observed in other jawed vertebrates.
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Affiliation(s)
- Arnaud Gaigher
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany.
| | - Alessia Rota
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Fabiana Neves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Javier Blasco-Aróstegui
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Faculty of Sciences, University of Lisbon, Campo Grande 016, 1749-016, Lisbon, Portugal
| | - Tereza Almeida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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17
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Wild Boar (Sus scrofa)—Fascioloides magna Interaction from the Perspective of the MHC Genes. Pathogens 2022; 11:pathogens11111359. [DOI: 10.3390/pathogens11111359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022] Open
Abstract
Fascioloidosis is a parasitic disease caused by a trematode Fascioloides magna. Since major histocompatibility complex (MHC) genes play an important role in the immune response, the aim of this study was to compare the potential differences in MHC class II SLA-DRB1 exon 2 genes between wild boar populations from infected (cases) and non-infected areas (controls). During the winter of 2021, a total of 136 wild boar tissue samples were collected, 39 cases and 97 controls. DNA was extracted and sequenced using the Illumina platform. Differences in distributions of allele combinations were calculated using the Chi-Square test for homogeneity and between proportions using the large-sample test and Fisher–Irwin test. Analysis revealed 19 previously described swine leucocyte antigen (SLA) alleles. The number of polymorphic sites was 79 (29.6%), with 99 mutations in total. Nucleotide diversity π was estimated at 0.11. Proportions of the alleles SLA-DRB1*12:05 (p = 0.0008379) and SLA-DRB1*0101 (p = 0.0002825) were statistically significantly higher in controls, and proportions of the SLA-DRB1*0602 (p = 0.006059) and SLA-DRB1*0901 (p = 0.0006601) in cases. Alleles SLA-DRB1*04:09, SLA-DRB1*0501, SLA-DRB1*11:09, and SLA-DRB1*1301 were detected only in cases, while SLA-DRB1*0404, SLA-DRB1*0701, SLA-DRB1*02:10, and SLA-DRB1*04:08 were present only in controls. We did not confirm the existence of specific alleles that could be linked to F. magna infection. Detected high variability of the MHC class II SLA-DRB1 exon 2 genes indicate high resistance potential against various pathogens.
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Evaluation of Genetic Diversity and Parasite-Mediated Selection of MHC Class I Genes in Emberiza godlewskii (Passeriformes: Emberizidae). DIVERSITY 2022. [DOI: 10.3390/d14110925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The major histocompatibility complex (MHC) is a multi-copy immune gene family in vertebrates. Its genes are highly variable and code for antigen-presenting molecules. Characterization of MHC genes in different species and investigating the mechanisms that shape MHC diversity is an important goal in understanding the evolution of biological diversity. Here we developed a next-generation sequencing (NGS) protocol to genotype the MHC class I genes of 326 Godlewski’s buntings (Emberiza godlewskii) sampled in the Western mountain area of Beijing from 2014 to 2016. A total of 184 functional alleles were identified, including both non-classical and classical alleles, clustering into nine supertypes. Compared with other passerine birds, the number of MHC class I alleles per individual in Godlewski’s buntings is high (mean 16.1 ± 3.3, median 16). In addition, we demonstrated signatures of historical and contemporary selection on MHC genes. Reflecting historical selection, ten amino acid sites in the antigen-binding domain showed signatures of balancing selection, eight of which exhibit high amino acid polymorphism. In terms of contemporary selection, we found that specific MHC supertypes were nominally associated with the infection of two malaria parasite lineages. These findings indicate the action of historical and possibly also contemporary balancing selection and suggest negative frequency-dependent or fluctuating selection as possible selection mechanisms.
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19
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Minias P, Palomar G, Dudek K, Babik W. Salamanders reveal novel trajectories of amphibian MHC evolution. Evolution 2022; 76:2436-2449. [PMID: 36000494 DOI: 10.1111/evo.14601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 07/06/2022] [Accepted: 07/29/2022] [Indexed: 01/22/2023]
Abstract
Genes of the major histocompatibility complex (MHC) code for immune proteins that are crucial for pathogen recognition in vertebrates. MHC research in nonmodel taxa has long been hampered by its genomic complexity that makes the locus-specific genotyping challenging. The recent progress in sequencing and genotyping methodologies allows an extensive phylogenetic coverage in studies of MHC evolution. Here, we analyzed the peptide-binding region of MHC class I (MHC-I) in 30 species of salamanders from six families representative of Urodela phylogeny. This extensive dataset revealed an extreme diversity of MHC-I in salamanders, both in terms of sequence diversity (about 3000 variants) and architecture (2-22 gene copies per species). The signal of positive selection was moderate and consistent between both peptide-binding domains, but varied greatly between genera. Positions of positively selected sites mostly coincided with human peptide-binding sites, suggesting similar structural properties of MHC-I molecules across distant vertebrate lineages. Finally, we provided evidence for the common intraexonic recombination at MHC-I and for the role of life history traits in the processes of MHC-I expansion/contraction. Our study revealed novel evolutionary trajectories of amphibian MHC and it contributes to the understanding of the mechanisms that generated extraordinary MHC diversity throughout vertebrate evolution.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland
| | - Gemma Palomar
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland.,Parasitology Unit, Department of Biomedicine and Biotechnology, Faculty of Pharmacy, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid, 28805, Spain
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, 30-387, Poland
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20
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Performance Comparison of Different Approaches in Genotyping MHC-DRB: The Contrast between Single-Locus and Multi-Locus Species. Animals (Basel) 2022; 12:ani12182452. [PMID: 36139311 PMCID: PMC9495155 DOI: 10.3390/ani12182452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Major histocompatibility complex (MHC) genes are widely recognised as valuable markers for wildlife genetic studies given their extreme polymorphism and functional importance in fitness-related traits. Newly developed genotyping methods, which rely on the use of next-generation sequencing (NGS), are gradually replacing traditional cloning and Sanger sequencing methods in MHC genotyping studies. Allele calling in NGS methods remains challenging due to extreme polymorphism and locus multiplication in the MHC coupled with allele amplification bias and the generation of artificial sequences. In this study, we compared the performance of molecular cloning with Illumina and Ion Torrent NGS sequencing in MHC-DRB genotyping of single-locus species (roe deer) and species with multiple DRB loci (red deer) in an attempt to adopt a reliable and straightforward method that does not require complex bioinformatic analyses. Our results show that all methods work similarly well in roe deer, but we demonstrate non-consistency in results across methods in red deer. With Illumina sequencing, we detected a maximum number of alleles in 10 red deer individuals (42), while other methods were somewhat less accurate as they scored 69–81% of alleles detected with Illumina sequencing.
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21
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LaFond J, Martin KR, Dahn H, Richmond JQ, Murphy RW, Rollinson N, Savage AE. Invasive Bullfrogs Maintain MHC Polymorphism Including Alleles Associated with Chytrid Fungal Infection. Integr Comp Biol 2022; 62:262-274. [PMID: 35588059 DOI: 10.1093/icb/icac044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across theinvasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.
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Affiliation(s)
- Jacob LaFond
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
- Department of Biology, University of Tampa, Tampa, FL 33606, USA
| | - Katherine R Martin
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Hollis Dahn
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Jonathan Q Richmond
- U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego, CA 92101, USA
| | - Robert W Murphy
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Njal Rollinson
- Department of Biology, University of Toronto, Toronto, ON, Canada
| | - Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
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22
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Patarroyo MA, Patarroyo ME, Pabón L, Alba MP, Bermudez A, Rugeles MT, Díaz-Arevalo D, Zapata-Builes W, Zapata MI, Reyes C, Suarez CF, Agudelo W, López C, Aza-Conde J, Melo M, Escamilla L, Oviedo J, Guzmán F, Silva Y, Forero M, Flórez-Álvarez L, Aguilar-Jimenez W, Moreno-Vranich A, Garry J, Avendaño C. SM-COLSARSPROT: Highly Immunogenic Supramutational Synthetic Peptides Covering the World's Population. Front Immunol 2022; 13:859905. [PMID: 35693819 PMCID: PMC9175637 DOI: 10.3389/fimmu.2022.859905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Fifty ~20-amino acid (aa)-long peptides were selected from functionally relevant SARS-CoV-2 S, M, and E proteins for trial B-21 and another 53 common ones, plus some new ones derived from the virus' main genetic variants for complementary trial C-21. Peptide selection was based on tremendous SARS-CoV-2 genetic variability for analysing them concerning vast human immunogenetic polymorphism for developing the first supramutational, Colombian SARS-protection (SM-COLSARSPROT), peptide mixture. Specific physicochemical rules were followed, i.e., aa predilection for polyproline type II left-handed (PPIIL) formation, replacing β-branched, aromatic aa, short-chain backbone H-bond-forming residues, π-π interactions (n→π* and π-CH), aa interaction with π systems, and molecular fragments able to interact with them, disrupting PPIIL propensity formation. All these modified structures had PPIIL formation propensity to enable target peptide interaction with human leukocyte antigen-DRβ1* (HLA-DRβ1*) molecules to mediate antigen presentation and induce an appropriate immune response. Such modified peptides were designed for human use; however, they induced high antibody titres against S, M, and E parental mutant peptides and neutralising antibodies when suitably modified and chemically synthesised for immunising 61 major histocompatibility complex class II (MHCII) DNA genotyped Aotus monkeys (matched with their corresponding HLA-DRβ1* molecules), predicted to cover 77.5% to 83.1% of the world's population. Such chemically synthesised peptide mixture represents an extremely pure, stable, reliable, and cheap vaccine for COVID-19 pandemic control, providing a new approach for a logical, rational, and soundly established methodology for other vaccine development.
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Affiliation(s)
- Manuel A. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel E. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabón
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P. Alba
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Adriana Bermudez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Diana Díaz-Arevalo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Isabel Zapata
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - César Reyes
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carlos F. Suarez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - William Agudelo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carolina López
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Miguel Melo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Luis Escamilla
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jairo Oviedo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Fanny Guzmán
- Núcleo de Biotecnología, Pontificia U. Católica de Valparaíso, Valparaíso, Chile
| | - Yolanda Silva
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Armando Moreno-Vranich
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jason Garry
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Facultad de Ciencias Agropecualrias, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
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23
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Antoł W, Palka JK, Sychta K, Dudek K, Prokop ZM. Gene conversion restores selfing in experimentally evolving C. elegans populations with fog-2 loss-of-function mutation. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000569. [PMID: 35601754 PMCID: PMC9121179 DOI: 10.17912/micropub.biology.000569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022]
Abstract
We have discovered a new case of gene conversion restoring ability of self-fertilization in obligatory outcrossing
Caenorhabditis elegans
populations. The
fog-2(q71)
mutation, used to transform the nematodes’ mating system from mostly self-fertilization to obligatory outcrossing, was spontaneously removed by replacing a fragment of
fog-2
gene with a fragment of its paralog,
ftr-1
. This has occurred spontaneously in experimental evolution with large populations, evolving with
fog-2(q71)
mutation for over a hundred generations, without addition mutagens or other factors promoting mutation accumulation. A converted
fog-2
allele restoring hermaphrodite sperm production was detected in five experimental populations. This raises the question about stability of obligatory outcrossing populations in long-term experiments.
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Affiliation(s)
- Weronika Antoł
- Jagiellonian University in Kraków, Institute of Environmental Sciences, Poland
,
Correspondence to: Weronika Antoł (
)
| | - Joanna K. Palka
- Jagiellonian University in Kraków, Institute of Environmental Sciences, Poland
| | - Karolina Sychta
- Jagiellonian University in Kraków, Institute of Environmental Sciences, Poland
,
Polish Academy of Sciences, Institute of Systematics and Evolution of Animals, Poland
| | - Katarzyna Dudek
- Jagiellonian University in Kraków, Institute of Environmental Sciences, Poland
| | - Zofia M. Prokop
- Jagiellonian University in Kraków, Institute of Environmental Sciences, Poland
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24
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Pikus E, Dunn PO, Minias P. High MHC diversity confers no advantage for phenotypic quality and reproductive performance in a wild bird. J Anim Ecol 2022; 91:1707-1718. [PMID: 35521665 PMCID: PMC9542035 DOI: 10.1111/1365-2656.13737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/24/2022] [Indexed: 11/28/2022]
Abstract
1. Genes of the major histocompatibility complex (MHC) encode antigen binding molecules and are an integral part of the acquired immune response of vertebrates. In general, high individual MHC diversity is expected to increase fitness by broadening the spectrum of pathogens recognized by the immune system, in accordance with the heterozygote advantage mechanism. On the other hand, the optimality hypothesis assumes that individuals with optimal (intermediate), rather than maximum diversity of the MHC will achieve the highest fitness because of inherent costs associated with expressing diverse MHC alleles. 2. Here, we tested for associations between individual diversity of the MHC class I and class II genes (binding antigens of intra- and extra-cellular pathogens, respectively) and a range of fitness-related traits (condition, ornament expression and reproduction) in an urban population of the Eurasian coot Fulica atra. 3. Contrary to our expectation, we found that high within-individual allelic diversity of MHC genes (both class I and II) was associated with poorer condition (lower blood haemoglobin concentrations), weaker expression of the putative ornament (smaller frontal shield), later onset of breeding and smaller clutches. An analysis of functional MHC allele clusters (supertypes) provided further support for negative associations of MHC diversity with phenotypic quality and reproductive performance, but most of these relationships could not be explained by the presence of specific maladaptive supertypes. Finally, we found little empirical support for the optimality hypothesis in the Eurasian coot. 4. Our results suggest that the costs of high MHC diversity outweighed any benefits associated with broad MHC repertoire, which could be driven by depauperate pathogen diversity in an urban landscape. To the best of our knowledge, this is one of the first studies providing consistent evidence for negative associations of MHC diversity with a range of fitness-related traits in a natural avian population.
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Affiliation(s)
- Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-, Milwaukee
| | - Piotr Minias
- 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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25
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Using de novo genome assembly and high-throughput sequencing to characterize the MHC region in a non-model bird, the Eurasian coot. Sci Rep 2022; 12:7031. [PMID: 35488050 PMCID: PMC9054815 DOI: 10.1038/s41598-022-11018-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
Genes of the Major Histocompatibility Complex (MHC) form a key component of vertebrate adaptive immunity, as they code for molecules which bind antigens of intra- and extracellular pathogens (MHC class I and II, respectively) and present them to T cell receptors. In general, MHC genes are hyper-polymorphic and high MHC diversity is often maintained within natural populations (via balancing selection) and within individuals (via gene duplications). Because of its complex architecture with tandems of duplicated genes, characterization of MHC region in non-model vertebrate species still poses a major challenge. Here, we combined de novo genome assembly and high-throughput sequencing to characterize MHC polymorphism in a rallid bird species, the Eurasian coot Fulica atra. An analysis of genome assembly indicated high duplication rate at MHC-I, which was also supported by targeted sequencing of peptide-binding exons (at least five MHC-I loci genotyped). We found high allelic richness at both MHC-I and MHC-II, although signature of diversifying selection and recombination (gene conversion) was much stronger at MHC-II. Our results indicate that Eurasian coot retains extraordinary polymorphism at both MHC classes (when compared to other non-passerine bird species), although they may be subject to different evolutionary mechanism.
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26
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Selection and demography drive range-wide patterns of MHC-DRB variation in mule deer. BMC Ecol Evol 2022; 22:42. [PMID: 35387584 PMCID: PMC8988406 DOI: 10.1186/s12862-022-01998-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Standing genetic variation is important especially in immune response-related genes because of threats to wild populations like the emergence of novel pathogens. Genetic variation at the major histocompatibility complex (MHC), which is crucial in activating the adaptive immune response, is influenced by both natural selection and historical population demography, and their relative roles can be difficult to disentangle. To provide insight into the influences of natural selection and demography on MHC evolution in large populations, we analyzed geographic patterns of variation at the MHC class II DRB exon 2 locus in mule deer (Odocoileus hemionus) using sequence data collected across their entire broad range. RESULTS We identified 31 new MHC-DRB alleles which were phylogenetically similar to other cervid MHC alleles, and one allele that was shared with white-tailed deer (Odocoileus virginianus). We found evidence for selection on the MHC including high dN/dS ratios, positive neutrality tests, deviations from Hardy-Weinberg Equilibrium (HWE) and a stronger pattern of isolation-by-distance (IBD) than expected under neutrality. Historical demography also shaped variation at the MHC, as indicated by similar spatial patterns of variation between MHC and microsatellite loci and a lack of association between genetic variation at either locus type and environmental variables. CONCLUSIONS Our results show that both natural selection and historical demography are important drivers in the evolution of the MHC in mule deer and work together to shape functional variation and the evolution of the adaptive immune response in large, well-connected populations.
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27
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Bracamonte SE, Hofmann MJ, Lozano-Martín C, Eizaguirre C, Barluenga M. Divergent and non-parallel evolution of MHC IIB in the Neotropical Midas cichlid species complex. BMC Ecol Evol 2022; 22:41. [PMID: 35365100 PMCID: PMC8974093 DOI: 10.1186/s12862-022-01997-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/21/2022] [Indexed: 01/09/2023] Open
Abstract
Background Ecological diversification is the result of divergent natural selection by contrasting habitat characteristics that favours the evolution of distinct phenotypes. This process can happen in sympatry and in allopatry. Habitat-specific parasite communities have the potential to drive diversification among host populations by imposing selective pressures on their host's immune system. In particular, the hyperdiverse genes of the major histocompatibility complex (MHC) are implicated in parasite-mediated host divergence. Here, we studied the extent of divergence at MHC, and discuss how it may have contributed to the Nicaraguan Midas cichlid species complex diversification, one of the most convincing examples of rapid sympatric parallel speciation. Results We genotyped the MHC IIB for individuals from six sympatric Midas cichlid assemblages, each containing species that have adapted to exploit similar habitats. We recovered large allelic and functional diversity within the species complex. While most alleles were rare, functional groups of alleles (supertypes) were common, suggesting that they are key to survival and that they were maintained during colonization and subsequent radiations. We identified lake-specific and habitat-specific signatures for both allelic and functional diversity, but no clear pattern of parallel divergence among ecomorphologically similar phenotypes. Conclusions Colonization and demographic effects of the fish could have contributed to MHC evolution in the Midas cichlid in conjunction with habitat-specific selective pressures, such as parasites associated to alternative preys or environmental features. Additional ecological data will help evaluating the role of host–parasite interactions in the Midas cichlid radiations and aid in elucidating the potential role of non-parallel features differentiating crater lake species assemblages. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01997-9.
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Affiliation(s)
- Seraina E Bracamonte
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Carlos Lozano-Martín
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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Buzan E, Potušek S, Duniš L, Pokorny B. Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia. Animals (Basel) 2022; 12:ani12060723. [PMID: 35327121 PMCID: PMC8944837 DOI: 10.3390/ani12060723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/23/2022] [Accepted: 03/10/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Disease prevention and appropriate wildlife management are among the major challenges in wildlife conservation. In the present study, we made a first assessment of the variability of major histocompatibility complex (MHC) genes in roe deer in Slovenia and evaluated local population adaptation by comparing MHC variability with neutral microsatellites. We discovered three new MHC DRB exon 2 alleles in addition to seven previously described in the literature. Moreover, we found evidence of historical positive selection, as selection analysis indicated that approx. 10% of the encoded amino acids were subjected to episodic positive selection. This study provides the basis for further research on immunogenetic variation in roe deer and highlights opportunities to incorporate genetic data into science-based population management. Abstract Disease control and containment in free-ranging populations is one of the greatest challenges in wildlife management. Despite the importance of major histocompatibility complex (MHC) genes for immune response, an assessment of the diversity and occurrence of these genes is still rare in European roe deer, the most abundant and widespread large mammal in Europe. Therefore, we examined immunogenetic variation in roe deer in Slovenia to identify species adaptation by comparing the genetic diversity of the MHC genes with the data on neutral microsatellites. We found ten MHC DRB alleles, three of which are novel. Evidence for historical positive selection on the MHC was found using the maximum likelihood codon method. Patterns of MHC allelic distribution were not congruent with neutral population genetic findings. The lack of population genetic differentiation in MHC genes compared to existing structure in neutral markers suggests that MHC polymorphism was influenced primarily by balancing selection and, to a lesser extent, by neutral processes such as genetic drift, with no clear evidence of local adaptation. Selection analyses indicated that approx. 10% of amino acids encoded under episodic positive selection. This study represents one of the first steps towards establishing an immunogenetic map of roe deer populations across Europe, aiming to better support science-based management of this important game species.
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Affiliation(s)
- Elena Buzan
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
- Environmental Protection College, Trg Mladosti 7, 3320 Velenje, Slovenia;
- Correspondence: ; Tel.: +38-65-6117570; Fax: +38-65-61175
| | - Sandra Potušek
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
| | - Luka Duniš
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
| | - Boštjan Pokorny
- Environmental Protection College, Trg Mladosti 7, 3320 Velenje, Slovenia;
- Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia
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29
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Ratcliffe FC, Garcia de Leaniz C, Consuegra S. MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax). Anim Genet 2022; 53:340-351. [PMID: 35274334 PMCID: PMC9314080 DOI: 10.1111/age.13184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/13/2022] [Accepted: 02/20/2022] [Indexed: 01/29/2023]
Abstract
Identifying population structuring in highly fecund marine species with high dispersal rates is challenging, but critical for conservation and stock delimitation for fisheries management. European sea bass (Dicentrarchus labrax) is a commercial species of fisheries and aquaculture relevance whose stocks are declining in the North Atlantic, despite management measures to protect them and identifying their fine population structure is needed for managing their exploitation. As for other marine fishes, neutral genetic markers indicate that eastern Atlantic sea bass form a panmictic population and is currently managed as arbitrarily divided stocks. The genes of the major histocompatibility complex (MHC) are key components of the adaptive immune system and ideal candidates to assess fine structuring arising from local selective pressures. We used Illumina sequencing to characterise allelic composition and signatures of selection at the MHC class I-α region of six D. labrax populations across the Atlantic range. We found high allelic diversity driven by positive selection, corresponding to moderate supertype diversity, with 131 alleles clustering into four to eight supertypes, depending on the Bayesian information criterion threshold applied, and a mean number of 13 alleles per individual. Alleles could not be assigned to particular loci, but private alleles allowed us to detect regional genetic structuring not found previously using neutral markers. Our results suggest that MHC markers can be used to detect cryptic population structuring in marine species where neutral markers fail to identify differentiation. This is particularly critical for fisheries management, and of potential use for selective breeding or identifying escapes from sea farms.
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Affiliation(s)
- Frances C Ratcliffe
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | | | - Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
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30
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Davies CS, Worsley SF, Maher KH, Komdeur J, Burke T, Dugdale HL, Richardson DS. Immunogenetic variation shapes the gut microbiome in a natural vertebrate population. MICROBIOME 2022; 10:41. [PMID: 35256003 PMCID: PMC8903650 DOI: 10.1186/s40168-022-01233-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The gut microbiome (GM) can influence many biological processes in the host, impacting its health and survival, but the GM can also be influenced by the host's traits. In vertebrates, Major Histocompatibility Complex (MHC) genes play a pivotal role in combatting pathogens and are thought to shape the host's GM. Despite this-and the documented importance of both GM and MHC variation to individual fitness-few studies have investigated the association between the GM and MHC in the wild. RESULTS We characterised MHC class I (MHC-I), MHC class II (MHC-II) and GM variation in individuals within a natural population of the Seychelles warbler (Acrocephalus sechellensis). We determined how the diversity and composition of the GM varied with MHC characteristics, in addition to environmental factors and other host traits. Our results show that the presence of specific MHC alleles, but not MHC diversity, influences both the diversity and composition of the GM in this population. MHC-I alleles, rather than MHC-II alleles, had the greatest impact on the GM. GM diversity was negatively associated with the presence of three MHC-I alleles (Ase-ua3, Ase-ua4, Ase-ua5), and one MHC-II allele (Ase-dab4), while changes in GM composition were associated with the presence of four different MHC-I alleles (Ase-ua1, Ase-ua7, Ase-ua10, Ase-ua11). There were no associations between GM diversity and TLR3 genotype, but GM diversity was positively correlated with genome-wide heterozygosity and varied with host age and field period. CONCLUSIONS These results suggest that components of the host's immune system play a role in shaping the GM of wild animals. Host genotype-specifically MHC-I and to a lesser degree MHC-II variation-can modulate the GM, although whether this occurs directly, or indirectly through effects on host health, is unclear. Importantly, if immune genes can regulate host health through modulation of the microbiome, then it is plausible that the microbiome could also influence selection on immune genes. As such, host-microbiome coevolution may play a role in maintaining functional immunogenetic variation within natural vertebrate populations. Video abstract.
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Affiliation(s)
- Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Kathryn H Maher
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles
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Martin KR, Mansfield KL, Savage AE. Adaptive evolution of major histocompatibility complex class I immune genes and disease associations in coastal juvenile sea turtles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211190. [PMID: 35154791 PMCID: PMC8825991 DOI: 10.1098/rsos.211190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/06/2022] [Indexed: 05/12/2023]
Abstract
Characterizing polymorphism at the major histocompatibility complex (MHC) genes is key to understanding the vertebrate immune response to disease. Despite being globally afflicted by the infectious tumour disease fibropapillomatosis (FP), immunogenetic variation in sea turtles is minimally explored. We sequenced the α 1 peptide-binding region of MHC class I genes (162 bp) from 268 juvenile green (Chelonia mydas) and 88 loggerhead (Caretta caretta) sea turtles in Florida, USA. We recovered extensive variation (116 alleles) and trans-species polymorphism. Supertyping analysis uncovered three functional MHC supertypes corresponding to the three well-supported clades in the phylogeny. We found significant evidence of positive selection at seven amino acid sites in the class I exon. Random forest modelling and risk ratio analysis of Ch. mydas alleles uncovered one allele weakly associated with smooth FP tumour texture, which may be associated with disease outcome. Our study represents the first characterization of MHC class I diversity in Ch. mydas and the largest sample of sea turtles used to date in any study of adaptive genetic variation, revealing tremendous genetic variation and high adaptive potential to viral pathogen threats. The novel associations we identified between MHC diversity and FP outcomes in sea turtles further highlight the importance of evaluating genetic predictors of disease, including MHC and other functional markers.
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Affiliation(s)
- Katherine R. Martin
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Katherine L. Mansfield
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
| | - Anna E. Savage
- Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA
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Individual copy number variation and extensive diversity between major MHC-DAB1 allelic lineages in the European bitterling. Immunogenetics 2022; 74:497-505. [PMID: 35015128 PMCID: PMC9467946 DOI: 10.1007/s00251-021-01251-4] [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: 11/08/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022]
Abstract
Polymorphism of the major histocompatibility complex (MHC), DAB1 gene was characterized for the first time in the European bitterling (Rhodeus amarus), a freshwater fish employed in studies of host-parasite coevolution and mate choice, taking advantage of newly designed primers coupled with high-throughput amplicon sequencing. Across 221 genotyped individuals, we detected 1–4 variants per fish, with 28% individuals possessing 3–4 variants. We identified 36 DAB1 variants, and they showed high sequence diversity mostly located within predicted antigen-binding sites, and both global and codon-specific excess of non-synonymous mutations. Despite deep divergence between two major allelic lineages, functional diversity was surprisingly low (3 supertypes). Overall, these findings suggest the role of positive and balancing selection in promotion and long-time maintenance of DAB1 polymorphism. Further investigations will clarify the role of pathogen-mediated selection to drive the evolution of DAB1 variation.
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Ning Y, Roberts NJ, Qi J, Peng Z, Long Z, Zhou S, Gu J, Hou Z, Yang E, Ren Y, Lang J, Liang Z, Zhang M, Ma J, Jiang G. Inbreeding status and implications for Amur tigers. Anim Conserv 2021. [DOI: 10.1111/acv.12761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Y. Ning
- College of Life Science Jilin Agricultural University Changchun China
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - N. J. Roberts
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - J. Qi
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
- School of Forestry Northeast Forestry University Harbin China
| | - Z. Peng
- School of Basic Medical Sciences Nanchang University Nanchang China
| | - Z. Long
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - S. Zhou
- Heilongjiang Research Institute of Wildlife Harbin China
| | - J. Gu
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - Z. Hou
- College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - E. Yang
- Wildlife Conservation Society Hunchun China
| | - Y. Ren
- Wildlife Conservation Society Hunchun China
| | - J. Lang
- Jilin Hunchun Amur Tiger National Nature Reserve Hunchun China
| | - Z. Liang
- Heilongjiang Laoyeling Amur Tiger National Nature Reserve Dongning China
| | - M. Zhang
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - J. Ma
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - G. Jiang
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
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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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Pikus E, Włodarczyk R, Jedlikowski J, Minias P. Urbanization processes drive divergence at the major histocompatibility complex in a common waterbird. PeerJ 2021; 9:e12264. [PMID: 34707940 PMCID: PMC8500109 DOI: 10.7717/peerj.12264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/16/2021] [Indexed: 11/20/2022] Open
Abstract
Urban sprawl is one of the most common landscape alterations occurring worldwide, and there is a growing list of species that are recognised to have adapted to urban life. To be successful, processes of urban colonization by wildlife require a broad spectrum of phenotypic (e.g., behavioural or physiological) adjustments, but evidence for genetic adaptations is much scarcer. One hypothesis proposes that different pathogen-driven selective pressures between urban and non-urban landscapes leads to adaptations in host immune genes. Here, we examined urbanization-related differentiation at the key pathogen-recognition genes of vertebrate adaptive immunity-the major histocompatibility complex (MHC)-in a common waterbird, the Eurasian coot (Fulica atra). Samples were collected from an old urban population (established before the 1950s), a new urban population (established in the 2000s), and two rural populations from central Poland. We found strong significant divergence (as measured with Jost's D) at the MHC class II between the old urban population and the remaining (new urban and rural) populations. Also, there was a moderate, but significant divergence at the MHC between the new urban population and two rural populations, while no divergence was found between the two rural populations. The total number of MHC alleles and the number of private (population-specific) MHC alleles was lower in old urban populations, as compared to the rural ones. These patterns of differentiation at the MHC were not consistent with patterns found for neutral genetic markers (microsatellites), which showed few differences between the populations. Our results indicate that MHC allele composition depended on the level of anthropogenic disturbance and the time which passed since urban colonization, possibly due to the processes of genotype sorting and local adaptation. As such, our study contributes to the understanding of genetic mechanisms associated with urbanization processes in wildlife.
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Affiliation(s)
- Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
| | - Jan Jedlikowski
- Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
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Salado I, Fernández-Gil A, Vilà C, Leonard JA. Automated genotyping of microsatellite loci from feces with high throughput sequences. PLoS One 2021; 16:e0258906. [PMID: 34695152 PMCID: PMC8544849 DOI: 10.1371/journal.pone.0258906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions.
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Affiliation(s)
- Isabel Salado
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- * E-mail: (JAL); (IS)
| | - Alberto Fernández-Gil
- Department of Conservation Biology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- * E-mail: (JAL); (IS)
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Patarroyo ME, Patarroyo MA, Alba MP, Pabon L, Rugeles MT, Aguilar-Jimenez W, Florez L, Bermudez A, Rout AK, Griesinger C, Suarez CF, Aza-Conde J, Reyes C, Avendaño C, Samacá J, Camargo A, Silva Y, Forero M, Gonzalez E. The First Chemically-Synthesised, Highly Immunogenic Anti-SARS-CoV-2 Peptides in DNA Genotyped Aotus Monkeys for Human Use. Front Immunol 2021; 12:724060. [PMID: 34539660 PMCID: PMC8446425 DOI: 10.3389/fimmu.2021.724060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Thirty-five peptides selected from functionally-relevant SARS-CoV-2 spike (S), membrane (M), and envelope (E) proteins were suitably modified for immunising MHC class II (MHCII) DNA-genotyped Aotus monkeys and matched with HLA-DRβ1* molecules for use in humans. This was aimed at producing the first minimal subunit-based, chemically-synthesised, immunogenic molecules (COLSARSPROT) covering several HLA alleles. They were predicted to cover 48.25% of the world’s population for 6 weeks (short-term) and 33.65% for 15 weeks (long-lasting) as they induced very high immunofluorescent antibody (IFA) and ELISA titres against S, M and E parental native peptides, SARS-CoV-2 neutralising antibodies and host cell infection. The same immunological methods that led to identifying new peptides for inclusion in the COLSARSPROT mixture were used for antigenicity studies. Peptides were analysed with serum samples from patients suffering mild or severe SARS-CoV-2 infection, thereby increasing chemically-synthesised peptides’ potential coverage for the world populations up to 62.9%. These peptides’ 3D structural analysis (by 1H-NMR acquired at 600 to 900 MHz) suggested structural-functional immunological association. This first multi-protein, multi-epitope, minimal subunit-based, chemically-synthesised, highly immunogenic peptide mixture highlights such chemical synthesis methodology’s potential for rapidly obtaining very pure, highly reproducible, stable, cheap, easily-modifiable peptides for inducing immune protection against COVID-19, covering a substantial percentage of the human population.
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Affiliation(s)
- Manuel E Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Universidad Santo Tomás, Bogotá, Colombia
| | - Manuel A Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P Alba
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabon
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María T Rugeles
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Colombia
| | | | - Lizdany Florez
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Colombia
| | - Adriana Bermudez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Ashok K Rout
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carlos F Suarez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - César Reyes
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Jhoan Samacá
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Anny Camargo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Yolanda Silva
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Edgardo Gonzalez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
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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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39
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Phillips KP, Cable J, Mohammed RS, Chmielewski S, Przesmycka KJ, van Oosterhout C, Radwan J. Functional immunogenetic variation, rather than local adaptation, predicts ectoparasite infection intensity in a model fish species. Mol Ecol 2021; 30:5588-5604. [PMID: 34415650 PMCID: PMC9292977 DOI: 10.1111/mec.16135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/07/2021] [Accepted: 08/11/2021] [Indexed: 11/28/2022]
Abstract
Natural host populations differ in their susceptibility to infection by parasites, and these intrapopulation differences are still an incompletely understood component of host‐parasite dynamics. In this study, we used controlled infection experiments with wild‐caught guppies (Poecilia reticulata) and their ectoparasite Gyrodactylus turnbulli to investigate the roles of local adaptation and host genetic composition (immunogenetic and neutral) in explaining differences in susceptibility to infection. We found differences between our four study host populations that were consistent between two parasite source populations, with no indication of local adaptation by either host or parasite at two tested spatial scales. Greater values of host population genetic variability metrics broadly aligned with lower population mean infection intensity, with the best alignments associated with major histocompatibility complex (MHC) “supertypes”. Controlling for intrapopulation differences and potential inbreeding variance, we found a significant negative relationship between individual‐level functional MHC variability and infection: fish carrying more MHC supertypes experienced infections of lower severity, with limited evidence for supertype‐specific effects. We conclude that population‐level differences in host infection susceptibility probably reflect variation in parasite selective pressure and/or host evolutionary potential, underpinned by functional immunogenetic variation.
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Affiliation(s)
- Karl P Phillips
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.,School of Biological Earth & Environmental Sciences, University College Cork, Cork, Ireland.,Marine Institute, Newport, Co. Mayo, Ireland
| | - Joanne Cable
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Ryan S Mohammed
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.,Department of Life Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Sebastian Chmielewski
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Karolina J Przesmycka
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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40
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Palomar G, Dudek K, Migalska M, Arntzen JW, Ficetola GF, Jelić D, Jockusch E, Martínez-Solano I, Matsunami M, Shaffer HB, Vörös J, Waldman B, Wielstra B, Babik W. Coevolution between MHC class I and Antigen Processing Genes in salamanders. Mol Biol Evol 2021; 38:5092-5106. [PMID: 34375431 PMCID: PMC8557411 DOI: 10.1093/molbev/msab237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins encoded by antigen-processing genes (APGs) provide major histocompatibility complex (MHC) class I (MHC-I) with antigenic peptides. In mammals, polymorphic multigenic MHC-I family is served by monomorphic APGs, whereas in certain nonmammalian species both MHC-I and APGs are polymorphic and coevolve within stable haplotypes. Coevolution was suggested as an ancestral gnathostome feature, presumably enabling only a single highly expressed classical MHC-I gene. In this view coevolution, while optimizing some aspects of adaptive immunity, would also limit its flexibility by preventing the expansion of classical MHC-I into a multigene family. However, some nonmammalian taxa, such as salamanders, have multiple highly expressed MHC-I genes, suggesting either that coevolution is relaxed or that it does not prevent the establishment of multigene MHC-I. To distinguish between these two alternatives, we use salamanders (30 species from 16 genera representing six families) to test, within a comparative framework, a major prediction of the coevolution hypothesis: the positive correlation between MHC-I and APG diversity. We found that MHC-I diversity explained both within-individual and species-wide diversity of two APGs, TAP1 and TAP2, supporting their coevolution with MHC-I, whereas no consistent effect was detected for the other three APGs (PSMB8, PSMB9, and TAPBP). Our results imply that although coevolution occurs in salamanders, it does not preclude the expansion of the MHC-I gene family. Contrary to the previous suggestions, nonmammalian vertebrates thus may be able to accommodate diverse selection pressures with flexibility granted by rapid expansion or contraction of the MHC-I family, while retaining the benefits of coevolution between MHC-I and TAPs.
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Affiliation(s)
- G Palomar
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - K Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - M Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - J W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA leiden, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, 2300 RA Leiden, The Netherlands
| | - G F Ficetola
- Department of Environmental Sciences and Policy, University of Milano, Italy.,Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes and Université Savoie Mont Blanc, Grenoble, France
| | - D Jelić
- Croatian Institute for Biodiversity, Zagreb, Croatia
| | - E Jockusch
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT USA
| | - I Martínez-Solano
- Museo Nacional de Ciencias Naturales (MNCN), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - M Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - H B Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - J Vörös
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - B Waldman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA.,School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - B Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA leiden, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, 2300 RA Leiden, The Netherlands
| | - W Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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41
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Talarico L, Marta S, Rossi AR, Crescenzo S, Petrosino G, Martinoli M, Tancioni L. Balancing selection, genetic drift, and human-mediated introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout. Ecol Evol 2021; 11:10026-10041. [PMID: 34367556 PMCID: PMC8328470 DOI: 10.1002/ece3.7760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/19/2022] Open
Abstract
The extraordinary polymorphism of major histocompatibility complex (MHC) genes is considered a paradigm of pathogen-mediated balancing selection, although empirical evidence is still scarce. Furthermore, the relative contribution of balancing selection to shape MHC population structure and diversity, compared to that of neutral forces, as well as its interaction with other evolutionary processes such as hybridization, remains largely unclear. To investigate these issues, we analyzed adaptive (MHC-DAB gene) and neutral (11 microsatellite loci) variation in 156 brown trout (Salmo trutta complex) from six wild populations in central Italy exposed to introgression from domestic hatchery lineages (assessed with the LDH gene). MHC diversity and structuring correlated with those at microsatellites, indicating the substantial role of neutral forces. However, individuals carrying locally rare MHC alleles/supertypes were in better body condition (a proxy of individual fitness/parasite load) regardless of the zygosity status and degree of sequence dissimilarity of MHC, hence supporting balancing selection under rare allele advantage, but not heterozygote advantage or divergent allele advantage. The association between specific MHC supertypes and body condition confirmed in part this finding. Across populations, MHC allelic richness increased with increasing admixture between native and domestic lineages, indicating introgression as a source of MHC variation. Furthermore, introgression across populations appeared more pronounced for MHC than microsatellites, possibly because initially rare MHC variants are expected to introgress more readily under rare allele advantage. Providing evidence for the complex interplay among neutral evolutionary forces, balancing selection, and human-mediated introgression in shaping the pattern of MHC (functional) variation, our findings contribute to a deeper understanding of the evolution of MHC genes in wild populations exposed to anthropogenic disturbance.
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Affiliation(s)
- Lorenzo Talarico
- Laboratory of Experimental Ecology and AquacultureDepartment of BiologyUniversity of Rome “Tor Vergata”RomeItaly
| | - Silvio Marta
- Department of Environmental Science and PolicyUniversity of MilanMilanItaly
| | - Anna Rita Rossi
- Department of Biology and Biotechnology C. DarwinUniversity of Rome “La Sapienza”RomeItaly
| | - Simone Crescenzo
- Department of Biology and Biotechnology C. DarwinUniversity of Rome “La Sapienza”RomeItaly
| | - Gerardo Petrosino
- Department of Biology and Biotechnology C. DarwinUniversity of Rome “La Sapienza”RomeItaly
| | - Marco Martinoli
- Laboratory of Experimental Ecology and AquacultureDepartment of BiologyUniversity of Rome “Tor Vergata”RomeItaly
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA)Centro di Zootecnia e AcquacolturaMonterotondoItaly
| | - Lorenzo Tancioni
- Laboratory of Experimental Ecology and AquacultureDepartment of BiologyUniversity of Rome “Tor Vergata”RomeItaly
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42
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Qin S, Dunn PO, Yang Y, Liu H, He K. Polymorphism and varying selection within the MHC class I of four Anas species. Immunogenetics 2021; 73:395-404. [PMID: 34195858 DOI: 10.1007/s00251-021-01222-9] [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: 02/16/2021] [Accepted: 06/23/2021] [Indexed: 10/21/2022]
Abstract
Ducks (Anatidae) are often vectors for the spread of pathogens because of their long-distance migrations. These migrations also expose ducks to a wide variety of pathogens in their wintering and breeding grounds, and, as a consequence, we might expect strong selection on their immune genes. Here, we studied exons 2 and 3 of the MHC class I in four species of Anas ducks (A. platyrhynchos, A. poecilorhyncha, A. formosa, and A. querquedula) using Illumina-sequencing. Both exons 2 and 3 code for the peptide-binding region of class I molecules; however, most previous studies of birds have only focused on exon 3. Here, we found stronger positive selection on exon 2 than exon 3, as indicated by more species with dN/dS > 1 and higher Wu-Kabat values. There was little evidence that divergence time influenced polymorphism, the numbers of identical alleles (partial α1 or α2 regions) among four Anas, or selection, suggesting that these widespread species might share similar levels of selection from pathogens. The high similarity of allele numbers, positively selected sites (PSS), conserved motifs, and variable protein sites (VPS) supported the persistence of trans-species polymorphism in Anas for at least 10 million years. Our study revealed exon 2 as a relatively unexplored source of variation in avian MHC class I, which should be considered in future studies.
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Affiliation(s)
- Shidi Qin
- College of Animal Science and Technology, College of Veterinary Medicine, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Agriculture and Forestry University, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Hangzhou, China
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, USA
| | - Yang Yang
- College of Animal Science and Technology, College of Veterinary Medicine, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Agriculture and Forestry University, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Hangzhou, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Agriculture and Forestry University, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Hangzhou, China.
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43
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Naito‐Liederbach AM, Sato Y, Nakajima N, Maeda T, Inoue T, Yamazaki T, Ogden R, Inoue‐Murayama M. Genetic diversity of the endangered Japanese golden eagle at neutral and functional loci. Ecol Res 2021. [DOI: 10.1111/1440-1703.12246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Yu Sato
- Wildlife Research Center Kyoto University Kyoto Japan
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Roslin UK
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies National Institute for Environmental Studies Tsukuba Japan
| | - Taku Maeda
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health Morioka Japan
| | - Takehiko Inoue
- Asian Raptor Research and Conservation Network Yasu Japan
| | - Toru Yamazaki
- Asian Raptor Research and Conservation Network Yasu Japan
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Roslin UK
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44
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Minias P, Włodarczyk R, Remisiewicz M, Cobzaru I, Janiszewski T. Distinct evolutionary trajectories of MHC class I and class II genes in Old World finches and buntings. Heredity (Edinb) 2021; 126:974-990. [PMID: 33824536 PMCID: PMC8178356 DOI: 10.1038/s41437-021-00427-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/08/2021] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Major histocompatibility complex (MHC) genes code for key proteins of the adaptive immune system, which present antigens from intra-cellular (MHC class I) and extra-cellular (MHC class II) pathogens. Because of their unprecedented diversity, MHC genes have long been an object of scientific interest, but due to methodological difficulties in genotyping of duplicated loci, our knowledge on the evolution of the MHC across different vertebrate lineages is still limited. Here, we compared the evolution of MHC class I and class II genes in three sister clades of common passerine birds, finches (Fringillinae and Carduelinae) and buntings (Emberizidae) using a uniform methodological (genotyping and data processing) approach and uniform sample sizes. Our analyses revealed contrasting evolutionary trajectories of the two MHC classes. We found a stronger signature of pervasive positive selection and higher allele diversity (allele numbers) at the MHC class I than class II. In contrast, MHC class II genes showed greater allele divergence (in terms of nucleotide diversity) and a much stronger recombination (gene conversion) signal. Gene copy numbers at both MHC class I and class II evolved via fluctuating selection and drift (Brownian Motion evolution), but the evolutionary rate was higher at class I. Our study constitutes one of few existing examples, where evolution of MHC class I and class II genes was directly compared using a multi-species approach. We recommend that re-focusing MHC research from single-species and single-class approaches towards multi-species analyses of both MHC classes can substantially increase our understanding MHC evolution in a broad phylogenetic context.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Magdalena Remisiewicz
- Bird Migration Research Station, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Ioana Cobzaru
- Institute of Biology Bucharest, Romanian Academy, Bucharest, Romania
| | - Tomasz Janiszewski
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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45
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Drzewińska-Chańko J, Włodarczyk R, Gajewski A, Rudnicka K, Dunn PO, Minias P. Immunocompetent birds choose larger breeding colonies. J Anim Ecol 2021; 90:2325-2335. [PMID: 34028816 DOI: 10.1111/1365-2656.13540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/17/2021] [Indexed: 11/27/2022]
Abstract
Optimal size of social groups may vary between individuals, depending on their phenotypic traits, such as dominance status, age or personality. Larger social groups often enhance transmission rates of pathogens and should be avoided by individuals with poor immune defences. In contrast, more immunocompetent individuals are expected to take advantage of larger group sizes (e.g. better protection, information transfer) with smaller extra costs from pathogen or parasite pressure. Here, we hypothesized that immunocompetence may be a key determinant of group size choice and tested this hypothesis in a colonial waterbird, the common tern Sterna hirundo. We used a unique experimental framework, where formation of breeding colonies of different sizes was induced under uniform environmental conditions. For this purpose, different-size patches of attractive nesting substrate (artificial floating rafts) were provided at a single site with limited availability of natural nesting habitat. Colony size was identified as the only significant predictor of both innate (natural antibody-mediated complement activation) and adaptive (immunoglobulin concentrations) immunological traits in the common terns, as more immunocompetent birds settled in larger experimental colonies. In contrast, we found no significant associations between colony size and genetic diversity of key pathogen-recognition receptors, toll-like receptors (TLRs) and the Major Histocompatibility Complex (MHC) or genome-wide heterozygosity. We conclude that settlement decisions may be flexible within individuals and, thus, are likely to be primarily determined by the current immunological status, rather than fixed immunogenetic traits. Our study sheds new light on the complex interface between immunity and sociality in animals.
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Affiliation(s)
- Joanna Drzewińska-Chańko
- Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
| | - Radosław Włodarczyk
- Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
| | - Adrian Gajewski
- Department of Immunology and Allergy, Medical University of Łódź, Łódź, Poland
| | - Karolina Rudnicka
- Faculty of Biology and Environmental Protection, Department of Immunology and Infectious Biology, University of Łódź, Łódź, Poland
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Piotr Minias
- Faculty of Biology and Environmental Protection, Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
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46
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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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47
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O'Connor EA, Westerdahl H. Trade-offs in expressed major histocompatibility complex diversity seen on a macroevolutionary scale among songbirds. Evolution 2021; 75:1061-1069. [PMID: 33666228 DOI: 10.1111/evo.14207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/07/2021] [Accepted: 02/17/2021] [Indexed: 12/30/2022]
Abstract
To survive organisms must defend themselves against pathogens. Classical Major Histocompatibility Complex (MHC) genes play a key role in pathogen defense by encoding molecules involved in pathogen recognition. MHC gene diversity influences the variety of pathogens individuals can recognize and respond to and has consequently been a popular genetic marker for disease resistance in ecology and evolution. However, MHC diversity is predominantly estimated using genomic DNA (gDNA) with little knowledge of expressed diversity. This limits our ability to interpret the adaptive significance of variation in MHC diversity, especially in species with very many MHC genes such as songbirds. Here, we address this issue using phylogenetic comparative analyses of the number of MHC class I alleles (MHC-I diversity) in gDNA and complementary DNA (cDNA), that is, expressed alleles, across 13 songbird species. We propose three theoretical relationships that could be expected between genomic and expressed MHC-I diversity on a macroevolutionary scale and test which of these are best supported. In doing so, we show that significantly fewer MHC-I alleles than the number available are expressed, suggesting that optimal MHC-I diversity could be achieved by modulating gene expression. Understanding the relationship between genomic and expressed MHC diversity is essential for interpreting variation in MHC diversity in an evolutionary context.
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Affiliation(s)
- Emily A O'Connor
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
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48
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Peng F, Ballare KM, Hollis Woodard S, den Haan S, Bolnick DI. What evolutionary processes maintain MHC IIꞵ diversity within and among populations of stickleback? Mol Ecol 2021; 30:1659-1671. [PMID: 33576071 PMCID: PMC8049082 DOI: 10.1111/mec.15840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 12/01/2022]
Abstract
Major Histocompatibility Complex (MHC) genes code for proteins that recognize foreign protein antigens to initiate T-cell-mediated adaptive immune responses. They are often the most polymorphic genes in vertebrate genomes. How evolution maintains this diversity remains of debate. Three main hypotheses seek to explain the maintenance of MHC diversity by invoking pathogen-mediated selection: heterozygote advantage, frequency-dependent selection, and fluctuating selection across landscapes or through time. Here, we use a large-scale field parasite survey in a stickleback metapopulation to test predictions derived from each of these hypotheses. We identify over 1000 MHC IIβ variants (alleles spanning paralogous genes) and find that many of them covary positively or negatively with parasite load, suggesting that these genes contribute to resistance or susceptibility. However, despite our large sample-size, we find no evidence for the widely cited stabilizing selection on MHC heterozygosity, in which individuals with an intermediate number of MHC variants have the lowest parasite burden. Nor do we observe a rare-variant advantage, or widespread fluctuating selection across populations. In contrast, we find that MHC diversity is best predicted by neutral genome-wide heterozygosity and between-population genomic divergence, suggesting neutral processes are important in shaping the pattern of metapopulation MHC diversity. Thus, although MHC IIβ is highly diverse and relevant to the type and intensity of macroparasite infection in these populations of stickleback, the main models of MHC evolution still provide little explanatory power in this system.
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Affiliation(s)
- Foen Peng
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Kimberly M. Ballare
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
| | | | | | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
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Trujillo AL, Hoffman EA, Becker CG, Savage AE. Spatiotemporal adaptive evolution of an MHC immune gene in a frog-fungus disease system. Heredity (Edinb) 2021; 126:640-655. [PMID: 33510466 PMCID: PMC8115231 DOI: 10.1038/s41437-020-00402-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 01/30/2023] Open
Abstract
Genetic diversity of major histocompatibility complex (MHC) genes is linked to reduced pathogen susceptibility in amphibians, but few studies also examine broad spatial and temporal patterns of MHC and neutral genetic diversity. Here, we characterized range-wide MHC diversity in the Northern leopard frog, Rana pipiens, a species found throughout North America that is experiencing disease-related declines. We used previously sequenced neutral markers (mitochondrial DNA and microsatellites), sequenced an expressed MHC class IIß gene fragment, and measured infection prevalence and intensity of the global fungal pathogen Batrachochytrium dendrobatidis (Bd) across 14 populations. Four populations were sampled across two decades, enabling temporal comparisons of selection and demography. We recovered 37 unique MHC alleles, including 17 that were shared across populations. Phylogenetic and population genetic patterns between MHC and neutral markers were incongruent, and five MHC codon positions associated with peptide binding were under positive selection. MHC heterozygosity, but not neutral marker heterozygosity, was a significant factor explaining spatial patterns of Bd prevalence, whereas only environmental variables predicted Bd intensity. MHC allelic richness (AR) decreased significantly over time but microsatellite-based AR did not, highlighting a loss of functional immunogenetic diversity that may be associated with Bd selective pressures. MHC supertype 4 was significantly associated with an elevated risk of Bd infection, whereas one supertype 2 allele was associated with a nearly significant reduced risk of Bd. Taken together, these results provide evidence that positive selection contributes to MHC class IIß evolution in R. pipiens and suggest that functional MHC differences across populations may contribute to disease adaptation.
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Affiliation(s)
- Alexa L. Trujillo
- grid.170430.10000 0001 2159 2859Department of Biology, University of Central Florida, Orlando, FL USA
| | - Eric A. Hoffman
- grid.170430.10000 0001 2159 2859Department of Biology, University of Central Florida, Orlando, FL USA
| | - C. Guilherme Becker
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, University of Alabama, Tuscaloosa, AL USA
| | - Anna E. Savage
- grid.170430.10000 0001 2159 2859Department of Biology, University of Central Florida, Orlando, FL USA
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Abstract
Background and aims Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question. Methods We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined. Results The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders. Conclusions Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.
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