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Yan J, Song C, Liang J, La Y, Lai J, Pan R, Huang Z, Li B, Zhang P. Moderate Genetic Diversity of MHC Genes in an Isolated Small Population of Black-and-White Snub-Nosed Monkeys ( Rhinopithecus bieti). Animals (Basel) 2024; 14:2276. [PMID: 39123802 PMCID: PMC11310952 DOI: 10.3390/ani14152276] [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: 06/11/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species.
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Affiliation(s)
- Jibing Yan
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Chunmei Song
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Jiaqi Liang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Yanni La
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Jiandong Lai
- Baima Snow Mountain National Nature Reserve Administrative Bureau, Diqing 674500, China;
| | - Ruliang Pan
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
- International Center of Biodiversity and Primat Conservation, Dali University, Dali 671003, China
- School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Zhipang Huang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China;
| | - Baoguo Li
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
- Shaanxi Institute of Zoology, Xi’an 710032, China
- College of Life Science, Yanan University, Yanan 710032, China
| | - Pei Zhang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
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He K, Liang C, Ma S, Liu H, Zhu Y. Copy number and selection of MHC genes in ruminants are related to habitat, average life span and diet. Gene 2024; 904:148179. [PMID: 38242373 DOI: 10.1016/j.gene.2024.148179] [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: 09/18/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The ruminants, as the main group of livestock, have been extensively studied in terms of their physiology, endocrinology, biochemistry, genetics, and nutrition. Despite the wide geographic distribution and habitat diversity of animals in this group, their ecology and evolution remain poorly understood. In this study, we analyzed the gene copy number, selection, and ecological and evolutionary processes that have affected the evolution of major histocompatibility complex (MHC) genes across ruminant lineages based on available genomic data. The 51 species analyzed represented all six families of ruminants. Our finding indicated that the architecture of the MHC region is conserved in ruminants, but with variable copy numbers of MHC-I, MHC-IIA, and MHC-IIB genes. No lineage-specific gene duplication was observed in the MHC genes. The phylogenetic generalized least squares regression (PGLS) model revealed association between ecological and biological factors (habitat and lifespan) and gene duplication in DQA and DQB, but not in DRB. The selection pressure of DQA and DQB were related with lifespan, diet, and the ratio of genetic repeat elements. These results suggest that the MHC evolution in ruminants, including copy number and selection, has been influenced by genetic repeat elements, pathogen exposure risk, and intrinsic cost of possessing multiple MHC genes.
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Affiliation(s)
- Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Chunhong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Shujuan Ma
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China.
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Ferreira D, San‐Jose LM, Roulin A, Gaigher A, Fumagalli L. Limited associations between MHC diversity and reproductive success in a bird species with biparental care. Ecol Evol 2024; 14:e10950. [PMID: 38384825 PMCID: PMC10879840 DOI: 10.1002/ece3.10950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 02/23/2024] Open
Abstract
The selective pressure from pathogens on individuals can have direct consequences on reproduction. Genes from the major histocompatibility complex (MHC) are central to the vertebrate adaptive immune system and pathogen resistance. In species with biparental care, each sex has distinct reproductive roles and levels of investment, and due to a trade-off with immunity, one can expect different selective regimes acting upon the MHC of each parent. Here, we addressed whether couples combine each other's variation at MHC loci to increase their breeding success. Specifically, we used a 23-year dataset from a barn owl population (Tyto alba) to understand how MHC class Iα and IIβ functional divergence and supertypes of each parent were associated with clutch size and fledging success. We did not detect associations between MHC diversity and supertypes with the clutch size or with the fledging success. In addition, to understand the relative contribution from the MHC of the genetic parents and the social parents, we analyzed the fledging success using only a cross-fostered dataset. We found several associations of weak-to-moderate effect sizes between the father's MHC and fledging success: (i) lower MHC-Iα divergence in the genetic father increases fledging success, which might improve paternal care during incubation, and (ii) one and two MHC-IIβ DAB2 supertypes in the social father decrease and increase, respectively, fledging success, which may affect the paternal care after hatching. Furthermore, fledging success increased when both parents did not carry MHC-IIβ DAB1 supertype 2, which could suggest conditional effects of this supertype. Although our study relied on a substantial dataset, we showed that the associations between MHC diversity and reproductive success remain scarce and of complex interpretation in the barn owl. Moreover, our results highlighted the need to incorporate more than one proxy of reproductive success and several MHC classes to capture more complex associations.
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Affiliation(s)
- Diana Ferreira
- Laboratory for Conservation Biology, Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - Luis M. San‐Jose
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRSUniversité Toulouse III Paul Sabatier, IRDToulouseFrance
| | - Alexandre Roulin
- Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - Arnaud Gaigher
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic ResourcesUniversity of PortoVairãoPortugal
- Research Unit for Evolutionary Immunogenomics, Department of BiologyUniversity of HamburgHamburgGermany
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne‐GenevaLausanne University Hospital and University of LausanneLausanneSwitzerland
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Vinkler M, Fiddaman SR, Těšický M, O'Connor EA, Savage AE, Lenz TL, Smith AL, Kaufman J, Bolnick DI, Davies CS, Dedić N, Flies AS, Samblás MMG, Henschen AE, Novák K, Palomar G, Raven N, Samaké K, Slade J, Veetil NK, Voukali E, Höglund J, Richardson DS, Westerdahl H. Understanding the evolution of immune genes in jawed vertebrates. J Evol Biol 2023; 36:847-873. [PMID: 37255207 PMCID: PMC10247546 DOI: 10.1111/jeb.14181] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
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Affiliation(s)
- Michal Vinkler
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Martin Těšický
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Anna E. Savage
- Department of BiologyUniversity of Central FloridaFloridaOrlandoUSA
| | - Tobias L. Lenz
- Research Unit for Evolutionary ImmunogenomicsDepartment of BiologyUniversity of HamburgHamburgGermany
| | | | - Jim Kaufman
- Institute for Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Neira Dedić
- Department of Botany and ZoologyMasaryk UniversityBrnoCzech Republic
| | - Andrew S. Flies
- Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmaniaAustralia
| | - M. Mercedes Gómez Samblás
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
- Department of ParasitologyUniversity of GranadaGranadaSpain
| | | | - Karel Novák
- Department of Genetics and BreedingInstitute of Animal SciencePragueUhříněvesCzech Republic
| | - Gemma Palomar
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Nynke Raven
- Department of ScienceEngineering and Build EnvironmentDeakin UniversityVictoriaWaurn PondsAustralia
| | - Kalifa Samaké
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Joel Slade
- Department of BiologyCalifornia State UniversityFresnoCaliforniaUSA
| | | | - Eleni Voukali
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Jacob Höglund
- Department of Ecology and GeneticsUppsala UniversitetUppsalaSweden
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Råberg L, Clough D, Hagström Å, Scherman K, Andersson M, Drews A, Strandh M, Tschirren B, Westerdahl H. MHC class II genotype-by-pathogen genotype interaction for infection prevalence in a natural rodent-Borrelia system. Evolution 2022; 76:2067-2075. [PMID: 35909235 PMCID: PMC9541904 DOI: 10.1111/evo.14590] [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: 02/23/2022] [Revised: 05/25/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
MHC genes are extraordinarily polymorphic in most taxa. Host-pathogen coevolution driven by negative frequency-dependent selection (NFDS) is one of the main hypotheses for the maintenance of such immunogenetic variation. Here, we test a critical but rarely tested assumption of this hypothesis-that MHC alleles affect resistance/susceptibility to a pathogen in a strain-specific way, that is, there is a host genotype-by-pathogen genotype interaction. In a field study of bank voles naturally infected with the tick-transmitted bacterium Borrelia afzelii, we tested for MHC class II (DQB) genotype-by-B. afzelii strain interactions for infection prevalence between 10 DQB alleles and seven strains. One allele (DQB*37) showed an interaction, such that voles carrying DQB*37 had higher prevalence of two strains and lower prevalence of one strain than individuals without the allele. These findings were corroborated by analyses of strain composition of infections, which revealed an effect of DQB*37 in the form of lower β diversity among infections in voles carrying the allele. Taken together, these results provide rare support at the molecular genetic level for a key assumption of models of antagonistic coevolution through NFDS.
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Affiliation(s)
- Lars Råberg
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | - Dagmar Clough
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | - Åsa Hagström
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | | | | | - Anna Drews
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | - Maria Strandh
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | - Barbara Tschirren
- Department of BiologyLund UniversityLundSE‐22362Sweden,Centre for Ecology and ConservationUniversity of ExeterPenrynTR10 9FEUnited Kingdom
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Migalska M, Przesmycka K, Alsarraf M, Bajer A, Behnke-Borowczyk J, Grzybek M, Behnke JM, Radwan J. Long term patterns of association between MHC and helminth burdens in the bank vole support Red Queen dynamics. Mol Ecol 2022; 31:3400-3415. [PMID: 35510766 PMCID: PMC9325469 DOI: 10.1111/mec.16486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/28/2022]
Abstract
Major histocompatibility complex (MHC) genes encode proteins crucial for adaptive immunity of vertebrates. Negative frequency-dependent selection (NFDS), resulting from adaptation of parasites to common MHC types, has been hypothesized to maintain high, functionally relevant polymorphism of MHC, but demonstration of this relationship has remained elusive. In particular, differentiation of NFDS from fluctuating selection, resulting from changes in parasite communities in time and space (FS), has proved difficult in short-term studies. Here, we used temporal data, accumulated through long-term monitoring of helminths infecting bank voles (Myodes glareolus), to test specific predictions of NFDS on MHC class II. Data were collected in three, moderately genetically differentiated subpopulations in Poland, which were characterized by some stable spatiotemporal helminth communities but also events indicating introduction of new species and loss of others. We found a complex association between individual MHC diversity and species richness, where intermediate numbers of DRB supertypes correlated with lowest species richness, but the opposite was true for DQB supertypes - arguing against universal selection for immunogenetic optimality. We also showed that particular MHC supertypes explain a portion of the variance in prevalence and abundance of helminths, but this effect was subpopulation-specific, which is consistent with both NFDS and FS. Finally, in line with NFDS, we found that certain helminths that have recently colonized or spread in a given subpopulation, more frequently or intensely infected voles with MHC supertypes that have been common in the recent past. Overall, our results highlight complex spatial and temporal patterns of MHC-parasite associations, the latter being consistent with Red Queen coevolutionary dynamics.
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Affiliation(s)
- Magdalena Migalska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Karolina Przesmycka
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Mohammed Alsarraf
- Department of Eco-epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Anna Bajer
- Department of Eco-epidemiology of Parasitic Diseases, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jolanta Behnke-Borowczyk
- Department of Forest Entomology and Pathology, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Wojska Polskiego 71c, 60-625, Poznań, Poland
| | - Maciej Grzybek
- Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Powstania Styczniowego 9B, 81-429, Gdynia, Poland
| | - Jerzy M Behnke
- School of Life Science, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jacek Radwan
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
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