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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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Torres FD, Borges ALDSB, Kolesnikovas C, Domit C, Barbosa CB, Carvalho-Costa FA, Di Azevedo MIN, Lilenbaum W. Pinnipeds carriers of pathogenic Leptospira: New data based on molecular characterization. Res Vet Sci 2023; 155:62-68. [PMID: 36634544 DOI: 10.1016/j.rvsc.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023]
Abstract
Leptospirosis is a bacterial disease caused by the infection of pathogenic strains of the genus Leptospira, endemic in tropical and subtropical regions. Although well documented in terrestrial animals and humans, little information is available on its distribution and impact on marine animals. Despite clinical manifestations that may occur, the occurrence of carriers was suggested in some species. Nevertheless, there are few studies regarding the infection by Leptospira sp. in marine mammals. In this context, and considering the One Health approach, the present aimed to investigate pinnipeds' role as Leptospira sp. carriers. Kidneys of 47 pinnipeds of two species, Arctocephalus australis (n = 40) and Arctocephalus tropicalis (n = 7) were collected. DNA was extracted and the diagnosis was performed through LipL32-PCR and genetic characterization based on secY gene sequencing. Phylogenetic analysis and haplotype networks were constructed. Pathogenic Leptospira sp. DNA was detected in 31.9% (15/47) of the tested pinnipeds. It was possible to amplify and sequence eight strains (6 for A. australis, 2 for A. tropicalis), all identified as L. interrogans, with high similarity with sequences from Icterohaemorrhagiae serogroup. Phylogenetic analysis revealed sequences from the present study grouped in species-specific unique clusters, but very close to others from humans, wild animals, and domestic animals. We demonstrate that pinnipeds could act as carriers, and play an important role in leptospirosis dynamics.
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Affiliation(s)
- Felipe D'Azeredo Torres
- Laboratory of Veterinary Bacteriology, Biomedical Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | | | | | - Camila Domit
- Laboratory of Ecology and Conservation, Center of Ocean Research, Paraná Federal University, Paraná, Brazil
| | | | | | | | - Walter Lilenbaum
- Laboratory of Veterinary Bacteriology, Biomedical Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil.
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Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Sci Rep 2022; 12:17933. [PMID: 36289307 PMCID: PMC9606363 DOI: 10.1038/s41598-022-21658-7] [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: 05/10/2022] [Accepted: 09/29/2022] [Indexed: 01/20/2023] Open
Abstract
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
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Sá ALAD, Baker PKB, Breaux B, Oliveira JM, Klautau AGCDM, Legatzki K, Luna FDO, Attademo FLN, Hunter ME, Criscitiello MF, Schneider MPC, Sena LDS. Novel insights on aquatic mammal MHC evolution: Evidence from manatee DQB diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 132:104398. [PMID: 35307479 DOI: 10.1016/j.dci.2022.104398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The low diversity in marine mammal major histocompatibility complex (MHC) appears to support the hypothesis of reduced pathogen selective pressure in aquatic systems compared to terrestrial environments. However, the lack of characterization of the aquatic and evolutionarily distant Sirenia precludes drawing more generalized conclusions. Therefore, we aimed to characterize the MHC DQB diversity of two manatee species and compare it with those reported for marine mammals. Our results identified 12 and 6 alleles in T. inunguis and T. manatus, respectively. Alleles show high rates of nonsynonymous substitutions, suggesting loci are evolving under positive selection. Among aquatic mammals, Pinnipeda DQB had smaller numbers of alleles, higher synonymous substitution rate, and a dN/dS ratio closer to 1, suggesting it may be evolving under more relaxed selection compared to fully aquatic mammals. This contradicts one of the predictions of the hypothesis that aquatic environments impose reduced pathogen pressure to mammalian immune system. These results suggest that the unique evolutionary trajectories of mammalian MHC may impose challenges in drawing ecoevolutionary conclusions from comparisons across distant vertebrate lineages.
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Affiliation(s)
- André Luiz Alves de Sá
- Laboratory of Applied Genetics (LGA), Socio-Environmental and Water Resources Institute (ISARH), Federal Rural University of the Amazon (UFRA), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil; Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
| | - Pamela Ketrya Barreiros Baker
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil
| | - Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Jairo Moura Oliveira
- Zoological Park of Santarém - Universidade da Amazônia (ZOOUNAMA), R. Belo Horizonte, 68030-150, Santarém, PA, Brazil
| | - Alex Garcia Cavalleiro de Macedo Klautau
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte (CEPNOR), Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil
| | - Kristian Legatzki
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte (CEPNOR), Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil
| | - Fábia de Oliveira Luna
- National Center for Research and Conservation of Aquatic Mammals, Chico Mendes Institute for Biodiversity Conservation (CMA), ICMBio, Rua Alexandre Herculano 197, 11050-031, Santos, SP, Brazil
| | - Fernanda Löffler Niemeyer Attademo
- National Center for Research and Conservation of Aquatic Mammals, Chico Mendes Institute for Biodiversity Conservation (CMA), ICMBio, Rua Alexandre Herculano 197, 11050-031, Santos, SP, Brazil
| | - Margaret Elizabeth Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA.
| | - Michael Frederick Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
| | - Leonardo Dos Santos Sena
- Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
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Duckworth EEM, Romoser KR, Ott JA, Deiss TC, Gulland FMD, Criscitiello MF. Using PacBio SMRT data for identification of class I MHC alleles in a wildlife species, Zalophus californianus (California sea lion). INFECTION GENETICS AND EVOLUTION 2020; 88:104700. [PMID: 33387691 DOI: 10.1016/j.meegid.2020.104700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Abstract
High allelic polymorphism and association with disease susceptibility has made the genes encoding major histocompatibility complex (MHC) antigen presentation molecules in humans, domesticated animals, and wildlife species of wide interest to ecologists, evolutionary biologists, and health specialists. The often multifaceted polygenism and extreme polymorphism of this immunogenetic system have made it especially difficult to characterize in non-model species. Here we compare and contrast the workflows of traditional Sanger sequencing of plasmid-cloned amplicons to Pacific Biosciences SMRT circular consensus sequencing (CCS) in their ability to capture alleles of MHC class I in a wildlife species where characterization of these genes was absent. We assessed two California sea lions (Zalophus californianus), a species suffering from a high prevalence of an aggressive cancer associated with a sexually transmitted gamma herpesvirus. In this pilot study, SMRT CCS proved superior in identifying more alleles from each animal than the more laborious plasmid cloning/Sanger workflow (12:7, 10:7), and no alleles were identified with the cloning/Sanger approach that were not identified by SMRT CCS. We discuss the advantages and disadvantages of each approach including cost, allele rarefaction, and sequence fidelity.
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Affiliation(s)
- Ellen E M Duckworth
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Kaitlyn R Romoser
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | | | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Molecular Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, TX 77807, USA.
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Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus). BMC Genet 2020; 21:83. [PMID: 32727360 PMCID: PMC7392685 DOI: 10.1186/s12863-020-00889-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type II genes into two subregions (IIa, IIb). Recombination rates are reportedly high between these subregions, and a lack of linkage has been documented in domestic ruminants. However, no study has yet examined the degree of linkage between these subregions in a wild ruminant. The white-tailed deer (Odocoileus virginianus), a popular ruminant of the Cervidae family, is habitually plagued by pathogens in its natural environment (e.g. Haemonchus contortus, Elaeophora). Due to the association between MHC haplotypes and disease susceptibility, a deeper understanding of MHC polymorphism and linkage between MHC genes can further aid in this species' successful management. We sequenced MHC-DRB exon 2 (IIa) and MHC-DOB exon 2 (IIb) on the MiSeq platform from an enclosed white-tailed deer population located in Alabama. RESULTS We identified 12 new MHC-DRB alleles, and resampled 7 alleles, which along with other published alleles brings the total number of documented alleles in white-tailed deer to 30 for MHC-DRB exon 2. The first examination of MHC-DOB in white-tailed deer found significantly less polymorphism (11 alleles), as was expected of a non-classical MHC gene. While MHC-DRB was found to be under positive, diversifying selection, MHC-DOB was found to be under purifying selection for white-tailed deer. We found no significant linkage disequilibrium between MHC-DRB and MHC-DOB, suggesting that these loci are unlikely to be closely linked. CONCLUSIONS Overall, this study identified 12 new MHC-DRB exon 2 alleles and characterized a new, non-classical, MHC II gene (MHC-DOB) for white-tailed deer. We also found a lack of significant linkage between these two loci, which supports previous findings of a chromosomal inversion within the MHC type II gene region in ruminants, and suggests that white-tailed deer may have a recombination hotspot between these MHC regions similar to that found for Bos taurus.
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Gagnon M, Yannic G, Boyer F, Côté SD. Adult survival in migratory caribou is negatively associated with MHC functional diversity. Heredity (Edinb) 2020; 125:290-303. [PMID: 32728043 DOI: 10.1038/s41437-020-0347-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 07/04/2020] [Accepted: 07/16/2020] [Indexed: 11/09/2022] Open
Abstract
Genes of the major histocompatibility complex (MHC) are involved in acquired immunity in vertebrates. Only a few studies have investigated the fitness consequences of MHC gene diversity in wild populations. Here, we looked at the association between annual survival and body mass and MHC-DRB exon 2 (MHC-DRB) genetic diversity, obtained from high-throughput sequencing, in two declining migratory caribou (Rangifer tarandus) herds. To disentangle the potential direct and general effects of MHC-DRB genetic diversity, we compared different indices of diversity that were either based on DNA-sequence variation or on physicochemical divergence of the translated peptides, thereby covering a gradient of allelic-to-functional diversity. We found that (1) body mass was not related to MHC-DRB diversity or genotype, and (2) adult survival probability was negatively associated with point accepted mutation distance, a corrected distance that considers the likelihood of each amino acid substitution to be accepted by natural selection. In addition, we found no evidence of fluctuating selection over time on MHC-DRB diversity. We concluded that direct effects were involved in the negative relationship between MHC functional diversity and survival, although the mechanism underlying this result remains unclear. A possible explanation could be that individuals with higher MHC diversity suffer higher costs of immunity (immunopathology). Our results suggest that genetic diversity is not always beneficial even in genes that are likely to be strongly shaped by balancing selection.
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Affiliation(s)
- Marianne Gagnon
- Département de Biologie, Caribou Ungava and Centre d'Études Nordiques, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Glenn Yannic
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.
| | - Frédéric Boyer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Steeve D Côté
- Département de Biologie, Caribou Ungava and Centre d'Études Nordiques, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
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Jo A, Lee HE, Kim HS. Identification and expression analysis of a novel miRNA derived from ERV-E1 LTR in Equus caballus. Gene 2018; 687:238-245. [PMID: 30453070 DOI: 10.1016/j.gene.2018.11.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Abstract
Horses (Equus caballus) have been domesticated and bred to enhance speed, strength, and agility. Members of the Equus caballus Endogenous Retrovirus (EqERV) family affect several of these abilities in horses. EqERV elements have been integrated in the horse genome during evolution and generate repeat elements such as long terminal repeats (LTRs). LTR sequences are involved in retrovirus replication and play an essential function in post-transcriptional control mechanisms, such as by providing binding sites for microRNAs (miRNAs) or generating miRNA precursors. In this study, we identified a novel miRNA derived from EqERV-E1 LTR using various bioinformatics tools. To examine the relationship between EqERV-E1 LTR and similar elements, we used BLAST2seq and phylogenetic analysis. LTR sequences were located in the untranslated region (UTR) of mRNAs and also formed the stem-loop secondary structure. The sequence was registered in the DDBJ database as LTR derived miRNA under the accession number corresponding to LC383797 (referred to eca-miR-1804). Quantitative polymerase chain reaction (qPCR) to confirm the expression of eca-miR-1804 and the similar miR-1255a, showed an almost identical expression pattern in eight different equine tissues. Therefore, these data imply that the LTR could function as an miRNA, which is expressed in the examined equine tissues. In addition, the current study provides inputs for additional functional studies concerning the LTR of other EqERV families.
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Affiliation(s)
- Ara Jo
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea; Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea.
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