1
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Heimeier D, Garland EC, Eichenberger F, Garrigue C, Vella A, Baker CS, Carroll EL. A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Mol Ecol Resour 2024; 24:e13955. [PMID: 38520161 DOI: 10.1111/1755-0998.13955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 03/25/2024]
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
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Affiliation(s)
- Dorothea Heimeier
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
| | - Ellen C Garland
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Franca Eichenberger
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Claire Garrigue
- UMR ENTROPIE, (IRD, Université de La Réunion, Université de la Nouvelle-Calédonie, IFREMER, CNRS, Laboratoire d'Excellence-CORAIL), Nouméa, New Caledonia
- Opération Cétacés, Nouméa, New Caledonia
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, Malta
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Corvallis, Oregon, USA
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
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2
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Day G, Robb K, Oxley A, Telonis-Scott M, Ujvari B. Organisation and evolution of the major histocompatibility complex class I genes in cetaceans. iScience 2024; 27:109590. [PMID: 38632986 PMCID: PMC11022044 DOI: 10.1016/j.isci.2024.109590] [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: 04/26/2023] [Revised: 09/30/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
A quarter of marine mammals are at risk of extinction, with disease and poor habitat quality contributing to population decline. Investigation of the Major Histocompatibility Complex (MHC) provides insight into species' capacity to respond to immune and environmental challenges. The eighteen available cetacean chromosome level genomes were used to annotate MHC Class I loci, and to reconstruct the phylogenetic relationship of the described loci. The highest number of loci was observed in the striped dolphin (Stenella coeruleoalba), while the least was observed in the pygmy sperm whale (Kogia breviceps) and rough toothed dolphin (Steno bredanensis). Of the species studied, Mysticetes had the most pseudogenes. Evolutionarily, MHC Class I diverged before the speciation of cetaceans. Yet, locus one was genomically and phylogenetically similar in many species, persisting over evolutionary time. This characterisation of MHC Class I in cetaceans lays the groundwork for future population genetics and MHC expression studies.
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Affiliation(s)
- Grace Day
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
- Marine Mammal Foundation, Melbourne 3194, VIC, Australia
| | - Kate Robb
- Marine Mammal Foundation, Melbourne 3194, VIC, Australia
| | - Andrew Oxley
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
| | - Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Melbourne 3125, VIC, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
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3
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Li X, Liu T, Li A, Xiao Y, Sun K, Feng J. Diversifying selection and climatic effects on major histocompatibility complex class
II
gene diversity in the greater horseshoe bat. Evol Appl 2023; 16:688-704. [PMID: 36969140 PMCID: PMC10033860 DOI: 10.1111/eva.13528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Heterogeneous pathogenic stress can shape major histocompatibility complex (MHC) diversity by influencing the functional plasticity of the immune response. Therefore, MHC diversity could reflect environmental stress, demonstrating its importance in uncovering the mechanisms of adaptive genetic variation. In this study, we combined neutral microsatellite loci, an immune-related MHC II-DRB locus, and climatic factors to unravel the mechanisms affecting the diversity and genetic differentiation of MHC genes in the greater horseshoe bat (Rhinolophus ferrumequinum), a species with a wide geographical distribution that has three distinct genetic lineages in China. First, increased genetic differentiation at the MHC locus among populations compared using microsatellites indicated diversifying selection. Second, the genetic differentiation of MHC and microsatellites were significantly correlated, suggesting that demographic processes exist. However, MHC genetic differentiation was significantly correlated with geographical distance among populations, even after controlling for the neutral markers, suggesting a major effect of selection. Third, although the MHC genetic differentiation was larger than that for microsatellites, there was no significant difference in the genetic differentiation between the two markers among genetic lineages, indicating the effect of balancing selection. Fourth, combined with climatic factors, MHC diversity and supertypes showed significant correlations with temperature and precipitation, but not with the phylogeographic structure of R. ferrumequinum, suggesting an effect of local adaptation driven by climate on MHC diversity. Moreover, the number of MHC supertypes varied between populations and lineages, suggesting regional characteristics and support for local adaptation. Taken together, the results of our study provide insights into the adaptive evolutionary driving forces at different geographic scales in R. ferrumequinum. In addition, climate factors may have played a vital role in driving adaptive evolution in this species.
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Affiliation(s)
- Xiaolin Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology, Ministry of Education Changchun China
| | - Tong Liu
- College of Life Science, Jilin Agricultural University Changchun China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology, Ministry of Education Changchun China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- College of Life Science, Jilin Agricultural University Changchun China
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4
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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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5
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Moreno-Santillán DD, Machain-Williams C, Hernández-Montes G, Ortega J. Transcriptomic analysis elucidates evolution of the major histocompatibility complex class I in neotropical bats. J Mammal 2022. [DOI: 10.1093/jmammal/gyac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The Order Chiroptera comprises more than 1,400 species, each with its evolutionary history and under unique selective pressures, among which are the host–pathogen interactions. Bats have coped with complex interactions with a broad spectrum of microbes throughout their evolutionary history, prompting the development of unique adaptations that allow them to co-exist with microbes with pathogenic potential more efficiently than other nonadapted species. In this sense, an extraordinary immune system with unique adaptations has been hypothesized in bats. To explore this, we focused on the major histocompatibility complex (MHC), which plays a crucial role in pathogen recognition and presentation to T cells to trigger the adaptive immune response. We analyzed MHC class I transcripts in five species, each from different families of New World bats. From RNA-seq data, we assembled a partial region of the MHC-I comprising the α1 and α2 domains, which are responsible for peptide binding and recognition. We described five putative functional variants, two of which have two independent insertions at the α2 domain. Our results suggest that this insertion appeared after the divergence of the order Chiroptera and may have an adaptive function in the defense against intracellular pathogens, providing evidence of positive selection and trans-specific polymorphism on the peptide-binding sites.
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Affiliation(s)
- Diana D Moreno-Santillán
- Department of Integrative Biology, University of California , Berkeley, California 94720-3200 , USA
| | - Carlos Machain-Williams
- Universidad Autónoma de Yucatán, Laboratorio de Arbovirología , Mérida, Yucatán 97000 , México
| | - Georgina Hernández-Montes
- Universidad Nacional Autónoma de México, Red de apoyo a la Investigación, Coordinación de la Investigación Científica entre Universidad y Red de Apoyo , Ciudad de México 14080 , México
| | - Jorge Ortega
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Departamento de Zoología, Posgrado en Ciencias Quimicobiológicas , Ciudad de México 11350 , México
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6
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Million KM, Lively CM. Trans‐specific polymorphism and the convergent evolution of supertypes in major histocompatibility complex class II genes in darters (
Etheostoma
). Ecol Evol 2022; 12:e8485. [PMID: 36311547 PMCID: PMC9601779 DOI: 10.1002/ece3.8485] [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: 08/15/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/24/2022] Open
Abstract
Major Histocompatibility Complex (MHC) genes are one of the most polymorphic gene groups known in vertebrates. MHC genes also exhibit allelic variants that are shared among taxa, referred to as trans‐specific polymorphism (TSP). The role that selection plays in maintaining such high diversity within species, as well as TSP, is an ongoing discussion in biology. In this study, we used deep‐sequencing techniques to characterize MHC class IIb gene diversity in three sympatric species of darters. We found at least 5 copies of the MHC gene in darters, with 126 genetic variants encoding 122 unique amino acid sequences. We identified four supertypes based on the binding properties of proteins encoded by the sequences. Although each species had a unique pool of variants, many variants were shared between species pairs and across all three species. Phylogenetic analysis showed that the variants did not group together monophyletically based on species identity or on supertype. An expanded phylogenetic analysis showed that some darter alleles grouped together with alleles from other percid fishes. Our findings show that TSP occurs in darters, which suggests that balancing selection is acting at the genotype level. Supertypes, however, are most likely evolving convergently, as evidenced by the fact that alleles do not form monophyletic groups based on supertype. Our research demonstrates that selection may be acting differently on MHC genes at the genotype and supertype levels, selecting for the maintenance of high genotypic diversity while driving the convergent evolution of similar MHC phenotypes across different species.
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Affiliation(s)
- Kara M. Million
- Department of Biology Indiana University Bloomington Indiana USA
| | - Curtis M. Lively
- Department of Biology Indiana University Bloomington Indiana USA
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7
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Batley KC, Sandoval-Castillo J, Kemper CM, Zanardo N, Tomo I, Beheregaray LB, Möller LM. Whole genomes reveal multiple candidate genes and pathways involved in the immune response of dolphins to a highly infectious virus. Mol Ecol 2021; 30:6434-6448. [PMID: 33675577 DOI: 10.1111/mec.15873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 01/02/2023]
Abstract
Wildlife species are challenged by various infectious diseases that act as important demographic drivers of populations and have become a great conservation concern particularly under growing environmental changes. The new era of whole genome sequencing provides new opportunities and avenues to explore the role of genetic variants in the plasticity of immune responses, particularly in non-model systems. Cetacean morbillivirus (CeMV) has emerged as a major viral threat to cetacean populations worldwide, contributing to the death of thousands of individuals of multiple dolphin and whale species. To understand the genomic basis of immune responses to CeMV, we generated and analysed whole genomes of 53 Indo-Pacific bottlenose dolphins (Tursiops aduncus) exposed to Australia's largest known CeMV-related mortality event that killed at least 50 dolphins from three different species. The genomic data set consisted of 10,168,981 SNPs anchored onto 23 chromosome-length scaffolds and 77 short scaffolds. Whole genome analysis indicated that levels of inbreeding in the dolphin population did not influence the outcome of an individual. Allele frequency estimates between survivors and nonsurvivors of the outbreak revealed 15,769 candidate SNPs, of which 689 were annotated to 295 protein coding genes. These included 50 genes with functions related to innate and adaptive immune responses, and cytokine signalling pathways and genes thought to be involved in immune responses to other morbilliviruses. Our study characterised genomic regions and pathways that may contribute to CeMV immune responses in dolphins. This represents a stride towards clarifying the complex interactions of the cetacean immune system and emphasises the value of whole genome data sets in understanding genetic elements that are essential for species conservation, including disease susceptibility and adaptation.
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Affiliation(s)
- Kimberley C Batley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | | | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Ikuko Tomo
- South Australian Museum, Adelaide, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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8
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MHC Genotyping by SSCP and Amplicon-Based NGS Approach in Chamois. Animals (Basel) 2020; 10:ani10091694. [PMID: 32962183 PMCID: PMC7552744 DOI: 10.3390/ani10091694] [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: 08/10/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 11/17/2022] Open
Abstract
Genes of the major histocompatibility complex (MHC) code for cell surface proteins essential for adaptive immunity. They show the most outstanding genetic diversity in vertebrates, which has been connected with various fitness traits and thus with the long-term persistence of populations. In this study, polymorphism of the MHC class II DRB locus was investigated in chamois with Single-Strand Conformation Polymorphism (SSCP)/Sanger genotyping and Ion Torrent S5 next-generation sequencing (NGS). From eight identified DRB variants in 28 individuals, five had already been described, and three were new, undescribed alleles. With conventional SSCP/Sanger sequencing, we were able to detect seven alleles, all of which were also detected with NGS. We found inconsistencies in the individual genotypes between the two methods, which were mainly caused by allelic dropout in the SSCP/Sanger method. Six out of 28 individuals were falsely classified as homozygous with SSCP/Sanger analysis. Overall, 25% of the individuals were identified as genotyping discrepancies between the two methods. Our results show that NGS technologies are better performing in sequencing highly variable regions such as the MHC, and they also have a higher detection capacity, thus allowing a more accurate description of the genetic composition, which is crucial for evolutionary and population genetic studies.
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9
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Latitudinal diversity gradient and cetaceans from the perspective of MHC genes. Immunogenetics 2020; 72:393-398. [PMID: 32564115 DOI: 10.1007/s00251-020-01171-9] [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: 12/17/2019] [Accepted: 06/05/2020] [Indexed: 01/07/2023]
Abstract
Pathogen diversity is a key source of selective pressure on immune system genes, shaping molecular evolution mainly on widely distributed or migratory organisms such as cetaceans. Here, we investigated the effects of latitudinal span migration, different biomes occupation, and pathogen-mediated selection on MHC DQB locus divergence on cetaceans. We applied some evolutionary genetics methods using a dataset of 15 species and 121 sequences, and we found a trend on greater MHC divergence on tropical species when compared with either temperate or migratory species. In addition, oceanic cetaceans exhibit greater MHC divergence. Here, we show that, despite there was a correlation between the diversity of MHC DQB alleles with the distribution of organisms, the pattern of diversity found is not completely explained by pathogenic pressure, suggesting that other factors must be investigated for a better understanding of the processes related to the diversity of MHC in cetaceans.
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10
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Manlik O, Krützen M, Kopps AM, Mann J, Bejder L, Allen SJ, Frère C, Connor RC, Sherwin WB. Is MHC diversity a better marker for conservation than neutral genetic diversity? A case study of two contrasting dolphin populations. Ecol Evol 2019; 9:6986-6998. [PMID: 31380027 PMCID: PMC6662329 DOI: 10.1002/ece3.5265] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia-one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty-three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population-for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human-induced changes to the coastal ecosystem it inhabits.
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Affiliation(s)
- Oliver Manlik
- Biology Department, College of ScienceUnited Arab Emirates UniversityAl AinUnited Arab Emirates
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Michael Krützen
- Department of AnthropologyUniversity of ZurichZurichSwitzerland
| | - Anna M. Kopps
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Janet Mann
- Department of Biology and Department of PsychologyGeorgetown UniversityWashingtonDistrict of Columbia
| | - Lars Bejder
- Marine Mammal Research Program, Hawai'i Institute of Marine BiologyUniversity of Hawai'i at ManoaKaneoheHonolulu
- Aquatic Megafauna Research Unit, School of Veterinary and Life SciencesMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Simon J. Allen
- School of Biological SciencesUniversity of BristolBristolUnited Kingdom
| | - Celine Frère
- Faculty of Science, Health, Education and EngineeringUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | | | - William B. Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Aquatic Megafauna Research Unit, School of Veterinary and Life SciencesMurdoch UniversityMurdochWestern AustraliaAustralia
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11
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de Sá ALA, Breaux B, Burlamaqui TCT, Deiss TC, Sena L, Criscitiello MF, Schneider MPC. The Marine Mammal Class II Major Histocompatibility Complex Organization. Front Immunol 2019; 10:696. [PMID: 31019512 PMCID: PMC6459222 DOI: 10.3389/fimmu.2019.00696] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/13/2019] [Indexed: 12/17/2022] Open
Abstract
Sirenians share with cetaceans and pinnipeds several convergent traits selected for the aquatic lifestyle. Living in water poses new challenges not only for locomotion and feeding but also for combating new pathogens, which may render the immune system one of the best tools aquatic mammals have for dealing with aquatic microbial threats. So far, only cetaceans have had their class II Major Histocompatibility Complex (MHC) organization characterized, despite the importance of MHC genes for adaptive immune responses. This study aims to characterize the organization of the marine mammal class II MHC using publicly available genomes. We located class II sequences in the genomes of one sirenian, four pinnipeds and eight cetaceans using NCBI-BLAST and reannotated the sequences using local BLAST search with exon and intron libraries. Scaffolds containing class II sequences were compared using dotplot analysis and introns were used for phylogenetic analysis. The manatee class II region shares overall synteny with other mammals, however most DR loci were translocated from the canonical location, past the extended class II region. Detailed analysis of the genomes of closely related taxa revealed that this presumed translocation is shared with all other living afrotherians. Other presumptive chromosome rearrangements in Afrotheria are the deletion of DQ loci in Afrosoricida and deletion of DP in E. telfairi. Pinnipeds share the main features of dog MHC: lack of a functional pair of DPA/DPB genes and inverted DRB locus between DQ and DO subregions. All cetaceans share the Cetartiodactyla inversion separating class II genes into two subregions: class IIa, with DR and DQ genes, and class IIb, with non-classic genes and a DRB pseudogene. These results point to three distinct and unheralded class II MHC structures in marine mammals: one canonical organization but lacking DP genes in pinnipeds; one bearing an inversion separating IIa and IIb subregions lacking DP genes found in cetaceans; and one with a translocation separating the most diverse class II gene from the MHC found in afrotherians and presumptive functional DR, DQ, and DP genes. Future functional research will reveal how these aquatic mammals cope with pathogen pressures with these divergent MHC organizations.
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Affiliation(s)
- André Luiz Alves de Sá
- Laboratory of Applied Genetics, Socio-Environmental and Water Resources Institute, Federal Rural University of the Amazon, Belém, Brazil.,Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| | - Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | | | - Thaddeus Charles Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Leonardo Sena
- Center of Biodiversity Advanced Studies, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| | - Michael Frederick Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
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12
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Dooley CT, Ferrer T, Pagán H, O’Corry-Crowe GM. Bridging immunogenetics and immunoproteomics: Model positional scanning library analysis for Major Histocompatibility Complex class II DQ in Tursiops truncatus. PLoS One 2018; 13:e0201299. [PMID: 30070993 PMCID: PMC6072028 DOI: 10.1371/journal.pone.0201299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/12/2018] [Indexed: 02/02/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) is a critical element in mounting an effective immune response in vertebrates against invading pathogens. Studies of MHC in wildlife populations have typically focused on assessing diversity within the peptide binding regions (PBR) of the MHC class II (MHC II) family, especially the DQ receptor genes. Such metrics of diversity, however, are of limited use to health risk assessment since functional analyses (where changes in the PBR are correlated to recognition/pathologies of known pathogen proteins), are difficult to conduct in wildlife species. Here we describe a means to predict the binding preferences of MHC proteins: We have developed a model positional scanning library analysis (MPSLA) by harnessing the power of mixture based combinatorial libraries to probe the peptide landscapes of distinct MHC II DQ proteins. The algorithm provided by NNAlign was employed to predict the binding affinities of sets of peptides generated for DQ proteins. These binding affinities were then used to retroactively construct a model Positional Scanning Library screen. To test the utility of the approach, a model screen was compared to physical combinatorial screens for human MHC II DP. Model library screens were generated for DQ proteins derived from sequence data from bottlenose dolphins from the Indian River Lagoon (IRL) and the Atlantic coast of Florida, and compared to screens of DQ proteins from Genbank for dolphin and three other cetaceans. To explore the peptide binding landscape for DQ proteins from the IRL, combinations of the amino acids identified as active were compiled into peptide sequence lists that were used to mine databases for representation in known proteins. The frequency of which peptide sequences predicted to bind the MHC protein are found in proteins from pathogens associated with marine mammals was found to be significant (p values <0.0001). Through this analysis, genetic variation in MHC (classes I and II) can now be associated with the binding repertoires of the expressed MHC proteins and subsequently used to identify target pathogens. This approach may be eventually applied to evaluate individual population and species risk for outbreaks of emerging diseases.
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Affiliation(s)
- Colette T. Dooley
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida, United States of America
| | - Tatiana Ferrer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Heidi Pagán
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Gregory M. O’Corry-Crowe
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
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13
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Awadi A, Ben Slimen H, Smith S, Knauer F, Makni M, Suchentrunk F. Positive selection and climatic effects on MHC class II gene diversity in hares (Lepus capensis) from a steep ecological gradient. Sci Rep 2018; 8:11514. [PMID: 30065344 PMCID: PMC6068193 DOI: 10.1038/s41598-018-29657-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/16/2018] [Indexed: 11/24/2022] Open
Abstract
In natural populations, allelic diversity of the major histocompatibility complex (MHC) is commonly interpreted as resulting from positive selection in varying spatiotemporal pathogenic landscapes. Composite pathogenic landscape data are, however, rarely available. We studied the spatial distribution of allelic diversity at two MHC class II loci (DQA, DQB) in hares, Lepus capensis, along a steep ecological gradient in North Africa and tested the role of climatic parameters for the spatial distribution of DQA and DQB proteins. Climatic parameters were considered to reflect to some extent pathogenic landscape variation. We investigated historical and contemporary forces that have shaped the variability at both genes, and tested for differential selective pressure across the ecological gradient by comparing allelic variation at MHC and neutral loci. We found positive selection on both MHC loci and significantly decreasing diversity from North to South Tunisia. Our multinomial linear models revealed significant effects of geographical positions that were correlated with mean annual temperature and precipitation on the occurrence of protein variants, but no effects of co-occurring DQA or DQB proteins, respectively. Diversifying selection, recombination, adaptation to local pathogenic landscapes (supposedly reflected by climate parameters) and neutral demographic processes have shaped the observed MHC diversity and differentiation patterns.
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Affiliation(s)
- Asma Awadi
- Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'Intérêt Agronomique, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.
| | - Hichem Ben Slimen
- Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'Intérêt Agronomique, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,Institut Supérieur de Biotechnologie de Béja, University of Jendouba, Avenue Habib Bourguiba Béja 9000, BP. 382, Béja, Tunisia
| | - Steve Smith
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Felix Knauer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
| | - Mohamed Makni
- Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'Intérêt Agronomique, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160, Vienna, Austria
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14
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Stejskalova K, Bayerova Z, Futas J, Hrazdilova K, Klumplerova M, Oppelt J, Splichalova P, Di Guardo G, Mazzariol S, Di Francesco CE, Di Francesco G, Terracciano G, Paiu RM, Ursache TD, Modry D, Horin P. Candidate gene molecular markers as tools for analyzing genetic susceptibility to morbillivirus infection in stranded Cetaceans. HLA 2017; 90:343-353. [DOI: 10.1111/tan.13146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 07/25/2017] [Accepted: 09/06/2017] [Indexed: 12/17/2022]
Affiliation(s)
- K. Stejskalova
- Department of Animal Genetics; University of Veterinary and Pharmaceutical Sciences; Brno Czech Republic
| | - Z. Bayerova
- Department of Animal Genetics; University of Veterinary and Pharmaceutical Sciences; Brno Czech Republic
| | - J. Futas
- Department of Animal Genetics; University of Veterinary and Pharmaceutical Sciences; Brno Czech Republic
- Ceitec VFU, RG Animal Immunogenomics; Brno Czech Republic
| | - K. Hrazdilova
- Ceitec VFU, RG Molecular Microbiology; Brno Czech Republic
| | - M. Klumplerova
- Department of Animal Genetics; University of Veterinary and Pharmaceutical Sciences; Brno Czech Republic
| | - J. Oppelt
- Ceitec MU, Masaryk University; Brno Czech Republic
- Faculty of Science, National Centre for Biomolecular Research; Masaryk University; Brno Czech Republic
| | - P. Splichalova
- Ceitec VFU, RG Animal Immunogenomics; Brno Czech Republic
| | - G. Di Guardo
- Faculty of Veterinary Medicine; University of Teramo; Teramo Italy
| | - S. Mazzariol
- Department of Comparative Biomedicine and Food Science, Viale dell'Università; University of Padua; Padua Italy
| | | | - G. Di Francesco
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”; Teramo Italy
| | - G. Terracciano
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”; Pisa Italy
| | | | - T. D. Ursache
- Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca; Cluj-Napoca Romania
| | - D. Modry
- Ceitec VFU, RG Molecular Microbiology; Brno Czech Republic
- Department of Pathology and Parasitology; University of Veterinary and Pharmaceutical Sciences; Brno Czech Republic
- Biology Center, Czech Academy of Sciences; České Budějovice Czech Republic
| | - P. Horin
- Department of Animal Genetics; University of Veterinary and Pharmaceutical Sciences; Brno Czech Republic
- Ceitec VFU, RG Animal Immunogenomics; Brno Czech Republic
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