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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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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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4
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Zhang Z, Sun X, Chen M, Li L, Ren W, Xu S, Yang G. Genomic Organization and Phylogeny of MHC Class II Loci in Cetaceans. J Hered 2019; 110:332-339. [PMID: 30844043 DOI: 10.1093/jhered/esz005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 01/26/2019] [Indexed: 01/01/2023] Open
Abstract
Cetaceans are a suborder of secondarily adapted aquatic mammals with an enigmatic history involving a transition from land to sea approximately 55 Mya. During the transition period, cetaceans would have faced many new pathogen challenges, but limited information is available about the adaptive immune system of these mammals. The major histocompatibility complex (MHC) family plays a key role in antigen recognition and presentation in adaptive immunity, which is believed to have evolved in response to pathogens. In the present study, MHC class II loci were characterized in 7 published cetacean genome assemblies and the genomic organization of cetaceans was compared with that of their terrestrial relatives, the cow, sheep, and pig. A total of 9 MHC class II loci were identified in the cetacean genomes: DRA, DRB, DQA, DQB, DPB, DOA, DOB, DMA, and DMB. Sequences from 8 of the 9 genes included intact coding regions and were presumably functional. The organization of the MHC class II loci was conserved across the examined mammalian species, whereas the orientation and number of the alpha and beta genes varied among the species. The phylogenetic reconstruction of all MHC genes from Cetartiodactyla suggested that alpha and beta genes had different topologies. Additionally, based on a phylogenetic reconstruction of the multi-locus DRB, 2 (DRB1 and DRB2) of the 4 putative gene copies were hypothesized to have duplicated and evolved during the radiation of cetaceans.
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Affiliation(s)
- Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaohui Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Meixiu Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lili Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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5
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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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6
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Zhang P, Huang K, Zhang B, Dunn DW, Chen D, Li F, Qi X, Guo S, Li B. High polymorphism in MHC-DRB genes in golden snub-nosed monkeys reveals balancing selection in small, isolated populations. BMC Evol Biol 2018. [PMID: 29534675 PMCID: PMC5851093 DOI: 10.1186/s12862-018-1148-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background Maintaining variation in immune genes, such as those of the major histocompatibility complex (MHC), is important for individuals in small, isolated populations to resist pathogens and parasites. The golden snub-nosed monkey (Rhinopithecus roxellana), an endangered primate endemic to China, has experienced a rapid reduction in numbers and severe population fragmentation over recent years. For this study, we measured the DRB diversity among 122 monkeys from three populations in the Qinling Mountains, and estimated the relative importance of different agents of selection in maintaining variation of DRB genes. Results We identified a total of 19 DRB sequences, in which five alleles were novel. We found high DRB variation in R. roxellana and three branches of evidence suggesting that balancing selection has contributed to maintaining MHC polymorphism over the long term in this species: i) different patterns of both genetic diversity and population differentiation were detected at MHC and neutral markers; ii) an excess of non-synonymous substitutions compared to synonymous substitutions at antigen binding sites, and maximum-likelihood-based random-site models, showed significant positive selection; and iii) phylogenetic analyses revealed a pattern of trans-species evolution for DRB genes. Conclusions High levels of DRB diversity in these R. roxellana populations may reflect strong selection pressure in this species. Patterns of genetic diversity and population differentiation, positive selection, as well as trans-species evolution, suggest that pathogen-mediated balancing selection has contributed to maintaining MHC polymorphism in R. roxellana over the long term. This study furthers our understanding of the role pathogen-mediated balancing selection has in maintaining variation in MHC genes in small and fragmented populations of free-ranging vertebrates. Electronic supplementary material The online version of this article (10.1186/s12862-018-1148-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pei Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Bingyi Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Dan Chen
- Middle School Affiliated to Northwest University, Xi'an, China
| | - Fan Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiaoguang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China. .,Xi'an Branch of Chinese Academy of Science, Xi'an, China.
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7
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Ruan R, Ruan J, Wan XL, Zheng Y, Chen MM, Zheng JS, Wang D. Organization and characteristics of the major histocompatibility complex class II region in the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). Sci Rep 2016; 6:22471. [PMID: 26932528 PMCID: PMC4773811 DOI: 10.1038/srep22471] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 02/16/2016] [Indexed: 11/30/2022] Open
Abstract
Little is known about the major histocompatibility complex (MHC) in the genome of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) (YFP) or other cetaceans. In this study, a high-quality YFP bacterial artificial chromosome (BAC) library was constructed. We then determined the organization and characterization of YFP MHC class II region by screening the BAC library, followed by sequencing and assembly of positive BAC clones. The YFP MHC class II region consists of two segregated contigs (218,725 bp and 328,435 bp respectively) that include only eight expressed MHC class II genes, three pseudo MHC genes and twelve non-MHC genes. The YFP has fewer MHC class II genes than ruminants, showing locus reduction in DRB, DQA, DQB, and loss of DY. In addition, phylogenic and evolutionary analyses indicated that the DRB, DQA and DQB genes might have undergone birth-and-death evolution, whereas the DQB gene might have evolved under positive selection in cetaceans. These findings provide an essential foundation for future work, such as estimating MHC genetic variation in the YFP or other cetaceans. This work is the first report on the MHC class II region in cetaceans and offers valuable information for understanding the evolution of MHC genome in cetaceans.
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Affiliation(s)
- Rui Ruan
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jue Ruan
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong 518120, China
| | - Xiao-Ling Wan
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yang Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Min-Min Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jin-Song Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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8
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Zhang X, Lin W, Zhou R, Gui D, Yu X, Wu Y. Low Major Histocompatibility Complex Class II Variation in the Endangered Indo-Pacific Humpback Dolphin (Sousa chinensis): Inferences About the Role of Balancing Selection. J Hered 2016; 107:143-52. [PMID: 26787544 PMCID: PMC5994972 DOI: 10.1093/jhered/esv138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/04/2015] [Indexed: 11/13/2022] Open
Abstract
It has been widely reported that the major histocompatibility complex (MHC) is under balancing selection due to its immune function across terrestrial and aquatic mammals. The comprehensive studies at MHC and other neutral loci could give us a synthetic evaluation about the major force determining genetic diversity of species. Previously, a low level of genetic diversity has been reported among the Indo-Pacific humpback dolphin (Sousa chinensis) in the Pearl River Estuary (PRE) using both mitochondrial marker and microsatellite loci. Here, the expression and sequence polymorphism of 2 MHC class II genes (DQB and DRB) in 32 S. chinensis from PRE collected between 2003 and 2011 were investigated. High ratios of non-synonymous to synonymous substitution rates, codon-based selection analysis, and trans-species polymorphism (TSP) support the hypothesis that balancing selection acted on S. chinensis MHC sequences. However, only 2 haplotypes were detected at either DQB or DRB loci. Moreover, the lack of deviation from the Hardy-Weinberg expectation at DRB locus combined with the relatively low heterozygosity at both DQB locus and microsatellite loci suggested that balancing selection might not be sufficient, which further suggested that genetic drift associated with historical bottlenecks was not mitigated by balancing selection in terms of the loss of MHC and neutral variation in S. chinensis. The combined results highlighted the importance of maintaining the genetic diversity of the endangered S. chinensis.
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Affiliation(s)
| | - Wenzhi Lin
- *These authors contributed equally to the work
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9
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Moreno-Santillán DD, Lacey EA, Gendron D, Ortega J. Genetic Variation at Exon 2 of the MHC Class II DQB Locus in Blue Whale (Balaenoptera musculus) from the Gulf of California. PLoS One 2016; 11:e0141296. [PMID: 26761201 PMCID: PMC4712016 DOI: 10.1371/journal.pone.0141296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/07/2015] [Indexed: 11/22/2022] Open
Abstract
The genes of the Major Histocompatibility Complex (MHC) play an important role in the vertebrate immune response and are among the most polymorphic genes known in vertebrates. In some marine mammals, MHC genes have been shown to be characterized by low levels of polymorphism compared to terrestrial taxa; this reduction in variation is often explained as a result of lower pathogen pressures in marine habitats. To determine if this same reduction in variation applies to the migratory population of blue whales (Balaenoptera musculus) that occurs in the Gulf of California, we genotyped a 172 bp fragment of exon 2 of the MHC Class II DQB locus for 80 members of this population. Twenty-two putatively functional DQB allotypes were identified, all of which were homologous with DQB sequences from other cetacean species. Up to 5 putative alleles per individual were identified, suggesting that gene duplication has occurred at this locus. Rates of non-synonymous to synonymous substitutions (ω) and maximum likelihood analyses of models of nucleotide variation provided potential evidence of ongoing positive selection at this exon. Phylogenetic analyses of DQB alleles from B. musculus and 16 other species of cetaceans revealed trans-specific conservation of MHC variants, suggesting that selection has acted on this locus over prolonged periods of time. Collectively our findings reveal that immunogenic variation in blue whales is comparable to that in terrestrial mammals, thereby providing no evidence that marine taxa are subject to reduced pathogen-induced selective pressures.
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Affiliation(s)
- Diana D Moreno-Santillán
- Laboratorio de Bioconservación y Manejo, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Eileen A Lacey
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Diane Gendron
- Laboratorio de Ecología de Cetáceos y Quelonios, Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, La Paz, BCS, México
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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Real-Monroy MD, Martínez-Méndez N, Ortega J. MHC-DRB Exon 2 Diversity of the Jamaican Fruit-Eating Bat (Artibeus jamaicensis) from Mexico. ACTA CHIROPTEROLOGICA 2014. [DOI: 10.3161/150811014x687260] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Gillett RM, Murray BW, White BN. Characterization of class I- and class II-like major histocompatibility complex loci in pedigrees of North Atlantic right whales. J Hered 2013; 105:188-202. [PMID: 24381183 DOI: 10.1093/jhered/est095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned to the locus Eugl-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with ≥ 4 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II sequences were significantly different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species.
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Affiliation(s)
- Roxanne M Gillett
- the Natural Resources DNA Profiling and Forensic Centre, Department of Biology, Trent University, 2140 East Bank Drive, Peterborough, Ontario K9J 7B8, Canada
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12
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Osborne AJ, Zavodna M, Chilvers BL, Robertson BC, Negro SS, Kennedy MA, Gemmell NJ. Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection. Heredity (Edinb) 2013; 111:44-56. [PMID: 23572124 PMCID: PMC3692317 DOI: 10.1038/hdy.2013.18] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Revised: 12/20/2012] [Accepted: 01/28/2013] [Indexed: 11/09/2022] Open
Abstract
Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.
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Affiliation(s)
- A J Osborne
- Centre for Reproduction and Genomics, Department of Anatomy, University of Otago, Dunedin, New Zealand.
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Weber DS, Van Coeverden De Groot PJ, Peacock E, Schrenzel MD, Perez DA, Thomas S, Shelton JM, Else CK, Darby LL, Acosta L, Harris C, Youngblood J, Boag P, Desalle R. Low MHC variation in the polar bear: implications in the face of Arctic warming? Anim Conserv 2013. [DOI: 10.1111/acv.12045] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- D. S. Weber
- Division of Natural Sciences; New College of Florida; Sarasota FL USA
- American Museum of Natural History; New York NY USA
| | | | - E. Peacock
- Department of Environment; The Government of Nunavut; Igloolik NU Canada
| | - M. D. Schrenzel
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - D. A. Perez
- American Museum of Natural History; New York NY USA
- Stevens Institute of Technology; Hoboken NJ USA
| | - S. Thomas
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - J. M. Shelton
- American Museum of Natural History; New York NY USA
- Brooklyn College; City University of New York; New York NY USA
| | | | - L. L. Darby
- American Museum of Natural History; New York NY USA
- Columbia University; New York NY USA
| | - L. Acosta
- American Museum of Natural History; New York NY USA
- Villanova University; Villanova PA USA
| | - C. Harris
- Biology Department; Queen's University; Kingston ON Canada
| | - J. Youngblood
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - P. Boag
- Biology Department; Queen's University; Kingston ON Canada
| | - R. Desalle
- American Museum of Natural History; New York NY USA
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14
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Nie C, Zhao J, Li Y, Wu X. Diversity and selection of MHC class IIb gene exon3 in Chinese alligator. Mol Biol Rep 2012; 40:295-301. [PMID: 23065218 DOI: 10.1007/s11033-012-2061-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 10/03/2012] [Indexed: 12/01/2022]
Abstract
Our study used MHC class IIb gene exon3 complete sequence as markers to investigate genetic variability, selection and population differentiation in Chinese alligator. In this study, 282 bp MHC IIb exon3 complete sequence was got, none of the sequences contained insertions/deletions or stop codons, suggesting that all sequences might come from functional molecules in the genome. The neighbor-joining (NJ) tree revealed that Xuangzhou and Changxing populations were genetically close related, while Wild population showed the most diverse from the other. Gene flow (Nm) was very higher than one, suggesting that inter-group gene flow may have occurred. Furthermore, the results showed that MHC IIb gene might be a good molecular marker, we think that this technology could be used for Chinese alligator breeding and releasing in future.
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Affiliation(s)
- Chuanpeng Nie
- College of Life Sciences, Institute of Traditional Chinese Medicine Resources, Anhui Normal University, Wuhu 241000, People's Republic of China
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15
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Xu S, Ju J, Zhou X, Wang L, Zhou K, Yang G. Considerable MHC diversity suggests that the functional extinction of baiji is not related to population genetic collapse. PLoS One 2012; 7:e30423. [PMID: 22272349 PMCID: PMC3260281 DOI: 10.1371/journal.pone.0030423] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 12/15/2011] [Indexed: 12/02/2022] Open
Abstract
To further extend our understanding of the mechanism causing the current nearly extinct status of the baiji (Lipotes vexillifer), one of the most critically endangered species in the world, genetic diversity at the major histocompatibility complex (MHC) class II DRB locus was investigated in the baiji. Nine highly divergent DRB alleles were identified in 17 samples, with an average of 28.4 (13.2%) nucleotide difference and 16.7 (23.5%) amino acid difference between alleles. The unexpectedly high levels of DRB allelic diversity in the baiji may partly be attributable to its evolutionary adaptations to the freshwater environment which is regarded to have a higher parasite diversity compared to the marine environment. In addition, balancing selection was found to be the main mechanisms in generating sequence diversity at baiji DRB gene. Considerable sequence variation at the adaptive MHC genes despite of significant loss of neutral genetic variation in baiji genome might suggest that intense selection has overpowered random genetic drift as the main evolutionary forces, which further suggested that the critically endangered or nearly extinct status of the baiji is not an outcome of genetic collapse.
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Affiliation(s)
- Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jianfeng Ju
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lian Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- * E-mail:
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16
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Ujvari B, Belov K. Major Histocompatibility Complex (MHC) markers in conservation biology. Int J Mol Sci 2011; 12:5168-86. [PMID: 21954351 PMCID: PMC3179158 DOI: 10.3390/ijms12085168] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/27/2011] [Accepted: 08/05/2011] [Indexed: 12/28/2022] Open
Abstract
Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a changing environment. In this way, loss of genetic polymorphism is linked with extinction risk. Recent advances in sequencing technologies mean that obtaining measures of genetic diversity at functionally important genes is within reach for conservation programs. A key region of the genome that should be targeted for population genetic studies is the Major Histocompatibility Complex (MHC). MHC genes, found in all jawed vertebrates, are the most polymorphic genes in vertebrate genomes. They play key roles in immune function via immune-recognition and -surveillance and host-parasite interaction. Therefore, measuring levels of polymorphism at these genes can provide indirect measures of the immunological fitness of populations. The MHC has also been linked with mate-choice and pregnancy outcomes and has application for improving mating success in captive breeding programs. The recent discovery that genetic diversity at MHC genes may protect against the spread of contagious cancers provides an added impetus for managing and protecting MHC diversity in wild populations. Here we review the field and focus on the successful applications of MHC-typing for conservation management. We emphasize the importance of using MHC markers when planning and executing wildlife rescue and conservation programs but stress that this should not be done to the detriment of genome-wide diversity.
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Affiliation(s)
- Beata Ujvari
- Faculty of Veterinary Science, University of Sydney, RMC Gunn Bldg, Sydney, NSW 2006, Australia; E-Mail:
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, RMC Gunn Bldg, Sydney, NSW 2006, Australia; E-Mail:
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17
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Xu S, Ren W, Zhou X, Zhou K, Yang G. Sequence polymorphism and geographical variation at a positively selected MHC-DRB gene in the finless porpoise (Neophocaena phocaenoides): implication for recent differentiation of the Yangtze finless porpoise? J Mol Evol 2010; 71:6-22. [PMID: 20563867 DOI: 10.1007/s00239-010-9357-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2009] [Accepted: 06/01/2010] [Indexed: 01/03/2023]
Abstract
Sequence polymorphism at the MHC class II DRB locus was investigated in three finless porpoise (Neophocaena phocaenoides) populations in Chinese waters. Intragenic recombination and strong positive selection were the main forces in generating sequence diversity in the DRB gene. MHC sequence diversity changed significantly along the study period. Significant decrease in heterozygosity and lost alleles have been detected in the Yangtze River population and South China Sea population since 1990. Furthermore, there is a trend of increasing population differentiation over time. Especially, the genetic differentiation between the Yangtze River population and the Yellow Sea population was very low prior to 1990 (F (ST) = 0.036, P = 0.009), but became very significant after 1990 (F (ST) = 0.134, P < 0.001), suggesting a recent augmentation of genetic differentiation between both populations probably in a relatively short-term period. Porpoises from the Yangtze River displayed divergent frequencies of shared and private alleles from those displayed by two marine populations, which suggest that the former riverine population has been under a different selection regime (characteristic of a fresh water environment) than that of its marine counterparts.
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Affiliation(s)
- Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210046, China
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18
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Du H, Zheng J, Wu M, Zhao Q, Wang D. High MHC DQB variation and asymmetric allelic distribution in the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis. Biochem Genet 2010; 48:433-49. [PMID: 20087659 DOI: 10.1007/s10528-009-9327-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2008] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
The endangered Yangtze finless porpoise is found in the middle and lower reaches of the Yangtze River and its adjoining big lakes. To explore the major histocompatibility complex (MHC) genetic diversity and allelic distribution patterns across its range, we investigated variation at DQB exon 2. From 76 porpoises, we identified 18 DQB sequences. The freshwater Yangtze populations had much higher allelic diversity than marine populations. Among these freshwater populations, the middle-reach population had higher allelic diversity than the lower-reach population. The high DQB diversity level, relative to that of a neutral mtDNA locus, suggests that balancing selection is acting at the DQB gene and that rapid evolution and local positive selection play critical roles in generating and retaining high MHC diversity in the freshwater population. As the balancing selection might be driven by environmental pathogens, we suggest that maintaining MHC variation should be a high priority in the conservation and management of this endangered population, especially as an ex situ conservation strategy.
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Affiliation(s)
- Hejun Du
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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19
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Sequence polymorphism and evolution of three cetacean MHC genes. J Mol Evol 2009; 69:260-75. [PMID: 19693422 DOI: 10.1007/s00239-009-9272-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 07/21/2009] [Accepted: 08/02/2009] [Indexed: 12/24/2022]
Abstract
Sequence variability at three major histocompatibility complex (MHC) genes (DQB, DRA, and MHC-I) of cetaceans was investigated in order to get an overall understanding of cetacean MHC evolution. Little sequence variation was detected at the DRA locus, while extensive and considerable variability were found at the MHC-I and DQB loci. Phylogenetic reconstruction and sequence comparison revealed extensive sharing of identical MHC alleles among different species at the three MHC loci examined. Comparisons of phylogenetic trees for these MHC loci with the trees reconstructed only based on non-PBR sites revealed that allelic similarity/identity possibly reflected common ancestry and were not due to adaptive convergence. At the same time, trans-species evolution was also evidenced that the allelic diversity of the three MHC loci clearly pre-dated species divergence events according to the relaxed molecular clock. It may be the forces of balancing selection acting to maintain the high sequence variability and identical alleles in trans-specific manner at the MHC-I and DQB loci.
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20
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Beineke A, Siebert U, Wohlsein P, Baumgärtner W. Immunology of whales and dolphins. Vet Immunol Immunopathol 2009; 133:81-94. [PMID: 19700205 DOI: 10.1016/j.vetimm.2009.06.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 05/08/2009] [Accepted: 06/22/2009] [Indexed: 11/25/2022]
Abstract
The increasing disease susceptibility in different whale and dolphin populations has led to speculation about a possible negative influence of environmental contaminants on the immune system and therefore on the health status of marine mammals. Despite current efforts in the immunology of marine mammals several aspects of immune functions in aquatic mammals remain unknown. However, assays for evaluating cellular immune responses, such as lymphocyte proliferation, respiratory burst as well as phagocytic and cytotoxic activity of leukocytes and humoral immune responses have been established for different cetacean species. Additionally, immunological and molecular techniques enable the detection and quantification of pro- and anti-inflammatory cytokines in lymphoid cells during inflammation or immune responses, respectively. Different T and B cell subsets as well as antigen-presenting cells can be detected by flow cytometry and immunohistochemistry. Despite great homologies between marine and terrestrial mammal lymphoid organs, some unique anatomical structures, particularly the complex lymphoepithelial laryngeal glands in cetaceans represent an adaptation to the marine environment. Additionally, physiological changes, such as age-related thymic atrophy and cystic degeneration of the "anal tonsil" of whales have to be taken into account when investigating these lymphoid structures. Systemic morbillivirus infections lead to fatalities in cetaceans associated with generalized lymphoid depletion. Similarly, chronic diseases and starvation are associated with a loss of functional lymphoid cells and decreased resistance against opportunistic infections. There is growing evidence for an immunotoxic effect of different environmental contaminants in whales and dolphins, as demonstrated in field studies. Furthermore, immunomodulatory properties of different persistent xenobiotics have been confirmed in cetacean lymphoid cells in vitro as well as in animal models in vivo. However, species-specific differences of the immune system and detoxification of xenobiotics between cetaceans and laboratory rodents have to be considered when interpreting these toxicological data for risk assessment in whales and dolphins.
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Affiliation(s)
- Andreas Beineke
- Department of Pathology, University of Veterinary Medicine, Bünteweg 17, 30559 Hannover, Germany
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21
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Barbisan F, Savio C, Bertorelle G, Patarnello T, Congiu L. Duplication polymorphism at MHC class II DRB1 locus in the wild boar (Sus scrofa). Immunogenetics 2008; 61:145-51. [DOI: 10.1007/s00251-008-0339-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 10/16/2008] [Indexed: 11/30/2022]
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22
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Xu S, Chen B, Zhou K, Yang G. High similarity at three MHC loci between the baiji and finless porpoise: Trans-species or convergent evolution? Mol Phylogenet Evol 2008; 47:36-44. [DOI: 10.1016/j.ympev.2007.05.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 04/28/2007] [Accepted: 05/30/2007] [Indexed: 10/23/2022]
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23
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Munguia-Vega A, Esquer-Garrigos Y, Rojas-Bracho L, Vazquez-Juarez R, Castro-Prieto A, Flores-Ramirez S. Genetic drift vs. natural selection in a long-term small isolated population: major histocompatibility complex class II variation in the Gulf of California endemic porpoise (Phocoena sinus). Mol Ecol 2007; 16:4051-65. [PMID: 17727623 DOI: 10.1111/j.1365-294x.2007.03319.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although many studies confirm long-term small isolated populations (e.g. island endemics) commonly sustain low neutral genetic variation as a result of genetic drift, it is less clear how selection on adaptive or detrimental genes interplay with random forces. We investigated sequence variation at two major histocompatibility complex (Mhc) class II loci on a porpoise endemic to the upper Gulf of California, México (Phocoena sinus, or vaquita). Its unique declining population is estimated around 500 individuals. Single-strand conformation polymorphism analysis revealed one putative functional allele fixed at the locus DQB (n = 25). At the DRB locus, we found two presumed functional alleles (n = 29), differing by a single nonsynonymous nucleotide substitution that could increase the stability at the dimer interface of alphabeta-heterodimers on heterozygous individuals. Identical trans-specific DQB1 and DRB1 alleles were identified between P. sinus and its closest relative, the Burmeister's porpoise (Phocoena spinipinnis). Comparison with studies on four island endemic mammals suggests fixation of one allele, due to genetic drift, commonly occurs at the DQA or DQB loci (effectively neutral). Similarly, deleterious alleles of small effect are also effectively neutral and can become fixed; a high frequency of anatomical malformations on vaquita gave empirical support to this prediction. In contrast, retention of low but functional polymorphism at the DRB locus was consistent with higher selection intensity. These observations indicated natural selection could maintain (and likely also purge) some crucial alleles even in the face of strong and prolonged genetic drift and inbreeding, suggesting long-term small populations should display low inbreeding depression. Low levels of Mhc variation warn about a high susceptibility to novel pathogens and diseases in vaquita.
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Affiliation(s)
- Adrian Munguia-Vega
- Centro de Investigaciones Biológicas del Noroeste, SC Mar Bermejo 195, Playa Palo Santa Rita. La Paz, Baja California Sur, México 23090.
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24
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Xu S, Sun P, Zhou K, Yang G. Sequence variability at three MHC loci of finless porpoises (Neophocaena phocaenoides). Immunogenetics 2007; 59:581-92. [PMID: 17486336 DOI: 10.1007/s00251-007-0223-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 03/31/2007] [Indexed: 11/29/2022]
Abstract
Major histocompatibility complex (MHC) class II DQB and DRA genes and class I gene of finless porpoises (Neophocaena phocaenoides) were investigated by single-strand conformation polymorphism and sequence analysis. The DRA, DQB, and MHC-I loci each contained 5, 14, and 34 unique sequences, respectively, and considerable sequence variation was found at the MHC-I and DQB loci. Gene duplication was manifested as three to five distinct sequences at each of the DQB and MHC-I loci from some individuals, and these sequences at each of the two loci separately clustered into four groups (cluster A, B, C, and D) based on the phylogenetic trees. Phylogenetic reconstruction revealed a trans-species pattern of evolution. Relatively high rates of non-synonymous (dN) vs synonymous (dS) substitution in the peptide-binding region (PBR) suggested balancing selection for maintaining polymorphisms at the MHC-I and DQB loci. In contrast, one single locus with little sequence variation was detected in the DRA gene, and no non-synonymous substitutions in the PBR indicated no balancing selection on this gene.
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Affiliation(s)
- Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 122 Ninghai Road, Nanjing 210097, China
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25
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Baker CS, Vant MD, Dalebout ML, Lento GM, O'Brien SJ, Yuhki N. Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (suborder: Mysticeti). Immunogenetics 2006; 58:283-96. [PMID: 16568262 DOI: 10.1007/s00251-006-0080-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Accepted: 12/21/2005] [Indexed: 10/24/2022]
Abstract
The molecular diversity and phylogenetic relationships of two class II genes of the baleen whale major histocompatibility complex were investigated and compared to toothed whales and out-groups. Amplification of the DQB exon 2 provided sequences showing high within-species and between-species nucleotide diversity and uninterrupted reading frames consistent with functional class II loci found in related mammals (e.g., ruminants). Cloning of amplified products indicated gene duplication in the humpback whale and triplication in the southern right whale, with average nucleotide diversity of 5.9 and 6.3%, respectively, for alleles of each species. Significantly higher nonsynonymous divergence at sites coding for peptide binding (32% for humpback and 40% for southern right) suggested that these loci were subject to positive (overdominant) selection. A population survey of humpback whales detected 23 alleles, differing by up to 21% of their inferred amino acid sequences. Amplification of the DRB exon 2 resulted in two groups of sequences. One was most similar to the DRB3 of the cow and present in all whales screened to date, including toothed whales. The second was most similar to the DRB2 of the cow and was found only in the bowhead and right whales. Both loci showed low diversity among species and apparent loss of function or altered function including interruption of reading frames. Finally, comparison of inferred protein sequence of the DRB3-like locus suggested convergence with the DQB, perhaps resulting from intergenic conversion or recombination.
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Affiliation(s)
- C S Baker
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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