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De Cahsan B, Kiemel K, Westbury MV, Lauritsen M, Autenrieth M, Gollmann G, Schweiger S, Stenberg M, Nyström P, Drews H, Tiedemann R. Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad. Ecol Evol 2021; 11:9776-9790. [PMID: 34306661 PMCID: PMC8293767 DOI: 10.1002/ece3.7805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/14/2021] [Accepted: 05/28/2021] [Indexed: 11/20/2022] Open
Abstract
Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation.
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Affiliation(s)
- Binia De Cahsan
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Katrin Kiemel
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | | | - Maike Lauritsen
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Marijke Autenrieth
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Günter Gollmann
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
| | - Silke Schweiger
- Herpetological CollectionNatural History Museum ViennaViennaAustria
| | | | | | - Hauke Drews
- Stiftung Naturschutz Schleswig‐HolsteinMolfseeGermany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic ZoologyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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Talarico L, Babik W, Marta S, Mattoccia M. Genetic drift shaped MHC IIB diversity of an endangered anuran species within the Italian glacial refugium. J Zool (1987) 2018. [DOI: 10.1111/jzo.12617] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- L. Talarico
- Department of Biology University of Tor Vergata Rome Italy
| | - W. Babik
- Institute of Environmental Sciences Jagiellonian University Kraków Poland
| | - S. Marta
- Department of Biology University of Tor Vergata Rome Italy
- Institute of Ecosystem Studies National Research Council Rome Italy
- Department of Environmental Sciences and Policy University of Milan Milan Italy
| | - M. Mattoccia
- Department of Biology University of Tor Vergata Rome Italy
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3
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Genetic variation and selection of MHC class I loci differ in two congeneric frogs. Genetica 2018; 146:125-136. [PMID: 29450668 DOI: 10.1007/s10709-018-0016-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
Abstract
Major histocompatibility complex (MHC) genes encode proteins in the acquired immune response pathway that often show distinctive selection-driven patterns in wild vertebrate populations. We examined genetic variation and signatures of selection in the MHC class I alpha 1 (A1)- and alpha 2 (A2)-domain encoding exons of two frog congeners [Agalychnis callidryas (n = 20) and A. lemur (n = 20)] from a single locality in Panama. We also investigated how historical demographic processes may have impacted MHC genetic diversity by analyzing a neutral mitochondrial marker. We found that both MHC domains were highly variable in both species, with both species likely expressing three loci. Our analyses revealed different signatures of selection between the two species, most notably that the A. callidryas A2 domain had experienced positive selection while the A2 domain of A. lemur had not. Diversifying selection acted on the same number of A1 and A2 allelic lineages, but on a higher percentage of A1 sites compared to A2 sites. Neutrality tests of mitochondrial haplotypes predominately indicated that the two species were at genetic equilibrium when the samples were collected. In addition, two historical tests of demography indicated both species have had relatively stable population sizes over the past 100,000 years; thus large population size changes are unlikely to have greatly influenced MHC diversity in either species during this time period. In conclusion, our results suggest that the impact of selection on MHC diversity varied between these two closely related species, likely due to a combination of distinct ecological conditions and past pathogenic pressures.
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Liu H, Xue F, Gong J, Wan Q, Fang S. Limited polymorphism of the functional MHC class II B gene in the black-spotted frog ( Pelophylax nigromaculatus) identified by locus-specific genotyping. Ecol Evol 2017; 7:9860-9868. [PMID: 29238521 PMCID: PMC5723586 DOI: 10.1002/ece3.3408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 07/31/2017] [Accepted: 08/19/2017] [Indexed: 12/23/2022] Open
Abstract
Amphibians can be more vulnerable to environmental changes and diseases than other species because of their complex life cycle and physiological requirements. Therefore, understanding the adaptation of amphibians to environmental changes is crucial for their conservation. Major histocompatibility complex (MHC) presents an excellent tool for the investigation of adaptive variations and the assessment of adaptive potential because it can be under strong diversifying selection. Here, we isolated the MHC class II B (MHCIIB) gene from cDNA sequences of the black-spotted frog (Pelophylax nigromaculatus), a widespread amphibian species in China, and designed locus-specific primers to characterize adaptive variability of this amphibian. Ten alleles were identified from 67 individual frogs of three populations and no more than two alleles were present in each individual animal. Furthermore, none of the sequences had indels or/and stop codons, which is in good agreement with locus-specific amplification of a functional gene. However, we found low polymorphism at both nucleotide and amino acid levels, even in the antigen-binding region. Purifying selection acting at this locus was supported by the findings that the dN/dS ratio across all alleles was below 1 and that negatively selected sites were detected by different methods. Allele frequency distributions were significantly different among geographic populations, indicating that physiographic factors may have strong effect on the genetic structure of the black-spotted frog. This study revealed limited polymorphism of three adjacent black-spotted frog populations at the functional MHCIIB locus, which may be attributed to region-specific differences. The locus-specific genotyping technique developed in this study would provide a foundation for future studies on adaptive divergence among different frog populations.
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Affiliation(s)
- Hong‐Yi Liu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Fei Xue
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Jie Gong
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Qiu‐Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
| | - Sheng‐Guo Fang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and State Conservation Centre for Gene Resources of Endangered WildlifeCollege of Life SciencesZhejiang UniversityHangzhouChina
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5
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Mulder KP, Cortazar-Chinarro M, Harris DJ, Crottini A, Campbell Grant EH, Fleischer RC, Savage AE. Evolutionary dynamics of an expressed MHC class IIβ locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 76:177-188. [PMID: 28587861 DOI: 10.1016/j.dci.2017.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.
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Affiliation(s)
- Kevin P Mulder
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Rua Padre Armando Quintas 7, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Maria Cortazar-Chinarro
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - D James Harris
- CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Rua Padre Armando Quintas 7, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Angelica Crottini
- CIBIO/InBIO, Research Centre in Biodiversity and Genetic Resources, Rua Padre Armando Quintas 7, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Evan H Campbell Grant
- United States Geological Survey, Patuxent Wildlife Research Center, SO Conte Anadromous Fish Research Lab, 1 Migratory Way, Turner Falls, MA 01376, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Anna E Savage
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Department of Biology, University of Central Florida, 4110 Libra Drive, Orlando, FL 32816, USA.
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6
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Didinger C, Eimes JA, Lillie M, Waldman B. Multiple major histocompatibility complex class I genes in Asian anurans: Ontogeny and phylogeny. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 70:69-79. [PMID: 28027939 DOI: 10.1016/j.dci.2016.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 06/06/2023]
Abstract
Amphibians, as the first terrestrial vertebrates, offer a window into early major histocompatibility complex (MHC) evolution. We characterized the MHC class I of two Korean amphibians, the Asiatic toad (Bufo gargarizans) and the Japanese tree frog (Hyla japonica). We found at least four transcribed MHC class I (MHC I) loci, the highest number confirmed in any anuran to date. Furthermore, we identified MHC I transcripts in terrestrial adults, and possibly in aquatic larvae, of both species. We conducted a phylogenetic analysis based on MHC I sequence data and found that B. gargarizans and H. japonica cluster together in the superfamily Nobleobatrachia. We further identified three supertypes shared by the two species. Our results reveal substantial variation in the number of MHC I loci in anurans and suggest that certain supertypes have particular physiochemical properties that may confer pathogen resistance.
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Affiliation(s)
- Chelsea Didinger
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - John A Eimes
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Mette Lillie
- Department of Medical Biochemistry and Microbiology (IMBIM), Genomics, Uppsala University, Box 582, 75123 Uppsala, Sweden
| | - Bruce Waldman
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea.
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7
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Savage AE, Zamudio KR. Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations. Proc Biol Sci 2016; 283:20153115. [PMID: 27009220 PMCID: PMC4822461 DOI: 10.1098/rspb.2015.3115] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/23/2016] [Indexed: 11/20/2022] Open
Abstract
Amphibians have been affected globally by the disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), and we are just now beginning to understand how immunogenetic variability contributes to disease susceptibility. Lineages of an expressed major histocompatibility complex (MHC) class II locus involved in acquired immunity are associated with chytridiomycosis susceptibility in controlled laboratory challenge assays. Here, we extend these findings to natural populations that vary both in exposure and response to Bd. We find that MHC alleles and supertypes associated with Bd survival in the field show a molecular signal of positive selection, while those associated with susceptibility do not, supporting the hypothesis that heritable Bd tolerance is rapidly evolving. We compare MHC supertypes to neutral loci to demonstrate where selection versus demography is shaping MHC variability. One population with Bd tolerance in nature shows a significant signal of directional selection for the same allele (allele Q) that was significantly associated with survival in an earlier laboratory study. Our findings indicate that selective pressure for Bd survival drives rapid immunogenetic adaptation in some natural populations, despite differences in environment and demography. Our field-based analysis of immunogenetic variation confirms that natural amphibian populations have the evolutionary potential to adapt to chytridiomycosis.
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Affiliation(s)
- Anna E Savage
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853, USA
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853, USA
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8
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Molecular characterization of MHC class II in the Australian invasive cane toad reveals multiple splice variants. Immunogenetics 2016; 68:449-460. [DOI: 10.1007/s00251-016-0919-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
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9
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Bataille A, Cashins SD, Grogan L, Skerratt LF, Hunter D, McFadden M, Scheele B, Brannelly LA, Macris A, Harlow PS, Bell S, Berger L, Waldman B. Susceptibility of amphibians to chytridiomycosis is associated with MHC class II conformation. Proc Biol Sci 2015; 282:rspb.2014.3127. [PMID: 25808889 PMCID: PMC4389617 DOI: 10.1098/rspb.2014.3127] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd) can cause precipitous population declines in its amphibian hosts. Responses of individuals to infection vary greatly with the capacity of their immune system to respond to the pathogen. We used a combination of comparative and experimental approaches to identify major histocompatibility complex class II (MHC-II) alleles encoding molecules that foster the survival of Bd-infected amphibians. We found that Bd-resistant amphibians across four continents share common amino acids in three binding pockets of the MHC-II antigen-binding groove. Moreover, strong signals of selection acting on these specific sites were evident among all species co-existing with the pathogen. In the laboratory, we experimentally inoculated Australian tree frogs with Bd to test how each binding pocket conformation influences disease resistance. Only the conformation of MHC-II pocket 9 of surviving subjects matched those of Bd-resistant species. This MHC-II conformation thus may determine amphibian resistance to Bd, although other MHC-II binding pockets also may contribute to resistance. Rescuing amphibian biodiversity will depend on our understanding of amphibian immune defence mechanisms against Bd. The identification of adaptive genetic markers for Bd resistance represents an important step forward towards that goal.
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Affiliation(s)
- Arnaud Bataille
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea
| | - Scott D Cashins
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Laura Grogan
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Lee F Skerratt
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - David Hunter
- New South Wales Office of Environment and Heritage, Biodiversity Conservation Section, Queanbeyan, New South Wales 2620, Australia
| | - Michael McFadden
- Taronga Conservation Society Australia, Herpetofauna Division, Mosman, New South Wales 2088, Australia
| | - Benjamin Scheele
- Fenner School of Environment and Society, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Laura A Brannelly
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Amy Macris
- Fenner School of Environment and Society, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Peter S Harlow
- Taronga Conservation Society Australia, Herpetofauna Division, Mosman, New South Wales 2088, Australia
| | - Sara Bell
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Lee Berger
- School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Bruce Waldman
- Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University, Seoul 151-747, South Korea
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10
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Mable BK, Kilbride E, Viney ME, Tinsley RC. Copy number variation and genetic diversity of MHC Class IIb alleles in an alien population of Xenopus laevis. Immunogenetics 2015; 67:591-603. [PMID: 26329765 PMCID: PMC4572066 DOI: 10.1007/s00251-015-0860-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/10/2015] [Indexed: 12/23/2022]
Abstract
Xenopus laevis (the African clawed frog), which originated through hybridisation and whole genome duplication, has been used as a model for genetics and development for many years, but surprisingly little is known about immune gene variation in natural populations. The purpose of this study was to use an isolated population of X. laevis that was introduced to Wales, UK in the past 50 years to investigate how variation at the MHC compares to that at other loci, following a severe population bottleneck. Among 18 individuals, we found nine alleles based on exon 2 sequences of the Class IIb region (which includes the peptide binding region). Individuals carried from one to three of the loci identified from previous laboratory studies. Genetic variation was an order of magnitude higher at the MHC compared with three single-copy nuclear genes, but all loci showed high levels of heterozygosity and nucleotide diversity and there was not an excess of homozygosity or decrease in diversity over time that would suggest extensive inbreeding in the introduced population. Tajima’s D was positive for all loci, which is consistent with a bottleneck. Moreover, comparison with published sequences identified the source of the introduced population as the Western Cape region of South Africa, where most commercial suppliers have obtained their stocks. These factors suggest that despite founding by potentially already inbred individuals, the alien population in Wales has maintained substantial genetic variation at both adaptively important and neutral genes.
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Affiliation(s)
- Barbara K Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Elizabeth Kilbride
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mark E Viney
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
| | - Richard C Tinsley
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
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11
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Huang ZQ, Sun XM, Dai JJ, Gu ML, Ye YS, Yao YF, Jiang RJ, Ma KL. Sequence diversity of the MHC Ⅱ DRB gene in Chinese tree shrews (Tupaia belangeri chinensis). BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Yu X, Zheng R, Zhang J, Shen B, Dong B. Genetic polymorphism of major histocompatibility complex class IIB alleles and pathogen resistance in the giant spiny frog Quasipaa spinosa. INFECTION GENETICS AND EVOLUTION 2014; 28:175-82. [PMID: 25269786 DOI: 10.1016/j.meegid.2014.09.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/28/2014] [Accepted: 09/22/2014] [Indexed: 12/31/2022]
Abstract
Major histocompatibility complex (MHC) genes are candidates for determining disease susceptibility due to their pivotal role in both innate and adaptive immune responses. Accordingly, the association between the genetic variation of MHC genes and the pathogen resistance has been investigated in numerous vertebrates. To date, however, little is reported in amphibians. In this study, we investigate the genetic variation at the MHC class IIB gene in the giant spiny frog Quasipaa spinosa, which has high commercial value in China. The full length of MHC class IIB cDNA was cloned from Q. spinosa by homology cloning and rapid amplification of cDNA end-polymerase chain reaction (RACE-PCR). Two MHC class IIB loci were identified in Q. spinosa. We also developed PCR primers for a portion of the second exon of the MHC class IIB gene. A total of 26 MHC class IIB alleles were identified. The dN rate was significantly higher than the dS rate in the putative peptide-binding region, thereby proving the positive selection hypothesis. In addition, individuals intraperitoneally injected with Aeromonas hydrophila were used to study the association between MHC class IIB alleles and pathogen resistance/susceptibility, to explore the specific alleles in balancing selection. Eighty frogs were used after exposure to A. hydrophila infection. Nine alleles were used to study the association between the alleles and disease resistance. Two alleles, namely, Pasa-DAB(∗)1301 and Pasa-DAB(∗)0901, were significantly associated with resistance against A. hydrophila. This study provides valuable information on the structure of the MHC class IIB gene and confirms the association between MHC class IIB gene alleles and disease resistance to bacterial infection in Q. spinosa. Moreover, pathogen resistance-related MHC markers can be used for the selective breeding of the giant spiny frog.
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Affiliation(s)
- Xiaoyun Yu
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Rongquan Zheng
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang 321004, China.
| | - Jiayong Zhang
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Bing Shen
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Baojuan Dong
- Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
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13
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Drift rather than selection dominates MHC class II allelic diversity patterns at the biogeographical range scale in natterjack toads Bufo calamita. PLoS One 2014; 9:e100176. [PMID: 24937211 PMCID: PMC4061088 DOI: 10.1371/journal.pone.0100176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 05/23/2014] [Indexed: 12/31/2022] Open
Abstract
Study of major histocompatibility complex (MHC) loci has gained great popularity in recent years, partly due to their function in protecting vertebrates from infections. This is of particular interest in amphibians on account of major threats many species face from emergent diseases such as chytridiomycosis. In this study we compare levels of diversity in an expressed MHC class II locus with neutral genetic diversity at microsatellite loci in natterjack toad (Bufo (Epidalea) calamita) populations across the whole of the species' biogeographical range. Variation at both classes of loci was high in the glacial refugium areas (REF) and much lower in postglacial expansion areas (PGE), especially in range edge populations. Although there was clear evidence that the MHC locus was influenced by positive selection in the past, congruence with the neutral markers suggested that historical demographic events were the main force shaping MHC variation in the PGE area. Both neutral and adaptive genetic variation declined with distance from glacial refugia. Nevertheless, there were also some indications from differential isolation by distance and allele abundance patterns that weak effects of selection have been superimposed on the main drift effect in the PGE zone.
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14
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Savage AE, Kiemnec-Tyburczy KM, Ellison AR, Fleischer RC, Zamudio KR. Conservation and divergence in the frog immunome: pyrosequencing and de novo assembly of immune tissue transcriptomes. Gene 2014; 542:98-108. [PMID: 24680726 DOI: 10.1016/j.gene.2014.03.051] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 03/06/2014] [Accepted: 03/26/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Frogs are a diverse group of vertebrates for which limited genomic resources are available. Natural frog populations face a multitude of threats, including habitat degradation, infectious disease, and environmental change. Characterizing the functional genomics of anuran tissues in general - and the immune system in particular - will enhance our knowledge of genetic and epigenetic responses to environmental threats and inform conservation and recovery efforts. RESULTS To increase the number of species with genomic datasets and characterize gene expression in immune-related tissues, we sequenced the transcriptomes of three tissues from two frogs (Espadarana prosoblepon and Lithobates yavapaiensis) on the Roche 454 GS FLX platform. Our sequencing produced 8881 E. prosoblepon and 5428 L. yavapaiensis annotated gene products after de novo assembly and Gene Ontology classification. Transcripts of the innate and acquired immune system were expressed in all three tissues. Inflammatory response and acquired immunity transcripts were significantly more diverged between E. prosoblepon and L. yavapaiensis compared to innate immunity and immune system development transcripts. Immune-related transcripts did not show an overall elevated rate of functional evolution, with the exception of glycosyl proteases, which include lysozymes, central bacterial and fungal-killing enzymes of the innate immune system. CONCLUSIONS The three frog transcriptomes provide more than 600 Mbp of new genomic data, and will serve as a valuable framework for future comparative studies of non-model anurans. Additionally, we show that immune gene divergence varies by functional group and that transcriptome studies can be useful in comparing rates of evolutionary change across gene families.
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Affiliation(s)
- Anna E Savage
- Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013, United States; Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Karen M Kiemnec-Tyburczy
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Amy R Ellison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
| | - Robert C Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian Institution, Washington, DC 20013, United States.
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, United States.
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15
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Shu YL, Hong P, Yang YW, Wu HL. An endemic frog harbors multiple expression loci with different patterns of variation in the MHC class II B gene. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:501-10. [DOI: 10.1002/jez.b.22525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 06/03/2013] [Accepted: 06/20/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Yi-Lin Shu
- College of Life Sciences; Anhui Normal University; Wuhu People's Republic of China
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province; Wuhu People's Republic of China
| | - Pei Hong
- College of Life Sciences; Anhui Normal University; Wuhu People's Republic of China
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province; Wuhu People's Republic of China
| | - Yi-Wen Yang
- College of Life Sciences; Anhui Normal University; Wuhu People's Republic of China
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province; Wuhu People's Republic of China
| | - Hai-Long Wu
- College of Life Sciences; Anhui Normal University; Wuhu People's Republic of China
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province; Wuhu People's Republic of China
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16
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Gong J, Sun QP, Xue F, Fang SG, Wan QH. Molecular Characterization of the Major Histocompatibility Complex Class Ia Gene in the Black-Spotted Frog, Pelophylax nigromaculata. Biochem Genet 2013; 51:876-88. [DOI: 10.1007/s10528-013-9614-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 12/21/2012] [Indexed: 12/13/2022]
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17
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Kiemnec-Tyburczy KM, Zamudio KR. Novel locus-specific primers for major histocompatibility complex class II alleles from glass frogs developed via genome walking. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9744-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Kiemnec-Tyburczy KM, Richmond JQ, Savage AE, Lips KR, Zamudio KR. Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication. Heredity (Edinb) 2012; 109:146-55. [PMID: 22549517 DOI: 10.1038/hdy.2012.22] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Comparative studies of major histocompatibility complex (MHC) genes across vertebrate species can reveal the evolutionary processes that shape the structure and function of immune regulatory proteins. In this study, we characterized MHC class I sequences from six frog species representing three anuran families (Hylidae, Centrolenidae and Ranidae). Using cDNA from our focal species, we amplified a total of 79 unique sequences spanning exons 2-4 that encode the extracellular domains of the functional alpha chain protein. We compared intra- and interspecific nucleotide and amino-acid divergence, tested for recombination, and identified codon sites under selection by estimating the rate of non-synonymous to synonymous substitutions with multiple codon-based maximum likelihood methods. We determined that positive (diversifying) selection was acting on specific amino-acid sites located within the domains that bind pathogen-derived peptides. We also found significant signals of recombination across the physical distance of the genes. Finally, we determined that all the six species expressed two or three putative classical class I loci, in contrast to the single locus condition of Xenopus laevis. Our results suggest that MHC evolution in anurans is a dynamic process and that variation in numbers of loci and genetic diversity can exist among taxa. Thus, the accumulation of genetic data for more species will be useful in further characterizing the relative importance of processes such as selection, recombination and gene duplication in shaping MHC loci among amphibian lineages.
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Affiliation(s)
- K M Kiemnec-Tyburczy
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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19
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Meng Z, Yang S, Fan B, Wang L, Lin H. Genetic variation and balancing selection at MHC class II exon 2 in cultured stocks and wild populations of orange-spotted grouper (Epinephelus coioides). GENETICS AND MOLECULAR RESEARCH 2012; 11:3869-81. [DOI: 10.4238/2012.november.12.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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20
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Nadachowska-Brzyska K, Zieliński P, Radwan J, Babik W. Interspecific hybridization increases MHC class II diversity in two sister species of newts. Mol Ecol 2011; 21:887-906. [PMID: 22066802 DOI: 10.1111/j.1365-294x.2011.05347.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Our understanding of the evolutionary mechanisms generating variation within the highly polymorphic major histocompatibility complex (MHC) genes remains incomplete. Assessing MHC variation across multiple populations, of recent and ancient divergence, may facilitate understanding of geographical and temporal aspects of variation. Here, we applied 454 sequencing to perform a large-scale, comprehensive analysis of MHC class II in the closely related, hybridizing newts, Lissotriton vulgaris (Lv) and Lissotriton montandoni (Lm). Our study revealed an extensive (299 alleles) geographically structured polymorphism. Populations at the southern margin of the Lv distribution, inhabited by old and distinct lineages (southern Lv), exhibited moderate MHC variation and strong population structure, indicating little gene flow or extensive local adaptation. Lissotriton vulgaris in central Europe and the northern Balkans (northern Lv) and almost all Lm populations had a high MHC variation. A much higher proportion of MHC alleles was shared between Lm and northern Lv than between Lm and southern Lv. Strikingly, the average pairwise F(ST) between northern Lv and Lm was significantly lower than between northern and southern Lv for MHC, but not for microsatellites. Thus, high MHC variation in Lm and northern Lv may result from gene flow between species. We hypothesize that the interspecific exchange of MHC genes may be facilitated by frequency-dependent selection. A marginally significant correlation between the MHC and microsatellite allelic richness indicates that demographic factors may have contributed to the present-day pattern of MHC variation, but unequivocal signatures of adaptive evolution in MHC class II sequences emphasize the role of selection on a longer timescale.
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Abstract
The emerging amphibian disease chytridiomycosis is caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Amphibian populations and species differ in susceptibility to Bd, yet we know surprisingly little about the genetic basis of this natural variation. MHC loci encode peptides that initiate acquired immunity in vertebrates, making them likely candidates for determining disease susceptibility. However, MHC genes have never been characterized in the context of chytridiomycosis. Here, we performed experimental Bd infections in laboratory-reared frogs collected from five populations that show natural variation in Bd susceptibility. We found that alleles of an expressed MHC class IIB locus associate with survival following Bd infection. Across populations, MHC heterozygosity was a significant predictor of survival. Within populations, MHC heterozygotes and individuals bearing MHC allele Q had a significantly reduced risk of death, and we detected a significant signal of positive selection along the evolutionary lineage leading to allele Q. Our findings demonstrate that immunogenetic variation affects chytridiomycosis survival under controlled experimental conditions, confirming that host genetic polymorphisms contribute to chytridiomycosis resistance.
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22
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Selection, trans-species polymorphism, and locus identification of major histocompatibility complex class IIβ alleles of New World ranid frogs. Immunogenetics 2010; 62:741-51. [DOI: 10.1007/s00251-010-0476-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 08/26/2010] [Indexed: 10/19/2022]
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23
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Canal D, Alcaide M, Anmarkrud JA, Potti J. Towards the simplification of MHC typing protocols: targeting classical MHC class II genes in a passerine, the pied flycatcher Ficedula hypoleuca. BMC Res Notes 2010; 3:236. [PMID: 20815923 PMCID: PMC2944132 DOI: 10.1186/1756-0500-3-236] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/05/2010] [Indexed: 11/13/2022] Open
Abstract
Background Major Histocompatibility Complex (MHC) has drawn the attention of evolutionary biologists due to its importance in crucial biological processes, such as sexual selection and immune response in jawed vertebrates. However, the characterization of classical MHC genes subjected to the effects of natural selection still remains elusive in many vertebrate groups. Here, we have tested the suitability of flanking intron sequences to guide the selective exploration of classical MHC genes driving the co-evolutionary dynamics between pathogens and their passerine (Aves, Order Passeriformes) hosts. Findings Intronic sequences flanking the usually polymorphic exon 2 were isolated from different species using primers sitting on conserved coding regions of MHC class II genes (β chain). Taking the pied flycatcher Ficedula hypoleuca as an example, we demonstrate that careful primer design can evade non-classical MHC gene and pseudogene amplification. At least four polymorphic and expressed loci were co-replicated using a single pair of primers in five non-related individuals (N = 28 alleles). The cross-amplification and preliminary inspection of similar MHC fragments in eight unrelated songbird taxa suggests that similar approaches can also be applied to other species. Conclusions Intron sequences flanking the usually polymorphic exon 2 may assist the specific investigation of classical MHC class II B genes in species characterized by extensive gene duplication and pseudogenization. Importantly, the evasion of non-classical MHC genes with a more specific function and non-functional pseudogenes may accelerate data collection and diminish lab costs. Comprehensive knowledge of gene structure, polymorphism and expression profiles may be useful not only for the selective examination of evolutionarily relevant genes but also to restrict chimera formation by minimizing the number of co-amplifying loci.
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Affiliation(s)
- David Canal
- Estación Biológica de Doñana - CSIC, Department of Evolutionary Ecology, Av, Américo Vespucio s/n, 41092 Seville, Spain.
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24
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Characterisation of MHC class II DRB genes in the northern tree shrew (Tupaia belangeri). Immunogenetics 2010; 62:613-22. [PMID: 20661731 DOI: 10.1007/s00251-010-0466-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 07/08/2010] [Indexed: 12/31/2022]
Abstract
Genes of the major histocompatibility complex (MHC) mainly code for proteins of the immune system of jawed vertebrates. In particular, MHC class I and II cell surface proteins are crucial for the self/non-self discrimination of the adaptive immune system and are the most polymorphic genes in vertebrates. Positive selection, gene duplications and pseudogenes shape the face of the MHC and reflect a highly dynamic evolution. Here, we present for the first time data of the highly polymorphic MHC class II DRB exon 2 of a representative of the mammalian order scandentia, the northern tree shrew Tupaia belangeri. We found up to eight different alleles per individual and determined haplotype constitution by intensively studying their inheritance. The alleles were assigned to four putative loci, all of which were polymorphic. Only the most polymorphic locus was subject to positive selection within the antigen binding sites and only alleles of this locus were transcribed.
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25
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Zeisset I, Beebee TJC. Larval fitness, microsatellite diversity and MHC class II diversity in common frog (Rana temporaria) populations. Heredity (Edinb) 2009; 104:423-30. [DOI: 10.1038/hdy.2009.157] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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26
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Characterisation of major histocompatibility complex class II alleles in the natterjack toad, Bufo calamita. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9096-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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27
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ZEISSET I, BEEBEE TJC. Molecular characterization of major histocompatibility complex class II alleles in the common frog,Rana temporaria. Mol Ecol Resour 2009; 9:738-45. [DOI: 10.1111/j.1755-0998.2009.02535.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Ekblom R, Saether SA, Fiske P, Kålås JA, Höglund J. Balancing selection, sexual selection and geographic structure in MHC genes of Great Snipe. Genetica 2008; 138:453-61. [PMID: 19052880 DOI: 10.1007/s10709-008-9335-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 11/17/2008] [Indexed: 11/28/2022]
Affiliation(s)
- Robert Ekblom
- Population Biology, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
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29
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Glaberman S, Caccone A. Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae). Immunogenetics 2008; 60:371-82. [PMID: 18488213 DOI: 10.1007/s00251-008-0298-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 04/09/2008] [Indexed: 11/30/2022]
Abstract
Over the last few decades, the major histocompatibility complex (MHC) has emerged as a model for understanding the influence of natural selection on genetic diversity in populations as well as for investigating the genetic basis of host resistance to pathogens. However, many vertebrate taxa remain underrepresented in the field of MHC research, preventing its application to studies of disease, evolution, and conservation genetics in these groups. This is particularly true for squamates, which are by far the most diversified order of non-avian reptiles but have not been the subject of any recent MHC studies. In this paper, we present MHC class I complementary DNA data from three squamate species in the subfamily Iguaninae (iguanas): the Galápagos marine iguana (Amblyrhynchus cristatus), the Galápagos land iguana (Conolophus subcristatus), and the green iguana (Iguana iguana). All sequences obtained are related to the few published class I genes from other squamates. There is evidence for multiple loci in each species, and the conserved alpha-3 domain appears to be evolving in a species-specific manner. Conversely, there is some indication of shared polymorphism between species in the peptide-binding alpha-1 and alpha-2 domains, suggesting that these two regions have different phylogenetic histories. The great similarity between alpha-3 sequences in marine iguanas in particular suggests that concerted evolution is acting to homogenize class I loci within species. However, while less likely, the data are also compatible with a birth and death model of evolution.
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Affiliation(s)
- Scott Glaberman
- Department of Ecology and Evolutionary Biology and the Yale Institute for Biospheric Studies, Yale University, 21 Sachem Street, New Haven, CT 06520-8105, USA.
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30
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BABIK W, PABIJAN M, RADWAN J. Contrasting patterns of variation in MHC loci in the Alpine newt. Mol Ecol 2008; 17:2339-55. [DOI: 10.1111/j.1365-294x.2008.03757.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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