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Some thoughts about what non-mammalian jawed vertebrates are telling us about antigen processing and peptide loading of MHC molecules. Curr Opin Immunol 2022; 77:102218. [PMID: 35687979 PMCID: PMC9586880 DOI: 10.1016/j.coi.2022.102218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/19/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022]
Abstract
The major histocompatibility complex (MHC) of mammals encodes highly polymorphic classical class I and class II molecules with crucial roles in immune responses, as well as various nonclassical molecules encoded by the MHC and elsewhere in the genome that have a variety of functions. These MHC molecules are supported by antigen processing and peptide loading pathways which are well-understood in mammals. This review considers what has been learned about the MHC, MHC molecules and the supporting pathways in non-mammalian jawed vertebrates. From the initial understanding from work with the chicken MHC, a great deal of diversity in the structure and function has been found. Are there underlying principles? The genomic organisation of the MHC varies enormously across jawed vertebrates. Total numbers of MHC genes vary among vertebrates, with only a few classical MHC genes. Some nonclassical MHC and classical pathway genes appear earlier than others. Obvious co-evolution within MHC pathways occurs in some species, but not others. The promiscuity of interactions may correlate with differences in genomic organisation.
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2
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He K, Liang CH, Zhu Y, Dunn P, Zhao A, Minias P. Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data. Front Genet 2022; 13:823686. [PMID: 35251132 PMCID: PMC8893315 DOI: 10.3389/fgene.2022.823686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/25/2022] [Indexed: 12/28/2022] Open
Abstract
The Major Histocompatibility Complex (MHC) is a hyper-polymorphic genomic region, which forms a part of the vertebrate adaptive immune system and is crucial for intra- and extra-cellular pathogen recognition (MHC-I and MHC-IIA/B, respectively). Although recent advancements in high-throughput sequencing methods sparked research on the MHC in non-model species, the evolutionary history of MHC gene structure is still poorly understood in birds. Here, to explore macroevolutionary patterns in the avian MHC architecture, we retrieved contigs with antigen-presenting MHC and MHC-related genes from available genomes based on third-generation sequencing. We identified: 1) an ancestral avian MHC architecture with compact size and tight linkage between MHC-I, MHC-IIA/IIB and MHC-related genes; 2) three major patterns of MHC-IIA/IIB unit organization in different avian lineages; and 3) lineage-specific gene translocation events (e.g., separation of the antigen-processing TAP genes from the MHC-I region in passerines), and 4) the presence of a single MHC-IIA gene copy in most taxa, showing evidence of strong purifying selection (low dN/dS ratio and low number of positively selected sites). Our study reveals long-term macroevolutionary patterns in the avian MHC architecture and provides the first evidence of important transitions in the genomic arrangement of the MHC region over the last 100 million years of bird evolution.
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Affiliation(s)
- Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
- *Correspondence: Ke He, ; Piotr Minias,
| | - Chun-hong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Peter Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Ayong Zhao
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łodz, Łódź, Poland
- *Correspondence: Ke He, ; Piotr Minias,
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3
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Arauco-Shapiro G, Schumacher KI, Boersma D, Bouzat JL. The role of demographic history and selection in shaping genetic diversity of the Galápagos penguin (Spheniscus mendiculus). PLoS One 2020; 15:e0226439. [PMID: 31910443 PMCID: PMC6946592 DOI: 10.1371/journal.pone.0226439] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/26/2019] [Indexed: 11/25/2022] Open
Abstract
Although many studies have documented the effects of demographic bottlenecks on the genetic diversity of natural populations, there is conflicting evidence of the roles that genetic drift and selection may play in driving changes in genetic variation at adaptive loci. We analyzed genetic variation at microsatellite and mitochondrial loci in conjunction with an adaptive MHC class II locus in the Galápagos penguin (Spheniscus mendiculus), a species that has undergone serial demographic bottlenecks associated with El Niño events through its evolutionary history. We compared levels of variation in the Galápagos penguin to those of its congener, the Magellanic penguin (Spheniscus magellanicus), which has consistently maintained a large population size and thus was used as a non-bottlenecked control. The comparison of neutral and adaptive markers in these two demographically distinct species allowed assessment of the potential role of balancing selection in maintaining levels of MHC variation during bottleneck events. Our analysis suggests that the lack of genetic diversity at both neutral and adaptive loci in the Galápagos penguin likely resulted from its restricted range, relatively low abundance, and history of demographic bottlenecks. The Galápagos penguin revealed two MHC alleles, one mitochondrial haplotype, and six alleles across five microsatellite loci, which represents only a small fraction of the diversity detected in Magellanic penguins. Despite the decreased genetic diversity in the Galápagos penguin, results revealed signals of balancing selection at the MHC, which suggest that selection can mitigate some of the effects of genetic drift during bottleneck events. Although Galápagos penguin populations have persisted for a long time, increased frequency of El Niño events due to global climate change, as well as the low diversity exhibited at immunological loci, may put this species at further risk of extinction.
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Affiliation(s)
- Gabriella Arauco-Shapiro
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Katelyn I. Schumacher
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Dee Boersma
- Center for Ecosystem Sentinels and Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Juan L. Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
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Hoover B, Alcaide M, Jennings S, Sin SYW, Edwards SV, Nevitt GA. Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach's storm-petrels (Oceanodroma leucorhoa). Mol Ecol 2018; 27:3371-3385. [PMID: 30010226 DOI: 10.1111/mec.14801] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/31/2018] [Accepted: 06/20/2018] [Indexed: 01/03/2023]
Abstract
Studies of MHC-based mate choice in wild populations often test hypotheses on species exhibiting female choice and male-male competition, which reflects the general prevalence of females as the choosy sex in natural systems. Here, we examined mutual mate-choice patterns in a small burrow-nesting seabird, the Leach's storm-petrel (Oceanodroma leucorhoa), using the major histocompatibility complex (MHC). The life history and ecology of this species are extreme: both partners work together to fledge a single chick during the breeding season, a task that requires regularly travelling hundreds of kilometres to and from foraging grounds over a 6- to 8-week provisioning period. Using a 5-year data set unprecedented for this species (n = 1078 adults and 925 chicks), we found a positive relationship between variation in the likelihood of female reproductive success and heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous reports rejecting disassortative mating as a mechanism for maintaining genetic polymorphism in this species, here we show that males make significant disassortative mate-choice decisions. Variability in female reproductive success suggests that the most common homozygous females (Ocle-DAB2*01/Ocle-DAB2*01) may be physiologically disadvantaged and, therefore, less preferred as lifelong partners for choosy males. The results from this study support the role of mate choice in maintaining high levels of MHC variability in a wild seabird species and highlight the need to incorporate a broader ecological framework and sufficient sample sizes into studies of MHC-based mating patterns in wild populations in general.
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Affiliation(s)
- Brian Hoover
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
| | - Miguel Alcaide
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sarah Jennings
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Gabrielle A Nevitt
- Graduate Group in Ecology, University of California, Davis, California
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California
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5
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Li C, Jiang J, Zhang Q, Wang X. Duplicated major histocompatibility complex class II genes in the tongue sole (Cynoglossus semilaevis
). Int J Immunogenet 2018; 45:210-224. [DOI: 10.1111/iji.12368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 02/25/2018] [Accepted: 03/22/2018] [Indexed: 12/26/2022]
Affiliation(s)
- C. Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding; College of Marine Life Sciences; Ocean University of China; Qingdao China
| | - J. Jiang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding; College of Marine Life Sciences; Ocean University of China; Qingdao China
| | - Q. Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding; College of Marine Life Sciences; Ocean University of China; Qingdao China
| | - X. Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding; College of Marine Life Sciences; Ocean University of China; Qingdao China
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Signatures of Crested Ibis MHC Revealed by Recombination Screening and Short-Reads Assembly Strategy. PLoS One 2016; 11:e0168744. [PMID: 27997612 PMCID: PMC5173252 DOI: 10.1371/journal.pone.0168744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 12/06/2016] [Indexed: 02/04/2023] Open
Abstract
Whole-genome shotgun (WGS) sequencing has become a routine method in genome research over the past decade. However, the assembly of highly polymorphic regions in WGS projects remains a challenge, especially for large genomes. Employing BAC library constructing, PCR screening and Sanger sequencing, traditional strategy is laborious and expensive, which hampers research on polymorphic genomic regions. As one of the most highly polymorphic regions, the major histocompatibility complex (MHC) plays a central role in the adaptive immunity of all jawed vertebrates. In this study, we introduced an efficient procedure based on recombination screening and short-reads assembly. With this procedure, we constructed a high quality 488-kb region of crested ibis MHC that consists of 3 superscaffolds and contains 50 genes. Our sequence showed comparable quality (97.29% identity) to traditional Sanger assembly, while the workload was reduced almost 7 times. Comparative study revealed distinctive features of crested ibis by exhibiting the COL11A2-BLA-BLB-BRD2 cluster and presenting both ADPRH and odorant receptor (OR) gene in the MHC region. Furthermore, the conservation of the BF-TAP1-TAP2 structure in crested ibis and other vertebrate lineages is interesting in light of the hypothesis that coevolution of functionally related genes in the primordial MHC is responsible for the appearance of the antigen presentation pathways at the birth of the adaptive immune system.
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The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola). Immunogenetics 2016; 69:175-186. [PMID: 27888301 DOI: 10.1007/s00251-016-0960-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 11/16/2016] [Indexed: 12/12/2022]
Abstract
Avian genomics, especially of non-model species, is in its infancy relative to mammalian genomics. Here, we describe the sequencing, assembly, and annotation of a new avian genome, that of the bananaquit Coereba flaveola (Passeriformes: Thraupidae). We produced ∼30-fold coverage of the genome with an assembly size of ca. 1.2 Gb, including approximately 16,500 annotated genes. Passerine birds, such as the bananaquit, are commonly infected by avian malarial parasites (Haemosporida), which presumably drive adaptive evolution of immunogenetic loci within the host genome. In the context of our research on the distribution of avian Haemosporida, we specifically characterized immune loci, including toll-like receptor (TLR) and major histocompatibility complex (MHC) genes. Additionally, we identified novel molecular markers in the form of single nucleotide polymorphisms (SNPs), both genome-wide and within identified immune loci. We discovered nine TLR genes and four MHC genes and identified five other TLR- or MHC- associated genes. Genome-wide, over 6 million high-quality SNPs were annotated, including 568 within TLR genes and 102 in MHC genes. This newly described genome and immune characterization expands the knowledge base for avian genomics and phylogenetics and allows for immune genotyping in the bananaquit, providing tools for the investigation of host-parasite coevolution.
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8
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Jarvi SI, Bianchi KR, Farias ME, Txakeeyang A, McFarland T, Belcaid M, Asano A. Characterization of class II β chain major histocompatibility complex genes in a family of Hawaiian honeycreepers: 'amakihi (Hemignathus virens). Immunogenetics 2016; 68:461-475. [PMID: 26971289 DOI: 10.1007/s00251-016-0908-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/19/2016] [Indexed: 12/19/2022]
Abstract
Hawaiian honeycreepers (Drepanidinae) have evolved in the absence of mosquitoes for over five million years. Through human activity, mosquitoes were introduced to the Hawaiian archipelago less than 200 years ago. Mosquito-vectored diseases such as avian malaria caused by Plasmodium relictum and Avipoxviruses have greatly impacted these vulnerable species. Susceptibility to these diseases is variable among and within species. Due to their function in adaptive immunity, the role of major histocompatibility complex genes (Mhc) in disease susceptibility is under investigation. In this study, we evaluate gene organization and levels of diversity of Mhc class II β chain genes (exon 2) in a captive-reared family of Hawaii 'amakihi (Hemignathus virens). A total of 233 sequences (173 bp) were obtained by PCR+1 amplification and cloning, and 5720 sequences were generated by Roche 454 pyrosequencing. We report a total of 17 alleles originating from a minimum of 14 distinct loci. We detected three linkage groups that appear to represent three distinct haplotypes. Phylogenetic analysis revealed one variable cluster resembling classical Mhc sequences (DAB) and one highly conserved, low variability cluster resembling non-classical Mhc sequences (DBB). High net evolutionary divergence values between DAB and DBB resemble that seen between chicken BLB system and YLB system genes. High amino acid identity among non-classical alleles from 12 species of passerines (DBB) and four species of Galliformes (YLB) was found, suggesting that these non-classical passerine sequences may be related to the Galliforme YLB sequences.
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Affiliation(s)
- Susan I Jarvi
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI, 96720, USA.
| | - Kiara R Bianchi
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI, 96720, USA
| | - Margaret Em Farias
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI, 96720, USA
| | - Ann Txakeeyang
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI, 96720, USA
| | - Thomas McFarland
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI, 96720, USA
| | - Mahdi Belcaid
- Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813, Kane'ohe, HI, USA
| | - Ashley Asano
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, HI, 96720, USA
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Gillingham MAF, Courtiol A, Teixeira M, Galan M, Bechet A, Cezilly F. Evidence of gene orthology and trans-species polymorphism, but not of parallel evolution, despite high levels of concerted evolution in the major histocompatibility complex of flamingo species. J Evol Biol 2015; 29:438-54. [DOI: 10.1111/jeb.12798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 11/12/2015] [Accepted: 11/15/2015] [Indexed: 11/30/2022]
Affiliation(s)
- M. A. F. Gillingham
- Equipe Ecologie Evolutive; UMR CNRS 6282 Biogéosciences; Université de Bourgogne; Dijon France
- Centre de Recherche de la Tour du Valat; Arles France
- Department of Evolutionary Genetics; Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
- Institute of Evolutionary Ecology and Conservation Genomics; University of Ulm; Ulm Germany
| | - A. Courtiol
- Department of Evolutionary Genetics; Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | - M. Teixeira
- Equipe Ecologie Evolutive; UMR CNRS 6282 Biogéosciences; Université de Bourgogne; Dijon France
| | - M. Galan
- UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); INRA EFPA; Montferrier-sur-Lez Cedex France
| | - A. Bechet
- Centre de Recherche de la Tour du Valat; Arles France
| | - F. Cezilly
- Equipe Ecologie Evolutive; UMR CNRS 6282 Biogéosciences; Université de Bourgogne; Dijon France
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Kohyama TI, Omote K, Nishida C, Takenaka T, Saito K, Fujimoto S, Masuda R. Spatial and temporal variation at major histocompatibility complex class IIB genes in the endangered Blakiston's fish owl. ZOOLOGICAL LETTERS 2015; 1:13. [PMID: 26605058 PMCID: PMC4657285 DOI: 10.1186/s40851-015-0013-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/25/2015] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Quantifying intraspecific genetic variation in functionally important genes, such as those of the major histocompatibility complex (MHC), is important in the establishment of conservation plans for endangered species. The MHC genes play a crucial role in the vertebrate immune system and generally show high levels of diversity, which is likely due to pathogen-driven balancing selection. The endangered Blakiston's fish owl (Bubo blakistoni) has suffered marked population declines on Hokkaido Island, Japan, during the past several decades due to human-induced habitat loss and fragmentation. We investigated the spatial and temporal patterns of genetic diversity in MHC class IIβ genes in Blakiston's fish owl, using massively parallel pyrosequencing. RESULTS We found that the Blakiston's fish owl genome contains at least eight MHC class IIβ loci, indicating recent gene duplications. An analysis of sequence polymorphism provided evidence that balancing selection acted in the past. The level of MHC variation, however, was low in the current fish owl populations in Hokkaido: only 19 alleles were identified from 174 individuals. We detected considerable spatial differences in MHC diversity among the geographically isolated populations. We also detected a decline of MHC diversity in some local populations during the past decades. CONCLUSIONS Our study demonstrated that the current spatial patterns of MHC variation in Blakiston's fish owl populations have been shaped by loss of variation due to the decline and fragmentation of populations, and that the short-term effects of genetic drift have counteracted the long-term effects of balancing selection.
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Affiliation(s)
- Tetsuo I Kohyama
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Keita Omote
- />Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Chizuko Nishida
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Takeshi Takenaka
- />FILIN, Hachiken 2 Jo Nishi 2, Nishi-ku, Sapporo 063-0842 Japan
| | - Keisuke Saito
- />Institute for Raptor Biomedicine, Kushiro, 084-0922 Japan
| | | | - Ryuichi Masuda
- />Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
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11
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Chen LC, Lan H, Sun L, Deng YL, Tang KY, Wan QH. Genomic organization of the crested ibis MHC provides new insight into ancestral avian MHC structure. Sci Rep 2015; 5:7963. [PMID: 25608659 PMCID: PMC4302302 DOI: 10.1038/srep07963] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/31/2014] [Indexed: 01/06/2023] Open
Abstract
The major histocompatibility complex (MHC) plays an important role in immune response. Avian MHCs are not well characterized, only reporting highly compact Galliformes MHCs and extensively fragmented zebra finch MHC. We report the first genomic structure of an endangered Pelecaniformes (crested ibis) MHC containing 54 genes in three regions spanning ~500 kb. In contrast to the loose BG (26 loci within 265 kb) and Class I (11 within 150) genomic structures, the Core Region is condensed (17 within 85). Furthermore, this Region exhibits a COL11A2 gene, followed by four tandem MHC class II αβ dyads retaining two suites of anciently duplicated “αβ” lineages. Thus, the crested ibis MHC structure is entirely different from the known avian MHC architectures but similar to that of mammalian MHCs, suggesting that the fundamental structure of ancestral avian class II MHCs should be “COL11A2-IIαβ1-IIαβ2.” The gene structures, residue characteristics, and expression levels of the five class I genes reveal inter-locus functional divergence. However, phylogenetic analysis indicates that these five genes generate a well-supported intra-species clade, showing evidence for recent duplications. Our analyses suggest dramatic structural variation among avian MHC lineages, help elucidate avian MHC evolution, and provide a foundation for future conservation studies.
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Affiliation(s)
- Li-Cheng Chen
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Hong Lan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Li Sun
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yan-Li Deng
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ke-Yi Tang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
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12
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Jan Ejsmond M, Radwan J, Wilson AB. Sexual selection and the evolutionary dynamics of the major histocompatibility complex. Proc Biol Sci 2014; 281:20141662. [PMID: 25339723 PMCID: PMC4213641 DOI: 10.1098/rspb.2014.1662] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/22/2014] [Indexed: 12/27/2022] Open
Abstract
The genes of the major histocompatibility complex (MHC) are a key component of the adaptive immune system and among the most variable loci in the vertebrate genome. Pathogen-mediated natural selection and MHC-based disassortative mating are both thought to structure MHC polymorphism, but their effects have proven difficult to discriminate in natural systems. Using the first model of MHC dynamics incorporating both survival and reproduction, we demonstrate that natural and sexual selection produce distinctive signatures of MHC allelic diversity with critical implications for understanding host-pathogen dynamics. While natural selection produces the Red Queen dynamics characteristic of host-parasite interactions, disassortative mating stabilizes allele frequencies, damping major fluctuations in dominant alleles and protecting functional variants against drift. This subtle difference generates a complex interaction between MHC allelic diversity and population size. In small populations, the stabilizing effects of sexual selection moderate the effects of drift, whereas pathogen-mediated selection accelerates the loss of functionally important genetic diversity. Natural selection enhances MHC allelic variation in larger populations, with the highest levels of diversity generated by the combined action of pathogen-mediated selection and disassortative mating. MHC-based sexual selection may help to explain how functionally important genetic variation can be maintained in populations of conservation concern.
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Affiliation(s)
- Maciej Jan Ejsmond
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Krakow, Poland Department of Arctic Biology, The University Centre in Svalbard, Box 156, 9171 Longyearbyen, Norway
| | - Jacek Radwan
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Anthony B Wilson
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland Department of Biology, Brooklyn College and The Graduate Center, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
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13
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Dearborn DC, Gager AB, Gilmour ME, McArthur AG, Hinerfeld DA, Mauck RA. Non-neutral evolution and reciprocal monophyly of two expressed Mhc class II B genes in Leach’s storm-petrel. Immunogenetics 2014; 67:111-23. [DOI: 10.1007/s00251-014-0813-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/30/2014] [Indexed: 12/21/2022]
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14
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Jones MR, Cheviron ZA, Carling MD. Variation in positively selected major histocompatibility complex class I loci in rufous-collared sparrows (Zonotrichia capensis). Immunogenetics 2014; 66:693-704. [DOI: 10.1007/s00251-014-0800-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/25/2014] [Indexed: 11/25/2022]
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15
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Halley YA, Dowd SE, Decker JE, Seabury PM, Bhattarai E, Johnson CD, Rollins D, Tizard IR, Brightsmith DJ, Peterson MJ, Taylor JF, Seabury CM. A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene. PLoS One 2014; 9:e90240. [PMID: 24621616 PMCID: PMC3951200 DOI: 10.1371/journal.pone.0090240] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/27/2014] [Indexed: 11/20/2022] Open
Abstract
Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts.
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Affiliation(s)
- Yvette A. Halley
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Scot E. Dowd
- Molecular Research LP, Shallowater, Texas, United States of America
| | - Jared E. Decker
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Paul M. Seabury
- ElanTech Inc., Greenbelt, Maryland, United States of America
| | - Eric Bhattarai
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Charles D. Johnson
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Dale Rollins
- Rolling Plains Quail Research Ranch, Rotan, Texas, United States of America
| | - Ian R. Tizard
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Donald J. Brightsmith
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Markus J. Peterson
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Burri R, Promerová M, Goebel J, Fumagalli L. PCR-based isolation of multigene families: lessons from the avian MHC class IIB. Mol Ecol Resour 2014; 14:778-88. [PMID: 24479469 DOI: 10.1111/1755-0998.12234] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/22/2014] [Accepted: 01/22/2014] [Indexed: 11/30/2022]
Abstract
The amount of sequence data available today highly facilitates the access to genes from many gene families. Primers amplifying the desired genes over a range of species are readily obtained by aligning conserved gene regions, and laborious gene isolation procedures can often be replaced by quicker PCR-based approaches. However, in the case of multigene families, PCR-based approaches bear the often ignored risk of incomplete isolation of family members. This problem is most prominent in gene families with highly variable and thus unpredictable number of gene copies among species, such as in the major histocompatibility complex (MHC). In this study, we (i) report new primers for the isolation of the MHC class IIB (MHCIIB) gene family in birds and (ii) share our experience with isolating MHCIIB genes from an unprecedented number of avian species from all over the avian phylogeny. We report important and usually underappreciated problems encountered during PCR-based multigene family isolation and provide a collection of measures to help significantly improving the chance of successfully isolating complete multigene families using PCR-based approaches.
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Affiliation(s)
- R Burri
- Laboratory for Conservation Biology, Department of Ecology and Evolution, University of Lausanne, CH-1015, Lausanne, Switzerland; Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden
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17
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Alcaide M, Muñoz J, Martínez-de la Puente J, Soriguer R, Figuerola J. Extraordinary MHC class II B diversity in a non-passerine, wild bird: the Eurasian Coot Fulica atra (Aves: Rallidae). Ecol Evol 2014; 4:688-98. [PMID: 24683452 PMCID: PMC3967895 DOI: 10.1002/ece3.974] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/30/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022] Open
Abstract
The major histocompatibility complex (MHC) hosts the most polymorphic genes ever described in vertebrates. The MHC triggers the adaptive branch of the immune response, and its extraordinary variability is considered an evolutionary consequence of pathogen pressure. The last few years have witnessed the characterization of the MHC multigene family in a large diversity of bird species, unraveling important differences in its polymorphism, complexity, and evolution. Here, we characterize the first MHC class II B sequences isolated from a Rallidae species, the Eurasian Coot Fulica atra. A next-generation sequencing approach revealed up to 265 alleles that translated into 251 different amino acid sequences (β chain, exon 2) in 902 individuals. Bayesian inference identified up to 19 codons within the presumptive peptide-binding region showing pervasive evidence of positive, diversifying selection. Our analyses also detected a significant excess of high-frequency segregating sites (average Tajima's D = 2.36, P < 0.05), indicative of balancing selection. We found one to six different alleles per individual, consistent with the occurrence of at least three MHC class II B gene duplicates. However, the genotypes comprised of three alleles were by far the most abundant in the population investigated (49.4%), followed by those with two (29.6%) and four (17.5%) alleles. We suggest that these proportions are in agreement with the segregation of MHC haplotypes differing in gene copy number. The most widespread segregating haplotypes, according to our findings, would contain one single gene or two genes. The MHC class II of the Eurasian Coot is a valuable system to investigate the evolutionary implications of gene copy variation and extensive variability, the greatest ever found, to the best of our knowledge, in a wild population of a non-passerine bird.
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Affiliation(s)
- Miguel Alcaide
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Joaquin Muñoz
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
- The University of Oklahoma Biological Station15389 Station Road, Kingston, Oklahoma, 73439
| | | | - Ramón Soriguer
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Jordi Figuerola
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
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18
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Knafler GJ, Fidler A, Jamieson IG, Robertson BC. Evidence for multiple MHC class II β loci in New Zealand's critically endangered kakapo, Strigops habroptilus. Immunogenetics 2013; 66:115-21. [PMID: 24352694 DOI: 10.1007/s00251-013-0750-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 11/26/2013] [Indexed: 01/25/2023]
Abstract
Immunologically important genes of the major histocompatibility complex (MHC) have been characterized in a number of avian species with the general finding of considerable variation in size and structural organization among organisms. A range of nonpasserines which represent early-diverging Neoave lineages have been described as having only one MHC class II β locus potentially leading to the conclusion that this is the ancestral condition. Here, we examine the monotypic, early-diverging, critically endangered kakapo, Strigops habroptilus, for allelic variation at MHC class II β exon 2, as part of species' recovery efforts. We found two to four confirmed sequence variants per individual indicating the presence of more than one MHC class II β locus. Given the kakapo's basal evolutionary status, evidence for multiple MHC class II β loci seems to counter the proposed mono-locus history of modern birds. However, MHC gene duplication, maintenance, and loss among and within bird species may confound avian relationships making it difficult to elucidate the ancestral state. This study adds essential data for disentangling the course of MHC structural evolution in birds.
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Affiliation(s)
- Gabrielle J Knafler
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand
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19
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Knafler GJ, Jamieson IG. Primers for the amplification of major histocompatibility complex class I and II loci in the recovering red-crowned parakeet. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-0063-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Paixão-Côrtes VR, Salzano FM, Bortolini MC. Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family. PLoS One 2013; 8:e73560. [PMID: 24023886 PMCID: PMC3759438 DOI: 10.1371/journal.pone.0073560] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 07/23/2013] [Indexed: 12/22/2022] Open
Abstract
Paired box (PAX) genes are transcription factors that play important roles in embryonic development. Although the PAX gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of PAX genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of PAX sequences from 188 chordates, which revealed restricted variation. The absence of PAX4 and PAX8 among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in PAX4, PAX7, and PAX8. This result indicates asymmetric evolution of PAX family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.
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Affiliation(s)
- Vanessa Rodrigues Paixão-Côrtes
- Departamento de Genética and Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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21
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Characteristics of MHC class I genes in house sparrows Passer domesticus as revealed by long cDNA transcripts and amplicon sequencing. J Mol Evol 2013; 77:8-21. [PMID: 23877344 DOI: 10.1007/s00239-013-9575-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/10/2013] [Indexed: 10/26/2022]
Abstract
In birds the major histocompatibility complex (MHC) organization differs both among and within orders; chickens Gallus gallus of the order Galliformes have a simple arrangement, while many songbirds of the order Passeriformes have a more complex arrangement with larger numbers of MHC class I and II genes. Chicken MHC genes are found at two independent loci, classical MHC-B and non-classical MHC-Y, whereas non-classical MHC genes are yet to be verified in passerines. Here we characterize MHC class I transcripts (α1 to α3 domain) and perform amplicon sequencing using a next-generation sequencing technique on exon 3 from house sparrow Passer domesticus (a passerine) families. Then we use phylogenetic, selection, and segregation analyses to gain a better understanding of the MHC class I organization. Trees based on the α1 and α2 domain revealed a distinct cluster with short terminal branches for transcripts with a 6-bp deletion. Interestingly, this cluster was not seen in the tree based on the α3 domain. 21 exon 3 sequences were verified in a single individual and the average numbers within an individual were nine and five for sequences with and without a 6-bp deletion, respectively. All individuals had exon 3 sequences with and without a 6-bp deletion. The sequences with a 6-bp deletion have many characteristics in common with non-classical MHC, e.g., highly conserved amino acid positions were substituted compared with the other alleles, low nucleotide diversity and just a single site was subject to positive selection. However, these alleles also have characteristics that suggest they could be classical, e.g., complete linkage and absence of a distinct cluster in a tree based on the α3 domain. Thus, we cannot determine for certain whether or not the alleles with a 6-bp deletion are non-classical based on our present data. Further analyses on segregation patterns of these alleles in combination with dating the 6-bp deletion through MHC characterization across the genus Passer may solve this matter in the future.
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22
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Aguilar JRD, Schut E, Merino S, Martínez J, Komdeur J, Westerdahl H. MHC class II B diversity in blue tits: a preliminary study. Ecol Evol 2013; 3:1878-89. [PMID: 23919136 PMCID: PMC3728931 DOI: 10.1002/ece3.598] [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: 02/28/2013] [Accepted: 04/17/2013] [Indexed: 12/18/2022] Open
Abstract
In this study, we partly characterize major histocompatibility complex (MHC) class II B in the blue tit (Cyanistes caeruleus). A total of 22 individuals from three different European locations: Spain, The Netherlands, and Sweden were screened for MHC allelic diversity. The MHC genes were investigated using both PCR-based methods and unamplified genomic DNA with restriction fragment length polymorphism (RFLP) and southern blots. A total of 13 different exon 2 sequences were obtained independently from DNA and/or RNA, thus confirming gene transcription and likely functionality of the genes. Nine out of 13 alleles were found in more than one country, and two alleles appeared in all countries. Positive selection was detected in the region coding for the peptide binding region (PBR). A maximum of three alleles per individual was detected by sequencing and the RFLP pattern consisted of 4-7 fragments, indicating a minimum number of 2-4 loci per individual. A phylogenetic analysis, demonstrated that the blue tit sequences are divergent compared to sequences from other passerines resembling a different MHC lineage than those possessed by most passerines studied to date.
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Affiliation(s)
- Juan Rivero-de Aguilar
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC)J. Gutiérrez Abascal 2, E-28006, Madrid, Spain
| | - Elske Schut
- Behavioural Ecology and Self-Organization, The University of GroningenPO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Santiago Merino
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC)J. Gutiérrez Abascal 2, E-28006, Madrid, Spain
| | - Javier Martínez
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de AlcaláAlcalá de Henares, E-28871, Madrid, Spain
| | - Jan Komdeur
- Behavioural Ecology and Self-Organization, The University of GroningenPO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Ecology Building, Lund UniversitySölvegatan 37, SE-22362, Lund, Sweden
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A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao). PLoS One 2013; 8:e62415. [PMID: 23667475 PMCID: PMC3648530 DOI: 10.1371/journal.pone.0062415] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/21/2013] [Indexed: 12/31/2022] Open
Abstract
Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (>1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N's). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two scarlet macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the scarlet macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the scarlet macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.
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Strand T, Wang B, Meyer-Lucht Y, Höglund J. Evolutionary history of black grouse major histocompatibility complex class IIB genes revealed through single locus sequence-based genotyping. BMC Genet 2013; 14:29. [PMID: 23617616 PMCID: PMC3652749 DOI: 10.1186/1471-2156-14-29] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 04/12/2013] [Indexed: 11/10/2022] Open
Abstract
Background Gene duplications are frequently observed in the Major Histocompatibility Complex (MHC) of many species, and as a consequence loci belonging to the same MHC class are often too similar to tell apart. In birds, single locus genotyping of MHC genes has proven difficult due to concerted evolution homogenizing sequences at different loci. But studies on evolutionary history, mode of selection and heterozygosity correlations on the MHC cannot be performed before it is possible to analyse duplicated genes separately. In this study we investigate the architecture and evolution of the MHC class IIB genes in black grouse. We developed a sequence-based genotyping method for separate amplification of the two black grouse MHC class IIB genes BLB1 and BLB2. Based on this approach we are able to study differences in structure and selection between the two genes in black grouse and relate these results to the chicken MHC structure and organization. Results Sequences were obtained from 12 individuals and separated into alleles using the software PHASE. We compared nucleotide diversity measures and employed selection tests for BLB1 and BLB2 to explore their modes of selection. Both BLB1 and BLB2 are transcribed and display classic characteristics of balancing selection as predicted for expressed MHC class IIB genes. We found evidence for both intra- and interlocus recombination or gene conversion, as well as indication for positive but differential selection at both loci. Moreover, the two loci appear to be linked. Phylogenetic analyses revealed orthology of the black grouse MHC class IIB genes to the respective BLB loci in chicken. Conclusions The results indicate that the duplication of the BLB gene occurred before the species divergence into black grouse, chicken and pheasant. Further, we conclude that BLB1 and BLB2 in black grouse are subjected to homogenizing concerted evolution due to interlocus genetic exchange after species divergence. The loci are in linkage disequilibrium, which is in line with the theory of tightly coevolving genes within the MHC under the minimal essential MHC hypothesis. Our results support the conclusion that MHC form and function in birds derived from studies on the domesticated chicken are not artefacts of the domestication process.
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Affiliation(s)
- Tanja Strand
- Population Biology and Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden
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Gohli J, Anmarkrud JA, Johnsen A, Kleven O, Borge T, Lifjeld JT. FEMALE PROMISCUITY IS POSITIVELY ASSOCIATED WITH NEUTRAL AND SELECTED GENETIC DIVERSITY IN PASSERINE BIRDS. Evolution 2013; 67:1406-19. [DOI: 10.1111/evo.12045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 12/17/2012] [Indexed: 12/16/2022]
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Wutzler R, Foerster K, Kempenaers B. MHC class I variation in a natural blue tit population (Cyanistes caeruleus). Genetica 2012; 140:349-64. [PMID: 23073914 DOI: 10.1007/s10709-012-9679-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 09/03/2012] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is central to the vertebrate immune system and its highly polymorphic genes are considered to influence several life-history traits of individuals. To characterize the MHC in a natural population of blue tits (Cyanistes caeruleus) we investigated the class I exon 3 diversity of more than 900 individuals. We designed two pairs of motif-specific primers that reliably amplify independent subsets of MHC alleles. Applying denaturing gradient gel electrophoresis (DGGE) we obtained 48 independently inherited units of unique band patterns (DGGE-haplogroups), which were validated in a segregation analysis within 105 families. In a second approach, we extensively sequenced 6 unrelated individuals to confirm that DGGE-haplogroup composition reflects individual allelic variation. The highest number of different DGGE-haplogroups in a single individual corresponded in 19 MHC exon 3 sequences, suggesting a minimum of 10 amplified MHC class I loci in the blue tit. In total, we identified 50 unique functional and 3 non-functional sequences. Functional sequences showed high levels of recombination and strong positive selection in the antigen binding region, whereas nucleotide diversity was comparatively low in the range of all passerine species. Finally, in a phylogenetic comparison of passerine MHC class I exon 3 sequences we discuss conflicting evolutionary signals possibly due to recent gene duplication, recombination events and concerted evolution. Our results indicate that the described method is suitable to effectively explore the MHC diversity and its ecological impacts in blue tits in future studies.
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Affiliation(s)
- R Wutzler
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82305 Seewiesen, Germany.
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Knafler GJ, Clark JA, Boersma PD, Bouzat JL. MHC diversity and mate choice in the magellanic penguin, Spheniscus magellanicus. ACTA ACUST UNITED AC 2012; 103:759-68. [PMID: 22952272 DOI: 10.1093/jhered/ess054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We estimated levels of diversity at the major histocompatibility complex (MHC) class II DRß1 gene in 50 breeding pairs of the Magellanic penguin and compared those to estimates from Humboldt and Galapagos penguins. We tested for positive selection and 2 conditions required for the evolution of MHC-based disassortative mating: 1) greater MHC diversity between breeding pairs compared to random mating, and 2) associations between MHC genotype and fitness. Cloning and sequencing of the DRß1 gene showed that Magellanic penguins had higher levels of genetic variation than Galapagos and Humboldt penguins. Sequence analysis revealed 45 alleles with 3.6% average proportion of nucleotide differences, nucleotide diversity of 0.030, and observed heterozygosity of 0.770. A gene phylogeny showed 9 allelic lineages with interspersed DRß1 sequences from Humboldt and Galapagos penguins, indicating ancestral polymorphisms. d (N)/d (S) ratios revealed evidence for positive selection. Analysis of breeding pairs showed no disassortative mating preferences. Significant MHC genotype/fitness associations in females suggest, however, that selection for pathogen resistance plays a more important role than mate choice in maintaining diversity at the MHC in the Magellanic penguin. The differential effect of MHC heterozygosity on fitness between the sexes is likely associated with the relative role of hatching and fledging rates as reliable indicators of overall fitness in males and females.
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28
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GANGOSO L, ALCAIDE M, GRANDE JM, MUÑOZ J, TALBOT SL, SONSTHAGEN SA, SAGE GK, FIGUEROLA J. Colonizing the world in spite of reduced MHC variation. J Evol Biol 2012; 25:1438-47. [DOI: 10.1111/j.1420-9101.2012.02529.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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29
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Ye Q, He K, Wu SY, Wan QH. Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant. PLoS One 2012; 7:e32154. [PMID: 22403630 PMCID: PMC3293878 DOI: 10.1371/journal.pone.0032154] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 01/19/2012] [Indexed: 12/02/2022] Open
Abstract
The bacterial artificial chromosome (BAC) system is widely used in isolation of large genomic fragments of interest. Construction of a routine BAC library requires several months for picking clones and arraying BACs into superpools in order to employ 4D-PCR to screen positive BACs, which might be time-consuming and laborious. The major histocompatibility complex (MHC) is a cluster of genes involved in the vertebrate immune system, and the classical avian MHC-B locus is a minimal essential one, occupying a 100-kb genomic region. In this study, we constructed a more effective reverse-4D BAC library for the golden pheasant, which first creates sub-libraries and then only picks clones of positive sub-libraries, and identified several MHC clones within thirty days. The full sequencing of a 97-kb reverse-4D BAC demonstrated that the golden pheasant MHC-B locus contained 20 genes and showed good synteny with that of the chicken. The notable differences between these two species were the numbers of class II B loci and NK genes and the inversions of the TAPBP gene and the TAP1-TAP2 region. Furthermore, the inverse TAP2-TAP1 was unique in the golden pheasant in comparison with that of chicken, turkey, and quail. The newly defined genomic structure of the golden pheasant MHC will give an insight into the evolutionary history of the avian MHC.
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Affiliation(s)
| | | | - Shao-Ying Wu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
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Alcaide M, Rodríguez A, Negro JJ. Sampling strategies for accurate computational inferences of gametic phase across highly polymorphic major histocompatibility complex loci. BMC Res Notes 2011; 4:151. [PMID: 21615903 PMCID: PMC3126723 DOI: 10.1186/1756-0500-4-151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 05/26/2011] [Indexed: 11/22/2022] Open
Abstract
Background Genes of the Major Histocompatibility Complex (MHC) are very popular genetic markers among evolutionary biologists because of their potential role in pathogen confrontation and sexual selection. However, MHC genotyping still remains challenging and time-consuming in spite of substantial methodological advances. Although computational haplotype inference has brought into focus interesting alternatives, high heterozygosity, extensive genetic variation and population admixture are known to cause inaccuracies. We have investigated the role of sample size, genetic polymorphism and genetic structuring on the performance of the popular Bayesian PHASE algorithm. To cover this aim, we took advantage of a large database of known genotypes (using traditional laboratory-based techniques) at single MHC class I (N = 56 individuals and 50 alleles) and MHC class II B (N = 103 individuals and 62 alleles) loci in the lesser kestrel Falco naumanni. Findings Analyses carried out over real MHC genotypes showed that the accuracy of gametic phase reconstruction improved with sample size as a result of the reduction in the allele to individual ratio. We then simulated different data sets introducing variations in this parameter to define an optimal ratio. Conclusions Our results demonstrate a critical influence of the allele to individual ratio on PHASE performance. We found that a minimum allele to individual ratio (1:2) yielded 100% accuracy for both MHC loci. Sampling effort is therefore a crucial step to obtain reliable MHC haplotype reconstructions and must be accomplished accordingly to the degree of MHC polymorphism. We expect our findings provide a foothold into the design of straightforward and cost-effective genotyping strategies of those MHC loci from which locus-specific primers are available.
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Affiliation(s)
- Miguel Alcaide
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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Ekblom R, Stapley J, Ball AD, Birkhead T, Burke T, Slate J. Genetic mapping of the major histocompatibility complex in the zebra finch (Taeniopygia guttata). Immunogenetics 2011; 63:523-30. [PMID: 21494955 DOI: 10.1007/s00251-011-0525-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/04/2011] [Indexed: 12/29/2022]
Abstract
Genes of the major histocompatibility complex (MHC) have received much attention in immunology, genetics, and ecology because they are highly polymorphic and play important roles in parasite resistance and mate choice. Until recently, the MHC of passerine birds was not well-described. However, the genome sequencing of the zebra finch (Taeniopygia guttata) has partially redressed this gap in our knowledge of avian MHC genes. Here, we contribute further to the understanding of the zebra finch MHC organization by mapping SNPs within or close to known MHC genes in the zebra finch genome. MHC class I and IIB genes were both mapped to zebra finch chromosome 16, and there was no evidence that MHC class I genes are located on chromosome 22 (as suggested by the genome assembly). We confirm the location in the MHC region on chromosome 16 for several other genes (BRD2, FLOT1, TRIM7.2, GNB2L1, and CSNK2B). Two of these (CSNK2B and FLOT1) have not previously been mapped in any other bird species. In line with previous results, we also find that orthologs to the immune-related genes B-NK and CLEC2D, which are part of the MHC region in chicken, are situated on zebra finch chromosome Z and not among other MHC genes in the zebra finch.
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Affiliation(s)
- Robert Ekblom
- Department of Population Biology and Conservation Biology, Uppsala University, Norbyvägen, Sweden.
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Characterisation of class II B MHC genes from a ratite bird, the little spotted kiwi (Apteryx owenii). Immunogenetics 2011; 63:223-33. [PMID: 21221966 DOI: 10.1007/s00251-010-0503-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Accepted: 12/11/2010] [Indexed: 12/15/2022]
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33
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Zagalska-Neubauer M, Babik W, Stuglik M, Gustafsson L, Cichoń M, Radwan J. 454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher. BMC Evol Biol 2010; 10:395. [PMID: 21194449 PMCID: PMC3024992 DOI: 10.1186/1471-2148-10-395] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 12/31/2010] [Indexed: 11/24/2022] Open
Abstract
Background Because of their functional significance, the Major Histocompatibility Complex (MHC) class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping. Results Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family. Conclusions 454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective, genotyping of MHC systems of virtually any complexity.
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Gómez D, Conejeros P, Marshall SH, Consuegra S. MHC evolution in three salmonid species: a comparison between class II alpha and beta genes. Immunogenetics 2010; 62:531-42. [PMID: 20521040 DOI: 10.1007/s00251-010-0456-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 05/15/2010] [Indexed: 11/26/2022]
Abstract
The genes of the major histocompatibility complex (MHC) are amongst the most variable in vertebrates and represent some of the best candidates to study processes of adaptive evolution. However, despite the number of studies available, most of the information on the structure and function of these genes come from studies in mammals and birds in which the MHC class I and II genes are tightly linked and class II alpha exhibits low variability in many cases. Teleost fishes are among the most primitive vertebrates with MHC and represent good organisms for the study of MHC evolution because their class I and class II loci are not physically linked, allowing for independent evolution of both classes of genes. We have compared the diversity and molecular mechanisms of evolution of classical MH class II alpha and class II beta loci in farm populations of three salmonid species: Oncorhynchus kisutch, Oncorhynchus mykiss and Salmo salar. We found single classical class II loci and high polymorphism at both class II alpha and beta genes in the three species. Mechanisms of evolution were common for both class II genes, with recombination and point mutation involved in generating diversity and positive selection acting on the peptide-binding residues. These results suggest that the maintenance of variability at the class IIalpha gene could be a mechanism to increase diversity in the MHC class II in salmonids in order to compensate for the expression of one single classical locus and to respond to a wider array of parasites.
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Affiliation(s)
- Daniela Gómez
- Instituto de Biología, Facultad de Ciencias Básicas y Matemáticas, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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Burri R, Salamin N, Studer RA, Roulin A, Fumagalli L. Adaptive Divergence of Ancient Gene Duplicates in the Avian MHC Class II. Mol Biol Evol 2010; 27:2360-74. [DOI: 10.1093/molbev/msq120] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Anmarkrud JA, Johnsen A, Bachmann L, Lifjeld JT. Ancestral polymorphism in exon 2 of bluethroat (Luscinia svecica) MHC class II B genes. J Evol Biol 2010; 23:1206-17. [PMID: 20456568 DOI: 10.1111/j.1420-9101.2010.01999.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The genes of the major histocompatibility complex (MHC) are important model genes for understanding selective forces in evolution. Here, we document, using a cloning and sequencing approach, high polymorphism at the exon 2 of the MHC class II B (MHCIIB) genes in the bluethroat (Luscinia svecica); a minimum of 61 unique alleles were detected in 20 individuals, and at least 11 functional loci. In addition, several pseudogenes were revealed. The specimens originated from three different bluethroat subspecies (azuricollis, cyanecula and svecica), and we also analysed four specimens of the closely related thrush nightingale (L. luscinia) for comparison. Phylogenetic analyses of the functional alleles revealed 258 equally parsimonious trees with poor statistical support for the majority of nodes. The distribution of the sequences in the trees point to an ancestral origin of the polymorphism in MHC class II B genes, a portion of which predated the phylogenetic split between the bluethroat and the thrush nightingale. Strong signatures of balancing selection were uncovered for the codons coding for the peptide-binding residues of the functional MHCIIB exon 2 alleles. Our results highlight the importance of duplication and recombination events for shaping passerine MHC and give insights in the evolutionary dynamics of MHC variation among closely related taxa.
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Affiliation(s)
- Jarl A Anmarkrud
- National Centre for Biosystematics, Natural History Museum, University of Oslo, Blindern, Oslo, Norway.
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37
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Balakrishnan CN, Ekblom R, Völker M, Westerdahl H, Godinez R, Kotkiewicz H, Burt DW, Graves T, Griffin DK, Warren WC, Edwards SV. Gene duplication and fragmentation in the zebra finch major histocompatibility complex. BMC Biol 2010; 8:29. [PMID: 20359332 PMCID: PMC2907588 DOI: 10.1186/1741-7007-8-29] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 04/01/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Due to its high polymorphism and importance for disease resistance, the major histocompatibility complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of particular interest because the chicken Gallus gallus, the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. It remains unclear the extent to which this organization describes the situation in other birds and whether it represents a derived or ancestral condition. The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. RESULTS The zebra finch MHC exhibits a complex structure and history involving gene duplication and fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content. Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes. CONCLUSION The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages.
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Affiliation(s)
- Christopher N Balakrishnan
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
- Current address: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, USA
| | - Robert Ekblom
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Population Biology and Conservation Biology, Uppsala University, Uppsala, Sweden
| | - Martin Völker
- Department of Biosciences, University of Kent, Kent, UK
| | | | - Ricardo Godinez
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Holly Kotkiewicz
- School of Medicine, Genome Sequencing Center, Washington University, St Louis, MO, USA
| | - David W Burt
- Roslin Institute, Division of Genetics & Genomics, University of Edinburgh, Edinburgh, UK
| | - Tina Graves
- School of Medicine, Genome Sequencing Center, Washington University, St Louis, MO, USA
| | | | - Wesley C Warren
- School of Medicine, Genome Sequencing Center, Washington University, St Louis, MO, USA
| | - Scott V Edwards
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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Bollmer JL, Dunn PO, Whittingham LA, Wimpee C. Extensive MHC Class II B Gene Duplication in a Passerine, the Common Yellowthroat (Geothlypis trichas). J Hered 2010; 101:448-60. [PMID: 20200139 DOI: 10.1093/jhered/esq018] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Jennifer L Bollmer
- Department of Biological Sciences, University of Wisconsin-Milwaukee, PO Box 413, Milwaukee, WI 53201, USA.
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Eimes JA, Bollmer JL, Dunn PO, Whittingham LA, Wimpee C. Mhc class II diversity and balancing selection in greater prairie-chickens. Genetica 2009; 138:265-71. [PMID: 19851875 DOI: 10.1007/s10709-009-9417-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 10/09/2009] [Indexed: 10/20/2022]
Abstract
The major histocompatibility complex (Mhc) of domestic chickens has been characterized as small and relatively simple compared with that of mammals. However, there is growing evidence that the Mhc of many bird lineages may be more complex, even within the Order Galliformes. In this study, we measured genetic variation and balancing selection at Mhc loci in another galliform, the greater prairie-chicken. We cloned and sequenced a 239 bp fragment of Mhc Class II beta-chain (BLB) exon 2 in 14 individuals. There was a total of 10 unique sequences and a minimum of four BLB loci. The d(N)/d(S) ratio at peptide-binding codons was significantly greater than one, suggesting balancing selection is acting on the BLB. We also recovered two YLB sequences, which clustered tightly with YLB sequences from three other species: domestic chicken, black grouse and common quail. The relatively large number of loci revealed in our study suggests that even closely related galliforms differ in the level of Mhc variation and structure.
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Affiliation(s)
- John A Eimes
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA.
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Promerová M, Albrecht T, Bryja J. Extremely high MHC class I variation in a population of a long-distance migrant, the Scarlet Rosefinch (Carpodacus erythrinus). Immunogenetics 2009; 61:451-61. [PMID: 19452149 DOI: 10.1007/s00251-009-0375-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 04/20/2009] [Indexed: 11/25/2022]
Affiliation(s)
- M Promerová
- Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Studenec 122, 675 02 Konesín, Czech Republic.
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Patterns of variation of the major histocompatibility complex class IIB loci in Chinese goose (Anser Cygnoides). Immunogenetics 2009; 61:443-50. [DOI: 10.1007/s00251-009-0374-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 04/15/2009] [Indexed: 11/26/2022]
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42
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Hughes AL, Friedman R. Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes. Mol Biol Evol 2008; 25:2681-8. [PMID: 18820253 DOI: 10.1093/molbev/msn207] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Both mean genomes size and the variance in genome size among species are smaller on average in birds (class Aves) than in the other tetrapod classes. In order to test whether loss of protein-coding genes has contributed to genome size reduction in birds, we compared the chicken genome and five mammalian genomes. Numbers of members (paralogs) were significantly lower in the chicken gene families than in the corresponding mammalian families. Phylogenetic analyses of chicken, mammal, and fish paralogs supported the hypothesis that chicken-specific loss of paralogs occurred much more frequently than mammal-specific gene duplications. Moreover, the phylogenetic analyses supported the hypothesis that a substantial majority of the paralogs lost in chicken originated from duplications prior to the most recent common ancestor of tetrapods and bony fishes. In addition to loss of paralogs, numerous gene families present in the mammalian genomes were missing in the chicken genome; over 1,000 of these families were found in bony fishes, implying presence of the family in the tetrapod ancestor. In the set of families with more members on average in the mammals than in the chicken, immune system function was associated with a greater degree of gene family size reduction in the chicken, consistent with other evidence that immune system gene families have become particularly compact in birds.
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Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, USA.
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