IHB OpenIR
Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes
Li, Zhiqiang1,2; Gan, Xiaoni1,2,3; He, Shunping1; He, SP, Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, 7th Donghu S Rd, Wuhan 430072, Hubei, Peoples R China
2009-10-01
Source PublicationJOURNAL OF MOLECULAR EVOLUTION
ISSN0022-2844
Volume69Issue:4Pages:346-359
AbstractWe investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus-Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.; We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus-Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.
SubtypeArticle
KeywordGenome Duplication Color Vision Gene Positive Selection Cyprinid Fish Cavefish Sinocyclocheilus
Subject AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
Department[Li, Zhiqiang; Gan, Xiaoni; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China; [Li, Zhiqiang; Gan, Xiaoni] Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China; [Gan, Xiaoni] Chinese Acad Sci, Wuhan Inst Virol, Wuhan 430071, Hubei, Peoples R China
DOI10.1007/s00239-009-9283-9
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Indexed BySCI
Funding OrganizationNational Natural Science Foundation of China (NSFC) [2007CB411600, 30530120] ; National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120] ; National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120] ; National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120]
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS KeywordPOSITIVE DARWINIAN SELECTION ; AMINO-ACID SITES ; ADAPTIVE EVOLUTION ; VISUAL PIGMENTS ; MOLECULAR EVOLUTION ; OPSIN GENES ; MAXIMUM-LIKELIHOOD ; PHYLOGENETIC ANALYSIS ; GENOME DUPLICATION ; SEQUENCE ALIGNMENT
WOS IDWOS:000271460600006
Funding OrganizationNational Natural Science Foundation of China (NSFC) [2007CB411600, 30530120] ; National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120] ; National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120] ; National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120]
Citation statistics
Cited Times:7[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/152342/7496
Collection中科院水生所知识产出(2009年前)
Corresponding AuthorHe, SP, Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, 7th Donghu S Rd, Wuhan 430072, Hubei, Peoples R China
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
3.Chinese Acad Sci, Wuhan Inst Virol, Wuhan 430071, Hubei, Peoples R China
Recommended Citation
GB/T 7714
Li, Zhiqiang,Gan, Xiaoni,He, Shunping,et al. Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes[J]. JOURNAL OF MOLECULAR EVOLUTION,2009,69(4):346-359.
APA Li, Zhiqiang,Gan, Xiaoni,He, Shunping,&He, SP, Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, 7th Donghu S Rd, Wuhan 430072, Hubei, Peoples R China.(2009).Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes.JOURNAL OF MOLECULAR EVOLUTION,69(4),346-359.
MLA Li, Zhiqiang,et al."Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes".JOURNAL OF MOLECULAR EVOLUTION 69.4(2009):346-359.
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