Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

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	Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes
	Li, Zhiqiang 1,2; Gan, Xiaoni 1,2,3; He, Shunping 1
刊名	JOURNAL OF MOLECULAR EVOLUTION
	2009-10-01
卷号	69 期号:4 页码:346-359
关键词	Genome duplication Color vision gene Positive selection Cyprinid fish Cavefish Sinocyclocheilus
ISSN号	0022-2844
通讯作者	He, SP, Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, 7th Donghu S Rd, Wuhan 430072, Hubei, Peoples R China
中文摘要	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.
英文摘要	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.
学科主题	Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
研究领域[WOS]	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
关键词[WOS]	POSITIVE DARWINIAN SELECTION ; AMINO-ACID SITES ; ADAPTIVE EVOLUTION ; VISUAL PIGMENTS ; MOLECULAR EVOLUTION ; OPSIN GENES ; MAXIMUM-LIKELIHOOD ; PHYLOGENETIC ANALYSIS ; GENOME DUPLICATION ; SEQUENCE ALIGNMENT
收录类别	SCI
资助信息	National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120]
语种	英语
WOS记录号	WOS:000271460600006
公开日期	2010-10-13
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/152342/7496]
专题	水生生物研究所_中科院水生所知识产出（2009年前）_期刊论文
作者单位	1.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
推荐引用方式 GB/T 7714	Li, Zhiqiang,Gan, Xiaoni,He, Shunping. 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.(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.