| 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 Publication | JOURNAL OF MOLECULAR EVOLUTION
 |
| ISSN | 0022-2844 |
| Volume | 69Issue:4Pages:346-359 |
| Abstract | 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.; 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. |
| Subtype | Article |
| Keyword | Genome Duplication Color Vision Gene Positive Selection Cyprinid Fish Cavefish Sinocyclocheilus |
| 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 |
| Subject Area | Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity |
| DOI | 10.1007/s00239-009-9283-9 |
| WOS Headings | Science & Technology ; Life Sciences & Biomedicine |
| Funding Organization | 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] ; National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120] |
| Indexed By | SCI |
| Language | 英语 |
| WOS Research Area | Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity |
| WOS Subject | Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity |
| WOS ID | WOS:000271460600006 |
| WOS Keyword | POSITIVE DARWINIAN SELECTION ; AMINO-ACID SITES ; ADAPTIVE EVOLUTION ; VISUAL PIGMENTS ; MOLECULAR EVOLUTION ; OPSIN GENES ; MAXIMUM-LIKELIHOOD ; PHYLOGENETIC ANALYSIS ; GENOME DUPLICATION ; SEQUENCE ALIGNMENT |
| Funding Organization | 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] ; National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120] |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ihb.ac.cn/handle/152342/7496 |
| Collection | 期刊论文 |
| Corresponding Author | He, SP, Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, 7th Donghu S Rd, Wuhan 430072, Hubei, Peoples R China |
| Affiliation | 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 |
| 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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