메뉴 건너뛰기




Volumn 6, Issue 9, 2011, Pages

Patterns of positive selection and neutral evolution in the Protein-Coding genes of Tetraodon and Takifugu

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE IMMUNITY; ARTICLE; BIOLOGICAL PHENOMENA AND FUNCTIONS; BRAIN FUNCTION; CONTROLLED STUDY; DEFENSE MECHANISM; ENVIRONMENT; EVOLUTION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC CODE; IMMUNE RESPONSE; MAMMAL; NONHUMAN; PATTERN RECOGNITION; POPULATION SIZE; PUFFER FISH; SIGNAL TRANSDUCTION; SPECIES DIFFERENTIATION; TETRAODON; TRANSCRIPTION REGULATION; ANIMAL; GENETIC DRIFT; GENETICS; TETRAODONTIFORMES;

EID: 80052754502     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024800     Document Type: Article
Times cited : (26)

References (59)
  • 1
    • 33745347447 scopus 로고    scopus 로고
    • The distribution of fitness effects of new deleterious amino acid mutations in humans
    • Eyre-Walker A, Woolfit M, Phelps T, (2006) The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 173: 891-900.
    • (2006) Genetics , vol.173 , pp. 891-900
    • Eyre-Walker, A.1    Woolfit, M.2    Phelps, T.3
  • 2
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, et al. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
    • (2005) Nature , vol.437 , pp. 69-87
    • Mikkelsen, T.S.1    Hillier, L.W.2    Eichler, E.E.3    Zody, M.C.4    Jaffe, D.B.5
  • 3
    • 0035963414 scopus 로고    scopus 로고
    • Protein dispensability and rate of evolution
    • Hirsh AE, Fraser HB, (2001) Protein dispensability and rate of evolution. Nature 411: 1046-1049.
    • (2001) Nature , vol.411 , pp. 1046-1049
    • Hirsh, A.E.1    Fraser, H.B.2
  • 4
    • 2942678187 scopus 로고    scopus 로고
    • Evolutionary rate depends on number of protein-protein interactions independently of gene expression level
    • Fraser HB, Hirsh AE, (2004) Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. 4 Bmc Evolutionary Biology.
    • (2004) Bmc Evolutionary Biology , vol.4
    • Fraser, H.B.1    Hirsh, A.E.2
  • 7
    • 1542286776 scopus 로고    scopus 로고
    • Mammalian housekeeping genes evolve more slowly than tissue-specific genes
    • Zhang LQ, Li WH, (2004) Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Molecular Biology and Evolution 21: 236-239.
    • (2004) Molecular Biology and Evolution , vol.21 , pp. 236-239
    • Zhang, L.Q.1    Li, W.H.2
  • 10
    • 38549153853 scopus 로고    scopus 로고
    • Human PAML browser: a database of positive selection on human genes using phylogenetic methods
    • Nickel GC, Tefft D, Adams MD, (2008) Human PAML browser: a database of positive selection on human genes using phylogenetic methods. Nucleic Acids Research 36: D800-D808.
    • (2008) Nucleic Acids Research , vol.36 , pp. 800-808
    • Nickel, G.C.1    Tefft, D.2    Adams, M.D.3
  • 12
    • 20444430245 scopus 로고    scopus 로고
    • A scan for positively selected genes in the genomes of humans and chimpanzees
    • Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. Plos Biology 3: 976-985.
    • (2005) Plos Biology , vol.3 , pp. 976-985
    • Nielsen, R.1    Bustamante, C.2    Clark, A.G.3    Glanowski, S.4    Sackton, T.B.5
  • 14
    • 33646244720 scopus 로고    scopus 로고
    • Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome
    • Arbiza L, Dopazo Jn, Dopazo Hn, (2006) Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome. PLoS Comput Biol 2: e38.
    • (2006) PLoS Comput Biol , vol.2
    • Arbiza, L.1    Dopazo, J.2    Dopazo, H.3
  • 15
    • 27844439855 scopus 로고    scopus 로고
    • Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    • Zhang JZ, Nielsen R, Yang ZH, (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution 22: 2472-2479.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 2472-2479
    • Zhang, J.Z.1    Nielsen, R.2    Yang, Z.H.3
  • 16
    • 34247352040 scopus 로고    scopus 로고
    • Evolutionary and biomedical insights from the rhesus macaque genome
    • Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234.
    • (2007) Science , vol.316 , pp. 222-234
    • Gibbs, R.A.1    Rogers, J.2    Katze, M.G.3    Bumgarner, R.4    Weinstock, G.M.5
  • 17
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
    • (2007) Nature , vol.450 , pp. 203-218
    • Clark, A.G.1    Eisen, M.B.2    Smith, D.R.3    Bergman, C.M.4    Oliver, B.5
  • 18
    • 20144371089 scopus 로고    scopus 로고
    • Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles
    • Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G, Dickson M, et al. (2005) Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307: 1928-1933.
    • (2005) Science , vol.307 , pp. 1928-1933
    • Colosimo, P.F.1    Hosemann, K.E.2    Balabhadra, S.3    Villarreal, G.4    Dickson, M.5
  • 19
    • 78649294100 scopus 로고    scopus 로고
    • Optimization of de novo transcriptome assembly from next-generation sequencing data
    • Surget-Groba Y, Montoya-Burgos JI, (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Research 20: 1432-1440.
    • (2010) Genome Research , vol.20 , pp. 1432-1440
    • Surget-Groba, Y.1    Montoya-Burgos, J.I.2
  • 20
    • 7244259101 scopus 로고    scopus 로고
    • Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
    • Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
    • (2004) Nature , vol.431 , pp. 946-957
    • Jaillon, O.1    Aury, J.M.2    Brunet, F.3    Petit, J.L.4    Stange-Thomann, N.5
  • 21
    • 42549089208 scopus 로고    scopus 로고
    • Evidence for Positive Selection in the C-terminal Domain of the Cholesterol Metabolism Gene PCSK9 Based on Phylogenetic Analysis in 14 Primate Species
    • Ding K, McDonough SJ, Kullo IJ, (2007) Evidence for Positive Selection in the C-terminal Domain of the Cholesterol Metabolism Gene PCSK9 Based on Phylogenetic Analysis in 14 Primate Species. Plos One 2.
    • (2007) Plos One , vol.2
    • Ding, K.1    McDonough, S.J.2    Kullo, I.J.3
  • 22
    • 77955593651 scopus 로고    scopus 로고
    • Molecular Evolution of the Primate Antiviral Restriction Factor Tetherin
    • Liu J, Chen KP, Wang JH, Zhang CY, (2010) Molecular Evolution of the Primate Antiviral Restriction Factor Tetherin. Plos One 5.
    • (2010) Plos One , vol.5
    • Liu, J.1    Chen, K.P.2    Wang, J.H.3    Zhang, C.Y.4
  • 24
    • 0027403961 scopus 로고
    • Unbiased Estimation of the Rates of Synonymous and Nonsynonymous Substitution
    • Li WH, (1993) Unbiased Estimation of the Rates of Synonymous and Nonsynonymous Substitution. Journal of Molecular Evolution 36: 96-99.
    • (1993) Journal of Molecular Evolution , vol.36 , pp. 96-99
    • Li, W.H.1
  • 25
    • 0027533924 scopus 로고
    • Evolution of the Zfx and Zfy Genes - Rates and Interdependence between the Genes
    • Pamilo P, Bianchi NO, (1993) Evolution of the Zfx and Zfy Genes- Rates and Interdependence between the Genes. Molecular Biology and Evolution 10: 271-281.
    • (1993) Molecular Biology and Evolution , vol.10 , pp. 271-281
    • Pamilo, P.1    Bianchi, N.O.2
  • 26
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang ZH, Nielsen R, (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution 17: 32-43.
    • (2000) Molecular Biology and Evolution , vol.17 , pp. 32-43
    • Yang, Z.H.1    Nielsen, R.2
  • 27
    • 0015722319 scopus 로고
    • Slightly Deleterious Mutant Substitutions in Evolution
    • Ohta T, (1973) Slightly Deleterious Mutant Substitutions in Evolution. Nature 246: 96-98.
    • (1973) Nature , vol.246 , pp. 96-98
    • Ohta, T.1
  • 28
    • 33847253862 scopus 로고    scopus 로고
    • Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model
    • Hobolth A, Christensen OF, Mailund T, Schierup MH, (2007) Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. Plos Genetics 3: 294-304.
    • (2007) Plos Genetics , vol.3 , pp. 294-304
    • Hobolth, A.1    Christensen, O.F.2    Mailund, T.3    Schierup, M.H.4
  • 29
    • 33745591114 scopus 로고    scopus 로고
    • Genetic evidence for complex speciation of humans and chimpanzees
    • Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D, (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441: 1103-1108.
    • (2006) Nature , vol.441 , pp. 1103-1108
    • Patterson, N.1    Richter, D.J.2    Gnerre, S.3    Lander, E.S.4    Reich, D.5
  • 30
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang ZH, Nielsen R, (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution 19: 908-917.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 908-917
    • Yang, Z.H.1    Nielsen, R.2
  • 33
    • 23244440415 scopus 로고    scopus 로고
    • Composition and evolution of the V2r vorneronasal receptor gene repertoire in mice and rats
    • Yang H, Shi P, Zhang YP, Zhang JZ, (2005) Composition and evolution of the V2r vorneronasal receptor gene repertoire in mice and rats. Genomics 86: 306-315.
    • (2005) Genomics , vol.86 , pp. 306-315
    • Yang, H.1    Shi, P.2    Zhang, Y.P.3    Zhang, J.Z.4
  • 34
    • 14644438648 scopus 로고    scopus 로고
    • Divergent V1R repertoires in five species: Amplification in rodents, decimation in primates, and a surprisingly small repertoire in dogs
    • Young JM, Kambere M, Trask BJ, Lane RP, (2005) Divergent V1R repertoires in five species: Amplification in rodents, decimation in primates, and a surprisingly small repertoire in dogs. Genome Research 15: 231-240.
    • (2005) Genome Research , vol.15 , pp. 231-240
    • Young, J.M.1    Kambere, M.2    Trask, B.J.3    Lane, R.P.4
  • 35
    • 33947149178 scopus 로고    scopus 로고
    • Comparative genomics of odorant and pheromone receptor genes in rodents
    • Zhang XH, Zhang XM, Firestein S, (2007) Comparative genomics of odorant and pheromone receptor genes in rodents. Genomics 89: 441-450.
    • (2007) Genomics , vol.89 , pp. 441-450
    • Zhang, X.H.1    Zhang, X.M.2    Firestein, S.3
  • 36
    • 0001816254 scopus 로고
    • The molecular nature of chemical stimuli in the aquatic environment
    • In: Atema J, Fay RR, Popper AN, Tavolga WN, editors, New York, Springer
    • Carr WES, (1988) The molecular nature of chemical stimuli in the aquatic environment. In: Atema J, Fay RR, Popper AN, Tavolga WN, editors. Sensory Biology of Aquatic Animals New York Springer pp. 3-27.
    • (1988) Sensory Biology of Aquatic Animals , pp. 3-27
    • Carr, W.E.S.1
  • 37
    • 46949083034 scopus 로고    scopus 로고
    • Neural processing, perception, and behavioral responses to natural chemical stimuli by fish and crustaceans
    • Derby CD, Sorensen PW, (2008) Neural processing, perception, and behavioral responses to natural chemical stimuli by fish and crustaceans. Journal of Chemical Ecology 34: 898-914.
    • (2008) Journal of Chemical Ecology , vol.34 , pp. 898-914
    • Derby, C.D.1    Sorensen, P.W.2
  • 38
    • 51349093264 scopus 로고    scopus 로고
    • Evolution of vertebrate visual pigments
    • Bowmaker JK, (2008) Evolution of vertebrate visual pigments. Vision Research 48: 2022-2041.
    • (2008) Vision Research , vol.48 , pp. 2022-2041
    • Bowmaker, J.K.1
  • 42
    • 26444526700 scopus 로고    scopus 로고
    • Neutral mutation as the source of genetic variation in life history traits
    • Brcic-Kostic K, (2005) Neutral mutation as the source of genetic variation in life history traits. Genetical Research 86: 53-63.
    • (2005) Genetical Research , vol.86 , pp. 53-63
    • Brcic-Kostic, K.1
  • 43
    • 28644440530 scopus 로고    scopus 로고
    • The signature of positive selection on standing genetic variation
    • Przeworski M, Coop G, Wall JD, (2005) The signature of positive selection on standing genetic variation. Evolution 59: 2312-2323.
    • (2005) Evolution , vol.59 , pp. 2312-2323
    • Przeworski, M.1    Coop, G.2    Wall, J.D.3
  • 45
    • 36749042777 scopus 로고    scopus 로고
    • Latent evolutionary potentials under the neutral mutational drift of an enzyme
    • Amitai G, Gupta RD, Tawfik DS, (2007) Latent evolutionary potentials under the neutral mutational drift of an enzyme. HSFP J 1: 67-78.
    • (2007) HSFP J , vol.1 , pp. 67-78
    • Amitai, G.1    Gupta, R.D.2    Tawfik, D.S.3
  • 46
    • 34447559360 scopus 로고    scopus 로고
    • Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution
    • Bloom JD, Romero PA, Lu ZY, Arnold FH, (2007) Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. 2 Biology Direct.
    • (2007) Biology Direct , vol.2
    • Bloom, J.D.1    Romero, P.A.2    Lu, Z.Y.3    Arnold, F.H.4
  • 47
    • 27844543705 scopus 로고    scopus 로고
    • Human SNPs reveal no evidence of frequent positive selection
    • Zhang LQ, Li WH, (2005) Human SNPs reveal no evidence of frequent positive selection. Molecular Biology and Evolution 22: 2504-2507.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 2504-2507
    • Zhang, L.Q.1    Li, W.H.2
  • 48
    • 68949202924 scopus 로고    scopus 로고
    • Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change
    • Eyre-Walker A, Keightley PD, (2009) Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change. Molecular Biology and Evolution 26: 2097-2108.
    • (2009) Molecular Biology and Evolution , vol.26 , pp. 2097-2108
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 49
    • 79960102692 scopus 로고    scopus 로고
    • Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals
    • doi:10.1093/gbe/evr041
    • Kai W, Kikuchi K, Tohari S, Chew AK, Tay A, et al. (2011) Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals. Genome Biology and Evolution doi:10.1093/gbe/evr041.
    • (2011) Genome Biology and Evolution
    • Kai, W.1    Kikuchi, K.2    Tohari, S.3    Chew, A.K.4    Tay, A.5
  • 52
    • 0014757386 scopus 로고
    • A General Method Applicable to Search for Similarities in Amino Acid Sequence of 2 Proteins
    • Needleman SB, Wunsch CD, (1970) A General Method Applicable to Search for Similarities in Amino Acid Sequence of 2 Proteins. Journal of Molecular Biology 48: 443-453.
    • (1970) Journal of Molecular Biology , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 53
    • 77951682635 scopus 로고    scopus 로고
    • KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
    • Wang D, Zhang Y, Zhang Z, Zhu J, Yu J, (2010) KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Genomics, Proteomics and Bioinformatics 8: 77-80.
    • (2010) Genomics, Proteomics and Bioinformatics , vol.8 , pp. 77-80
    • Wang, D.1    Zhang, Y.2    Zhang, Z.3    Zhu, J.4    Yu, J.5
  • 54
    • 33747835539 scopus 로고    scopus 로고
    • Computing Ka and Ks with a consideration of unequal transitional substitutions
    • Zhang Z, Li J, Yu J, (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evolutionary Biology 6: 44.
    • (2006) BMC Evolutionary Biology , vol.6 , pp. 44
    • Zhang, Z.1    Li, J.2    Yu, J.3
  • 55
    • 67650067467 scopus 로고    scopus 로고
    • Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates
    • Wang DP, Wan HL, Zhang S, Yu J, (2009) Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biology Direct 4: 20.
    • (2009) Biology Direct , vol.4 , pp. 20
    • Wang, D.P.1    Wan, H.L.2    Zhang, S.3    Yu, J.4
  • 56
    • 48449104617 scopus 로고    scopus 로고
    • GOEAST: a web-based software toolkit for gene ontology enrichment analysis
    • doi:10.1093/nar/gkn1276
    • Zheng Q, Wang X-J, (2008) GOEAST: a web-based software toolkit for gene ontology enrichment analysis. Nucleic Acids Research 36 doi:10.1093/nar/gkn1276.
    • (2008) Nucleic Acids Research , vol.36
    • Zheng, Q.1    Wang, X.-J.2
  • 57
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Benjamini Y, Yekutieli D, (2001) The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 29: 1165-1188.
    • (2001) Annals of Statistics , vol.29 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 58
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: find statistically overrepresented Gene Ontologies within a group of genes
    • Beissbarth T, Speed TP, (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464-1465.
    • (2004) Bioinformatics , vol.20 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.