메뉴 건너뛰기




Volumn 6, Issue 3, 2013, Pages 412-422

A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals

Author keywords

Hearing; Phylomedicine; Positive selection; Purifying selection

Indexed keywords


EID: 84875682200     PISSN: 17524563     EISSN: 17524571     Source Type: Journal    
DOI: 10.1111/eva.12047     Document Type: Article
Times cited : (14)

References (52)
  • 4
    • 34547793042 scopus 로고    scopus 로고
    • Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites
    • Anisimova, M., and Z. H. Yang 2007. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Molecular Biology and Evolution 24:1219-1228.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1219-1228
    • Anisimova, M.1    Yang, Z.H.2
  • 5
    • 45549107624 scopus 로고    scopus 로고
    • UniPrime: a workflow-based platform for improved universal primer design
    • Bekaert, M., and E. C. Teeling 2008. UniPrime: a workflow-based platform for improved universal primer design. Nucleic Acids Research 36:e56.
    • (2008) Nucleic Acids Research , vol.36
    • Bekaert, M.1    Teeling, E.C.2
  • 8
    • 40849106619 scopus 로고    scopus 로고
    • Quiet as a mouse: dissecting the molecular and genetic basis of hearing
    • Brown, S. D. M., R. E. Hardisty-Hughes, and P. Mburu 2008. Quiet as a mouse: dissecting the molecular and genetic basis of hearing. Nature Reviews Genetics 9:277-290.
    • (2008) Nature Reviews Genetics , vol.9 , pp. 277-290
    • Brown, S.D.M.1    Hardisty-Hughes, R.E.2    Mburu, P.3
  • 9
    • 33644660937 scopus 로고    scopus 로고
    • Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans
    • Burk-Herrick, A., M. Scally, H. Amrine-Madsen, M. J. Stanhope, and M. S. Springer 2006. Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans. Mammalian Genome 17:257-270.
    • (2006) Mammalian Genome , vol.17 , pp. 257-270
    • Burk-Herrick, A.1    Scally, M.2    Amrine-Madsen, H.3    Stanhope, M.J.4    Springer, M.S.5
  • 10
    • 80051968181 scopus 로고    scopus 로고
    • Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
    • Cooper, G. M., and J. Shendure 2011. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews Genetics 12:628-640.
    • (2011) Nature Reviews Genetics , vol.12 , pp. 628-640
    • Cooper, G.M.1    Shendure, J.2
  • 11
    • 84859934504 scopus 로고    scopus 로고
    • Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence
    • Davies, K. T., J. A. Cotton, J. D. Kirwan, E. C. Teeling, and S. J. Rossiter 2011. Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence. Heredity (Edinb) 108:480-489.
    • (2011) Heredity (Edinb) , vol.108 , pp. 480-489
    • Davies, K.T.1    Cotton, J.A.2    Kirwan, J.D.3    Teeling, E.C.4    Rossiter, S.J.5
  • 12
    • 13544251711 scopus 로고    scopus 로고
    • Myosin XVa and whirlin, two deafness gene products required for hair bundle growth, are located at the stereocilia tips and interact directly
    • Delprat, B., V. Michel, R. Goodyear, Y. Yamasaki, N. Michalski, A. El-Amraoui, I. Perfettini et al. 2005. Myosin XVa and whirlin, two deafness gene products required for hair bundle growth, are located at the stereocilia tips and interact directly. Human Molecular Genetics 14:401-410.
    • (2005) Human Molecular Genetics , vol.14 , pp. 401-410
    • Delprat, B.1    Michel, V.2    Goodyear, R.3    Yamasaki, Y.4    Michalski, N.5    El-Amraoui, A.6    Perfettini, I.7
  • 13
    • 77957911916 scopus 로고    scopus 로고
    • Hearing impairment: a panoply of genes and functions
    • Dror, A. A., and K. B. Avraham 2010. Hearing impairment: a panoply of genes and functions. Neuron 68:293-308.
    • (2010) Neuron , vol.68 , pp. 293-308
    • Dror, A.A.1    Avraham, K.B.2
  • 15
    • 29244448344 scopus 로고    scopus 로고
    • The sensory and motor roles of auditory hair cells
    • Fettiplace, R., and C. M. Hackney 2006. The sensory and motor roles of auditory hair cells. Nature Reviews Neuroscience 7:19-29.
    • (2006) Nature Reviews Neuroscience , vol.7 , pp. 19-29
    • Fettiplace, R.1    Hackney, C.M.2
  • 16
    • 71049176982 scopus 로고    scopus 로고
    • Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species
    • Genome 10K Community of Scientists
    • Genome 10K Community of Scientists 2009. Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. Journal of Heredity 100:659-674.
    • (2009) Journal of Heredity , vol.100 , pp. 659-674
  • 19
    • 45949109669 scopus 로고    scopus 로고
    • MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    • Kumar, S., M. Nei, J. Dudley, and K. Tamura 2008. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9:299-306.
    • (2008) Briefings in Bioinformatics , vol.9 , pp. 299-306
    • Kumar, S.1    Nei, M.2    Dudley, J.3    Tamura, K.4
  • 20
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar, P., S. Henikoff, and P. C. Ng 2009. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols 4:1073-1082.
    • (2009) Nature Protocols , vol.4 , pp. 1073-1082
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 21
    • 84856088973 scopus 로고    scopus 로고
    • Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations
    • Kumar, S., J. T. Dudley, A. Filipski, and L. Liu 2011. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics 27:377-386.
    • (2011) Trends in Genetics , vol.27 , pp. 377-386
    • Kumar, S.1    Dudley, J.T.2    Filipski, A.3    Liu, L.4
  • 22
    • 84866111524 scopus 로고    scopus 로고
    • Evolutionary diagnosis method for variants in personal exomes
    • Kumar, S., M. Sanderford, V. E. Gray, J. P. Ye, and L. Liu 2012. Evolutionary diagnosis method for variants in personal exomes. Nature Methods 9:855-856.
    • (2012) Nature Methods , vol.9 , pp. 855-856
    • Kumar, S.1    Sanderford, M.2    Gray, V.E.3    Ye, J.P.4    Liu, L.5
  • 24
    • 80055117714 scopus 로고    scopus 로고
    • Hereditary hearing loss: from human mutation to mechanism
    • Lenz, D. R., and K. B. Avraham 2011. Hereditary hearing loss: from human mutation to mechanism. Hearing Research 281:3-10.
    • (2011) Hearing Research , vol.281 , pp. 3-10
    • Lenz, D.R.1    Avraham, K.B.2
  • 26
    • 74549195621 scopus 로고    scopus 로고
    • The hearing gene Prestin unites echolocating bats and whales
    • Li, Y., Z. Liu, P. Shi, and J. Zhang . 2010. The hearing gene Prestin unites echolocating bats and whales. Current Biology 20:R55-R56.
    • (2010) Current Biology , vol.20
    • Li, Y.1    Liu, Z.2    Shi, P.3    Zhang, J.4
  • 28
    • 78049285239 scopus 로고    scopus 로고
    • Cetaceans on a molecular fast track to ultrasonic hearing
    • Liu, Y., S. J. Rossiter, X. Han, J. A. Cotton, and S. Zhang . 2010b. Cetaceans on a molecular fast track to ultrasonic hearing. Current Biology 20:1834-1839.
    • (2010) Current Biology , vol.20 , pp. 1834-1839
    • Liu, Y.1    Rossiter, S.J.2    Han, X.3    Cotton, J.A.4    Zhang, S.5
  • 29
  • 30
    • 84862865765 scopus 로고    scopus 로고
    • The voltage-gated potassium channel subfamily KQT member 4 (KCNQ4) displays parallel evolution in echolocating bats
    • Liu, Y., N. Han, L. F. Franchini, H. Xu, F. Pisciottano, A. B. Elgoyhen, K. E. Rajan et al. 2012. The voltage-gated potassium channel subfamily KQT member 4 (KCNQ4) displays parallel evolution in echolocating bats. Molecular Biology and Evolution 29:1441-1450.
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 1441-1450
    • Liu, Y.1    Han, N.2    Franchini, L.F.3    Xu, H.4    Pisciottano, F.5    Elgoyhen, A.B.6    Rajan, K.E.7
  • 31
    • 0003903482 scopus 로고    scopus 로고
    • 2nd ed. Oxford: Oxford University Press, England, UK.
    • MacDonald, D. 2009. The Encyclopedia of Mammals, 2nd ed. Oxford: Oxford University Press, England, UK.
    • (2009) The Encyclopedia of Mammals
    • MacDonald, D.1
  • 32
    • 79960976768 scopus 로고    scopus 로고
    • UniProt Knowledgebase: a hub of integrated protein data
    • bar009
    • Magrane, M., and U. Consortium 2011. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011:bar009.
    • (2011) Database (Oxford) , vol.2011
    • Magrane, M.1    Consortium, U.2
  • 33
    • 80055070300 scopus 로고    scopus 로고
    • Impacts of the cretaceous terrestrial revolution and KPg extinction on mammal diversification
    • Meredith, R. W., J. E. Janecka, J. Gatesy, O. A. Ryder, C. A. Fisher, E. C. Teeling, A. Goodbla et al. 2011. Impacts of the cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334:521-524.
    • (2011) Science , vol.334 , pp. 521-524
    • Meredith, R.W.1    Janecka, J.E.2    Gatesy, J.3    Ryder, O.A.4    Fisher, C.A.5    Teeling, E.C.6    Goodbla, A.7
  • 35
    • 34948880109 scopus 로고    scopus 로고
    • Mutational spectrum of MYO15A: the large N-terminal extension of myosin XVA is required for hearing
    • Nal, N., Z. M. Ahmed, E. Erkal, O. M. Alper, G. Luleci, O. Dinc, A. M. Waryah et al. 2007. Mutational spectrum of MYO15A: the large N-terminal extension of myosin XVA is required for hearing. Human Mutation 28:1014-1019.
    • (2007) Human Mutation , vol.28 , pp. 1014-1019
    • Nal, N.1    Ahmed, Z.M.2    Erkal, E.3    Alper, O.M.4    Luleci, G.5    Dinc, O.6    Waryah, A.M.7
  • 37
    • 80053189298 scopus 로고    scopus 로고
    • Predicting the functional impact of protein mutations: application to cancer genomics
    • Reva, B., Y. Antipin, and C. Sander 2011. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Research 39:e118.
    • (2011) Nucleic Acids Research , vol.39
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 38
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen, S., and H. Skaletsky 2000. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132:365-386.
    • (2000) Methods in Molecular Biology , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 39
    • 84864063616 scopus 로고    scopus 로고
    • Parallel evolution of auditory genes for echolocation in bats and toothed whales
    • Shen, Y. Y., L. Liang, G. S. Li, R. W. Murphy, and Y. P. Zhang 2012. Parallel evolution of auditory genes for echolocation in bats and toothed whales. PLoS Genetics 8:e1002788.
    • (2012) PLoS Genetics , vol.8
    • Shen, Y.Y.1    Liang, L.2    Li, G.S.3    Murphy, R.W.4    Zhang, Y.P.5
  • 41
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 42
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML Web servers
    • Stamatakis, A., P. Hoover, and J. Rougemont 2008. A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology 57:758-771.
    • (2008) Systematic Biology , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 43
    • 0033983669 scopus 로고    scopus 로고
    • A take on the tectorial membrane
    • Steel, K. P. 2000. A take on the tectorial membrane. Nature Genetics 24:104.
    • (2000) Nature Genetics , vol.24 , pp. 104
    • Steel, K.P.1
  • 44
    • 0037230001 scopus 로고    scopus 로고
    • Pervasive adaptive evolution in mammalian fertilization proteins
    • Swanson, W. J., R. Nielsen, and Q. F. Yang 2003. Pervasive adaptive evolution in mammalian fertilization proteins. Molecular Biology and Evolution 20:18-20.
    • (2003) Molecular Biology and Evolution , vol.20 , pp. 18-20
    • Swanson, W.J.1    Nielsen, R.2    Yang, Q.F.3
  • 45
    • 12844251802 scopus 로고    scopus 로고
    • A molecular phylogeny for bats illuminates biogeography and the fossil record
    • Teeling, E. C., M. S. Springer, O. Madsen, P. Bates, S. J. O'Brien, and W. J. Murphy 2005. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307:580-584.
    • (2005) Science , vol.307 , pp. 580-584
    • Teeling, E.C.1    Springer, M.S.2    Madsen, O.3    Bates, P.4    O'Brien, S.J.5    Murphy, W.J.6
  • 46
    • 67649388061 scopus 로고    scopus 로고
    • Hear, hear: the convergent evolution of echolocation in bats?
    • Teeling, E. C. 2009. Hear, hear: the convergent evolution of echolocation in bats? Trends in Ecology s; Evolution 24:351-354.
    • (2009) Trends in Ecology & Evolution , vol.24 , pp. 351-354
    • Teeling, E.C.1
  • 47
    • 84866080200 scopus 로고    scopus 로고
    • Phylogenies, fossils and functional genes: The evolution of echolocation in bats
    • G. F. Gunnell, and N. B. Simmons, eds. -, Cambridge University Press, Cambridge.
    • Teeling, E. C., S. Dool, and M. S. Springer . 2012. Phylogenies, fossils and functional genes: The evolution of echolocation in bats. In G. F. Gunnell, and N. B. Simmons, eds. Evolutionary History of Bats: Fossils, Molecules, and Morphology, pp. 1-21, Cambridge University Press, Cambridge.
    • (2012) Evolutionary History of Bats: Fossils, Molecules, and Morphology , pp. 1-21
    • Teeling, E.C.1    Dool, S.2    Springer, M.S.3
  • 48
    • 77954161995 scopus 로고    scopus 로고
    • Genetics and pathological mechanisms of Usher syndrome
    • Yan, D., and X. Z. Liu 2010. Genetics and pathological mechanisms of Usher syndrome. Journal of Human Genetics 55:327-335.
    • (2010) Journal of Human Genetics , vol.55 , pp. 327-335
    • Yan, D.1    Liu, X.Z.2
  • 49
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang, Z. H. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution 15:568-573.
    • (1998) Molecular Biology and Evolution , vol.15 , pp. 568-573
    • Yang, Z.H.1
  • 50
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: phylogenetic analysis by maximum likelihood
    • Yang, Z. H. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24:1586-1591.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1586-1591
    • Yang, Z.H.1
  • 51
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical Bayes inference of amino acid sites under positive selection
    • Yang, Z. H., W. S. W. Wong, and R. Nielsen 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution 22:1107-1118.
    • (2005) Molecular Biology and Evolution , vol.22 , pp. 1107-1118
    • Yang, Z.H.1    Wong, W.S.W.2    Nielsen, R.3
  • 52
    • 27844439855 scopus 로고    scopus 로고
    • Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    • Zhang, J. Z., R. Nielsen, and Z. H. Yang 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.