메뉴 건너뛰기




Volumn 95, Issue 9, 2008, Pages 1166-1176

Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): Dramatic intron size variation and footprint of ancestral recombination

Author keywords

Ancestral recombination; Intron size variation; MITE; PHOT gene duplicates; Species level phylogenetics; Verbena complex

Indexed keywords

CHLOROPLAST; DICOTYLEDON; DNA; EVOLUTION; GENE; HYBRIDIZATION; PHYLOGENETICS; PHYLOGENY;

EID: 51349110642     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.0800133     Document Type: Article
Times cited : (25)

References (42)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • AKAIKE, H. 1974. A new look at the statistical model identification. IEEE Transactions of Automatic Control 19:716-723.
    • (1974) IEEE Transactions of Automatic Control , vol.19 , pp. 716-723
    • AKAIKE, H.1
  • 4
    • 51349122241 scopus 로고    scopus 로고
    • BOTTA, S. M. 1989. Studies in the South American genus Junellia (Verbenaceae, Verbenoideae). I. Delimitation and infrageneric divisions. Darwiniana (San Isidro) 29:371-396.
    • BOTTA, S. M. 1989. Studies in the South American genus Junellia (Verbenaceae, Verbenoideae). I. Delimitation and infrageneric divisions. Darwiniana (San Isidro) 29:371-396.
  • 6
    • 34249700809 scopus 로고    scopus 로고
    • Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from Melanoplus grasshoppers
    • CARSTENS, B. C., AND L. L. KNOWLES. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from Melanoplus grasshoppers. Systematic Biology 56:400-411.
    • (2007) Systematic Biology , vol.56 , pp. 400-411
    • CARSTENS, B.C.1    KNOWLES, L.L.2
  • 8
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • DEGNAN, J. H., AND N. A. ROSENBERG. 2006. Discordance of species trees with their most likely gene trees. PLOS Genetics 2:762-768.
    • (2006) PLOS Genetics , vol.2 , pp. 762-768
    • DEGNAN, J.H.1    ROSENBERG, N.A.2
  • 10
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • DELSUC, F., H. BRINKMANN, AND H. PHILIPPE. 2005. Phylogenomics and the reconstruction of the tree of life. Nature Reviews. Genetics 6:361-375.
    • (2005) Nature Reviews. Genetics , vol.6 , pp. 361-375
    • DELSUC, F.1    BRINKMANN, H.2    PHILIPPE, H.3
  • 13
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies-An approach using the bootstrap
    • FELSENSTEIN, J. 1985. Confidence limits on phylogenies-An approach using the bootstrap. Evolution 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • FELSENSTEIN, J.1
  • 14
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • FITCH, W. M. 1970. Distinguishing homologous from analogous proteins. Systematic Zoology 19:99-113.
    • (1970) Systematic Zoology , vol.19 , pp. 99-113
    • FITCH, W.M.1
  • 15
    • 0035984048 scopus 로고    scopus 로고
    • Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants
    • FULTON, T. M., R. VAN DER HOEVEN, N. T. EANNETTA, AND S. D. Tanksley. 2002. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. The Plant Cell 14:1457-1467.
    • (2002) The Plant Cell , vol.14 , pp. 1457-1467
    • FULTON, T.M.1    VAN DER HOEVEN, R.2    EANNETTA, N.T.3    Tanksley, S.D.4
  • 16
    • 0033753825 scopus 로고    scopus 로고
    • Sister-Scanning: A Monte Carlo procedure for assessing signals in recombinant sequences
    • GIBBS, M. J., J. S. ARMSTRONG, AND A. J. GIBBS. 2000. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics (Oxford, England) 16:573-582.
    • (2000) Bioinformatics (Oxford, England) , vol.16 , pp. 573-582
    • GIBBS, M.J.1    ARMSTRONG, J.S.2    GIBBS, A.J.3
  • 17
    • 33749389724 scopus 로고    scopus 로고
    • Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
    • HAWKINS, J. S., H. KIM, J. D. NASON, R. A. WING, AND J. F. WENDEL. 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Research 16:1252-1261.
    • (2006) Genome Research , vol.16 , pp. 1252-1261
    • HAWKINS, J.S.1    KIM, H.2    NASON, J.D.3    WING, R.A.4    WENDEL, J.F.5
  • 18
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • D. Futuyma and J. Antonovics [eds, Oxford University Press, Oxford, UK
    • HUDSON, R. R. 1990. Gene genealogies and the coalescent process. In D. Futuyma and J. Antonovics [eds.], Oxford surveys in evolutionary biology, vol. 7, 1-44. Oxford University Press, Oxford, UK.
    • (1990) Oxford surveys in evolutionary biology , vol.7 , pp. 1-44
    • HUDSON, R.R.1
  • 19
    • 33646594138 scopus 로고    scopus 로고
    • From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Philosophical Transactions of the Royal Society, B
    • HUGHES, C. E., R. J. EASTWOOD, AND C. D. BAILEY. 2006. From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Philosophical Transactions of the Royal Society, B, Biological Sciences 361:211-225.
    • (2006) Biological Sciences , vol.361 , pp. 211-225
    • HUGHES, C.E.1    EASTWOOD, R.J.2    BAILEY, C.D.3
  • 20
    • 0035912211 scopus 로고    scopus 로고
    • Phototropin-related NPL1 controls chloroplast relocation induced by blue light
    • JARILLO, J. A., H. GABRYS, J. CAPEL, J. M. ALONSO, J. R. ECKER, AND A. R. Cashmore. 2001. Phototropin-related NPL1 controls chloroplast relocation induced by blue light. Nature 410:952-954.
    • (2001) Nature , vol.410 , pp. 952-954
    • JARILLO, J.A.1    GABRYS, H.2    CAPEL, J.3    ALONSO, J.M.4    ECKER, J.R.5    Cashmore, A.R.6
  • 21
    • 0035896393 scopus 로고    scopus 로고
    • Arabidopsis NPL1: A phototropin homolog controlling the chloroplast high-light avoidance response
    • KAGAWA, T., T. SAKAI, N. SUETSUGU, K. OIKAWA, S. ISHIGURO, T. KATO, S. TABATA, ET AL. 2001. Arabidopsis NPL1: A phototropin homolog controlling the chloroplast high-light avoidance response. Science 291:2138-2141.
    • (2001) Science , vol.291 , pp. 2138-2141
    • KAGAWA, T.1    SAKAI, T.2    SUETSUGU, N.3    OIKAWA, K.4    ISHIGURO, S.5    KATO, T.6    TABATA, S.7    ET AL.8
  • 22
    • 0035818967 scopus 로고    scopus 로고
    • phot1 and phot2 mediate blue light regulation of stomatal opening
    • KINOSHITA, T., M. DOI, N. SUETSUGU, T. KAGAWA, M. WADA, AND K. SHIMAZAKI. 2001. phot1 and phot2 mediate blue light regulation of stomatal opening. Nature 414:656-660.
    • (2001) Nature , vol.414 , pp. 656-660
    • KINOSHITA, T.1    DOI, M.2    SUETSUGU, N.3    KAGAWA, T.4    WADA, M.5    SHIMAZAKI, K.6
  • 23
    • 33847302458 scopus 로고    scopus 로고
    • Inconsistency of phylogenetic estimates from concatenated data under coalescence
    • KUBATKO, L. S., AND J. H. DEGNAN. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56:17-24.
    • (2007) Systematic Biology , vol.56 , pp. 17-24
    • KUBATKO, L.S.1    DEGNAN, J.H.2
  • 24
    • 34548575126 scopus 로고    scopus 로고
    • Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
    • LIU, L., AND D. K. PEARL. 2007. Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 56:504-514.
    • (2007) Systematic Biology , vol.56 , pp. 504-514
    • LIU, L.1    PEARL, D.K.2
  • 25
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • MADDISON, W. P. 1997. Gene trees in species trees. Systematic Biology 46:523-536.
    • (1997) Systematic Biology , vol.46 , pp. 523-536
    • MADDISON, W.P.1
  • 26
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • MADDISON, W. P., AND L. L. KNOWLES. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55:21-30.
    • (2006) Systematic Biology , vol.55 , pp. 21-30
    • MADDISON, W.P.1    KNOWLES, L.L.2
  • 27
    • 13444251528 scopus 로고    scopus 로고
    • RDP2: Recombination detection and analysis from sequence alignments
    • MARTIN, D. P., C. WILLIAMSON, AND D. POSADA. 2005. RDP2: Recombination detection and analysis from sequence alignments. Bioinformatics (Oxford, England) 21:260-262.
    • (2005) Bioinformatics (Oxford, England) , vol.21 , pp. 260-262
    • MARTIN, D.P.1    WILLIAMSON, C.2    POSADA, D.3
  • 30
    • 0003626439 scopus 로고    scopus 로고
    • Website, University of Oxford, Oxford, UK
    • RAMBAUT, A. 1996. Se-Al: Sequence Alignment Editor. Website http://evolve.zoo.ox.ac.uk/. University of Oxford, Oxford, UK.
    • (1996) Se-Al: Sequence Alignment Editor
    • RAMBAUT, A.1
  • 31
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • RONQUIST, F., AND J. P. HUELSENBECK. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (Oxford, England) 19:1572-1574.
    • (2003) Bioinformatics (Oxford, England) , vol.19 , pp. 1572-1574
    • RONQUIST, F.1    HUELSENBECK, J.P.2
  • 32
    • 0942283320 scopus 로고    scopus 로고
    • The genera of Verbenaceae in the southeastern United States
    • SANDERS, R. W. 2001. The genera of Verbenaceae in the southeastern United States. Harvard Papers in Botany 5:303-358.
    • (2001) Harvard Papers in Botany , vol.5 , pp. 303-358
    • SANDERS, R.W.1
  • 33
    • 0032413101 scopus 로고    scopus 로고
    • Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons
    • SANMIGUEL, P., AND J. L. BENNETZEN. 1998. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annals of Botany 82:37-44.
    • (1998) Annals of Botany , vol.82 , pp. 37-44
    • SANMIGUEL, P.1    BENNETZEN, J.L.2
  • 34
  • 35
    • 34250767339 scopus 로고    scopus 로고
    • Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III
    • SHAW, J., E. B. LICKEY, E. E. SCHILLING, AND R. L. SMALL. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. American Journal of Botany 94:275-288.
    • (2007) American Journal of Botany , vol.94 , pp. 275-288
    • SHAW, J.1    LICKEY, E.B.2    SCHILLING, E.E.3    SMALL, R.L.4
  • 37
    • 0032229478 scopus 로고    scopus 로고
    • The tortoise and the hare: Choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group
    • SMALL, R. L., J. A. RYBURN, R. C. CRONN, T. SEELANAN, AND J. F. WENDEL. 1998. The tortoise and the hare: Choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85:1301-1315.
    • (1998) American Journal of Botany , vol.85 , pp. 1301-1315
    • SMALL, R.L.1    RYBURN, J.A.2    CRONN, R.C.3    SEELANAN, T.4    WENDEL, J.F.5
  • 38
    • 0026708873 scopus 로고
    • Analyzing the mosaic structure of genes
    • SMITH, J. M. 1992. Analyzing the mosaic structure of genes. Journal of Molecular Evolution 34:126-129.
    • (1992) Journal of Molecular Evolution , vol.34 , pp. 126-129
    • SMITH, J.M.1
  • 40
    • 23844543047 scopus 로고    scopus 로고
    • LTR retrotransposons and flowering plant genome size: Emergence of the increase/decrease model
    • VITTE, C., AND O. PANAUD. 2005. LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenetic and Genome Research 110:91-107.
    • (2005) Cytogenetic and Genome Research , vol.110 , pp. 91-107
    • VITTE, C.1    PANAUD, O.2
  • 41
    • 33751344142 scopus 로고    scopus 로고
    • Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the euasterid plant clade
    • WU, F. N., L. A. MUELLER, D. CROUZILLAT, V. PÉTIARD, AND S. D. TANKSLEY. 2006. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the euasterid plant clade. Genetics 174:1407-1420.
    • (2006) Genetics , vol.174 , pp. 1407-1420
    • WU, F.N.1    MUELLER, L.A.2    CROUZILLAT, D.3    PÉTIARD, V.4    TANKSLEY, S.D.5
  • 42
    • 44949253887 scopus 로고    scopus 로고
    • A species-level phylogenetic study of the Verbena complex (Verbenaceae) indicates two independent intergeneric chloroplast transfers
    • YUAN, Y. W., AND R. G. OLMSTEAD. 2008. A species-level phylogenetic study of the Verbena complex (Verbenaceae) indicates two independent intergeneric chloroplast transfers. Molecular Phylogenetics and Evolution 48:23-33.
    • (2008) Molecular Phylogenetics and Evolution , vol.48 , pp. 23-33
    • YUAN, Y.W.1    OLMSTEAD, R.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.