메뉴 건너뛰기




Volumn 222, Issue 1, 2019, Pages 565-575

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)

Author keywords

bryophytes; compositional heterogeneity; land plants; life cycle; phylogenomics; substitutional saturation

Indexed keywords

BRYOPHYTE; CHLOROPLAST; GENOMICS; HETEROGENEITY; LIFE CYCLE; PHYLOGENETICS; PHYLOGENY; PROTEIN; VASCULAR PLANT;

EID: 85058051129     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.15587     Document Type: Article
Times cited : (94)

References (69)
  • 1
    • 47249122561 scopus 로고    scopus 로고
    • A site- and time-heterogeneous model of amino acid replacement
    • Blanquart S, Lartillot N. 2008. A site- and time-heterogeneous model of amino acid replacement. Molecular Biology and Evolution 25: 842–858.
    • (2008) Molecular Biology and Evolution , vol.25 , pp. 842-858
    • Blanquart, S.1    Lartillot, N.2
  • 2
    • 84993842127 scopus 로고
    • Are codon usage patterns in unicellular organisms determined by selection-mutation balance?
    • Bulmer M. 1988. Are codon usage patterns in unicellular organisms determined by selection-mutation balance? Journal of Evolutionary Biology 1: 15–26.
    • (1988) Journal of Evolutionary Biology , vol.1 , pp. 15-26
    • Bulmer, M.1
  • 4
    • 84863338313 scopus 로고    scopus 로고
    • Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set
    • Chang Y, Graham SW. 2011. Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set. American Journal of Botany 98: 839–849.
    • (2011) American Journal of Botany , vol.98 , pp. 839-849
    • Chang, Y.1    Graham, S.W.2
  • 5
    • 84994448773 scopus 로고    scopus 로고
    • Terrace aware data structure for phylogenomic inference from supermatrices
    • Chernomor O, von Haeseler A, Minh BQ. 2016. Terrace aware data structure for phylogenomic inference from supermatrices. Systematic Biology 65: 997–1008.
    • (2016) Systematic Biology , vol.65 , pp. 997-1008
    • Chernomor, O.1    von Haeseler, A.2    Minh, B.Q.3
  • 6
    • 84902994618 scopus 로고    scopus 로고
    • Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants
    • Civáň P, Foster PG, Embley MT, Seneca A, Cox CJ. 2014. Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants. Genome Biology and Evolution 6: 897–911.
    • (2014) Genome Biology and Evolution , vol.6 , pp. 897-911
    • Civáň, P.1    Foster, P.G.2    Embley, M.T.3    Seneca, A.4    Cox, C.J.5
  • 8
    • 85054541689 scopus 로고    scopus 로고
    • Land plant molecular phylogenetics: a review with comments on evaluating incongruence among phylogenies
    • in press
    • Cox CJ. 2018. Land plant molecular phylogenetics: a review with comments on evaluating incongruence among phylogenies. Critical Reviews in Plant Sciences, in press, doi: 10.1080/07352689.2018.1482443.
    • (2018) Critical Reviews in Plant Sciences
    • Cox, C.J.1
  • 10
    • 84894600564 scopus 로고    scopus 로고
    • Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions
    • Cox CJ, Li B, Foster PG, Embley TM, Civáň P. 2014. Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions. Systematic Biology 63: 272–279.
    • (2014) Systematic Biology , vol.63 , pp. 272-279
    • Cox, C.J.1    Li, B.2    Foster, P.G.3    Embley, T.M.4    Civáň, P.5
  • 11
  • 12
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff MO, ed., Washington DC, USA, National Biomedical Research Foundation
    • Dayhoff MO, Schwartz RM, Orcutt BC. 1978. A model of evolutionary change in proteins. In: Dayhoff MO, ed. Atlas of protein sequence and structure, vol. 5. Washington DC, USA: National Biomedical Research Foundation, 345–352.
    • (1978) Atlas of protein sequence and structure , vol.5 , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 13
    • 3242701529 scopus 로고    scopus 로고
    • Modeling compositional heterogeneity
    • Foster PG. 2004. Modeling compositional heterogeneity. Systematic Biology 53: 485–495.
    • (2004) Systematic Biology , vol.53 , pp. 485-495
    • Foster, P.G.1
  • 15
    • 77949936124 scopus 로고    scopus 로고
    • Plastid genome sequencing, comparative genomics, and phylogenomics: current status and prospects
    • Gao L, Su YJ, Wang T. 2010. Plastid genome sequencing, comparative genomics, and phylogenomics: current status and prospects. Journal of Systematics and Evolution 48: 77–93.
    • (2010) Journal of Systematics and Evolution , vol.48 , pp. 77-93
    • Gao, L.1    Su, Y.J.2    Wang, T.3
  • 16
    • 84948136797 scopus 로고    scopus 로고
    • The evolution of body form in bryophytes
    • Goffinet B, Buck WR. 2013. The evolution of body form in bryophytes. Annual Plant Reviews 45: 51–89.
    • (2013) Annual Plant Reviews , vol.45 , pp. 51-89
    • Goffinet, B.1    Buck, W.R.2
  • 17
    • 84927071428 scopus 로고    scopus 로고
    • Morphology, anatomy, and classification of the Bryophyta
    • Goffinet B, Shaw AJ, eds., Cambridge, UK, Cambridge University Press
    • Goffinet B, Buck WR, Shaw AJ. 2009. Morphology, anatomy, and classification of the Bryophyta. In: Goffinet B, Shaw AJ, eds. Bryophyte biology. Cambridge, UK: Cambridge University Press, 55–138.
    • (2009) Bryophyte biology , pp. 55-138
    • Goffinet, B.1    Buck, W.R.2    Shaw, A.J.3
  • 18
    • 0020491327 scopus 로고
    • Codon usage in bacteria: correlation with gene expressivity
    • Gouy M, Gautier C. 1982. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Research 10: 7055–7074.
    • (1982) Nucleic Acids Research , vol.10 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 19
    • 74549125386 scopus 로고    scopus 로고
    • SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
    • Gouy M, Guindon S, Gascuel O. 2009. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27: 221–224.
    • (2009) Molecular Biology and Evolution , vol.27 , pp. 221-224
    • Gouy, M.1    Guindon, S.2    Gascuel, O.3
  • 21
    • 51349148323 scopus 로고    scopus 로고
    • Homologous versus antithetic alternation of generations and the origin of sporophytes
    • Haig D. 2008. Homologous versus antithetic alternation of generations and the origin of sporophytes. Botanical Review 74: 395–418.
    • (2008) Botanical Review , vol.74 , pp. 395-418
    • Haig, D.1
  • 22
    • 70450237691 scopus 로고    scopus 로고
    • What is the danger of the anomaly zone for empirical phylogenetics?
    • Huang H, Knowles LL. 2009. What is the danger of the anomaly zone for empirical phylogenetics? Systematic Biology 58: 527–536.
    • (2009) Systematic Biology , vol.58 , pp. 527-536
    • Huang, H.1    Knowles, L.L.2
  • 23
    • 33745810231 scopus 로고    scopus 로고
    • Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
    • Inagaki Y, Roger AJ. 2006. Phylogenetic estimation under codon models can be biased by codon usage heterogeneity. Molecular Phylogenetics and Evolution 40: 428–434.
    • (2006) Molecular Phylogenetics and Evolution , vol.40 , pp. 428-434
    • Inagaki, Y.1    Roger, A.J.2
  • 24
    • 4644327551 scopus 로고    scopus 로고
    • Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study
    • Inagaki Y, Simpson AG, Dacks JB, Roger AJ. 2004. Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study. Systematic Biology 53: 582–593.
    • (2004) Systematic Biology , vol.53 , pp. 582-593
    • Inagaki, Y.1    Simpson, A.G.2    Dacks, J.B.3    Roger, A.J.4
  • 25
    • 33645850710 scopus 로고    scopus 로고
    • Phylogenomics: the beginning of incongruence?
    • Jeffroy O, Brinkmann H. 2006. Phylogenomics: the beginning of incongruence? TRENDS in Genetics 22: 225–231.
    • (2006) TRENDS in Genetics , vol.22 , pp. 225-231
    • Jeffroy, O.1    Brinkmann, H.2
  • 26
    • 0035861514 scopus 로고    scopus 로고
    • The closest living relatives of land plants
    • Karol KG. 2001. The closest living relatives of land plants. Science 294: 2351–2353.
    • (2001) Science , vol.294 , pp. 2351-2353
    • Karol, K.G.1
  • 28
    • 33645816587 scopus 로고    scopus 로고
    • Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
    • Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evolutionary Biology 6: 29.
    • (2006) BMC Evolutionary Biology , vol.6 , pp. 29
    • Keane, T.M.1    Creevey, C.J.2    Pentony, M.M.3    Naughton, T.J.4    Mclnerney, J.O.5
  • 30
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
    • Lartillot N, Lepage T, Blanquart S. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25: 2286–2288.
    • (2009) Bioinformatics , vol.25 , pp. 2286-2288
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 31
    • 84864598680 scopus 로고    scopus 로고
    • Origin of land plants revisited in the light of sequence contamination and missing data
    • Laurin-Lemay S, Brinkmann H, Philippe H. 2012. Origin of land plants revisited in the light of sequence contamination and missing data. Current Biology 22: R593–R594.
    • (2012) Current Biology , vol.22 , pp. R593-R594
    • Laurin-Lemay, S.1    Brinkmann, H.2    Philippe, H.3
  • 33
    • 84859178717 scopus 로고    scopus 로고
    • Major transitions in the evolution of early land plants: a bryological perspective
    • Ligrone R, Duckett JG, Renzaglia KS. 2012. Major transitions in the evolution of early land plants: a bryological perspective. Annals of Botany 109: 851–871.
    • (2012) Annals of Botany , vol.109 , pp. 851-871
    • Ligrone, R.1    Duckett, J.G.2    Renzaglia, K.S.3
  • 34
    • 84909618628 scopus 로고    scopus 로고
    • Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias
    • Liu Y, Cox CJ, Wang W, Goffinet B. 2014. Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. Systematic Biology 63: 862–878.
    • (2014) Systematic Biology , vol.63 , pp. 862-878
    • Liu, Y.1    Cox, C.J.2    Wang, W.3    Goffinet, B.4
  • 36
    • 84874918225 scopus 로고    scopus 로고
    • Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates
    • Magallón S, Hilu KW, Quandt D. 2013. Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates. American Journal of Botany 100: 556–573.
    • (2013) American Journal of Botany , vol.100 , pp. 556-573
    • Magallón, S.1    Hilu, K.W.2    Quandt, D.3
  • 38
    • 0033844505 scopus 로고    scopus 로고
    • The evolution of base composition and phylogenetic inference
    • Mooers AØ, Holmes EC. 2000. The evolution of base composition and phylogenetic inference. Trends in Ecology & Evolution 15: 365–369.
    • (2000) Trends in Ecology & Evolution , vol.15 , pp. 365-369
    • Mooers, A.Ø.1    Holmes, E.C.2
  • 41
    • 84922362345 scopus 로고    scopus 로고
    • IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
    • Nguyen LT, Schmidt HS, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32: 268–274.
    • (2015) Molecular Biology and Evolution , vol.32 , pp. 268-274
    • Nguyen, L.T.1    Schmidt, H.S.2    von Haeseler, A.3    Minh, B.Q.4
  • 42
    • 71249116114 scopus 로고    scopus 로고
    • The evolution of the land plant life cycle
    • Niklas KJ, Kutschera U. 2010. The evolution of the land plant life cycle. New Phytologist 185: 27–41.
    • (2010) New Phytologist , vol.185 , pp. 27-41
    • Niklas, K.J.1    Kutschera, U.2
  • 43
    • 0032784470 scopus 로고    scopus 로고
    • Molecular phylogenetic analysis among bryophytes and tracheophytes based on combined data of plasmid coded genes and the 18S rRNA gene
    • Nishiyama T, Kato M. 1999. Molecular phylogenetic analysis among bryophytes and tracheophytes based on combined data of plasmid coded genes and the 18S rRNA gene. Molecular Biology and Evolution 16: 1027–1036.
    • (1999) Molecular Biology and Evolution , vol.16 , pp. 1027-1036
    • Nishiyama, T.1    Kato, M.2
  • 49
    • 78650304100 scopus 로고    scopus 로고
    • Synonymous but not the same: the causes and consequences of codon bias
    • Plotkin JB, Kudla G. 2011. Synonymous but not the same: the causes and consequences of codon bias. Nature Reviews Genetics 12: 32–42.
    • (2011) Nature Reviews Genetics , vol.12 , pp. 32-42
    • Plotkin, J.B.1    Kudla, G.2
  • 54
    • 84871849373 scopus 로고    scopus 로고
    • Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study
    • Rota-Stabelli O, Lartillot N, Philippe H, Pisani D. 2012. Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study. Systematic Biology 62: 121–133.
    • (2012) Systematic Biology , vol.62 , pp. 121-133
    • Rota-Stabelli, O.1    Lartillot, N.2    Philippe, H.3    Pisani, D.4
  • 56
    • 85058050906 scopus 로고
    • Bryophyta
    • von Zittel KA, eds., München & Leipzig, Germany, R. Oldenbourg
    • Schimper WP. 1879. Bryophyta. In: von Zittel KA, eds. Handbuch der palaeontologie, vol. 2. München & Leipzig, Germany: R. Oldenbourg.
    • (1879) Handbuch der palaeontologie, vol. 2
    • Schimper, W.P.1
  • 58
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313.
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 60
    • 0001174620 scopus 로고
    • Did multicellular plants invade the land?
    • Stebbins GL, Hill GJC. 1980. Did multicellular plants invade the land? American Naturalist 115: 342–353.
    • (1980) American Naturalist , vol.115 , pp. 342-353
    • Stebbins, G.L.1    Hill, G.J.C.2
  • 61
    • 11144317388 scopus 로고    scopus 로고
    • Adaptive basis of codon usage in the haploid moss Physcomitrella patens
    • Stenøien HK. 2005. Adaptive basis of codon usage in the haploid moss Physcomitrella patens. Heredity 94: 87.
    • (2005) Heredity , vol.94 , pp. 87
    • Stenøien, H.K.1
  • 62
    • 35748943561 scopus 로고    scopus 로고
    • On reduced amino acid alphabets for phylogenetic inference
    • Susko E, Roger AJ. 2007. On reduced amino acid alphabets for phylogenetic inference. Molecular Biology and Evolution 24: 2139–2150.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 2139-2150
    • Susko, E.1    Roger, A.J.2
  • 63
    • 84855858792 scopus 로고    scopus 로고
    • Broad phylogenomic sampling and the sister lineage of land plants
    • Timme RE, Bachvaroff TR, Delwiche CF. 2012. Broad phylogenomic sampling and the sister lineage of land plants. PLoS ONE 7: e29696.
    • (2012) PLoS ONE , vol.7
    • Timme, R.E.1    Bachvaroff, T.R.2    Delwiche, C.F.3
  • 64
    • 0014669335 scopus 로고
    • New concepts of kingdoms of organisms
    • Whittaker RH. 1969. New concepts of kingdoms of organisms. Science 163: 150–160.
    • (1969) Science , vol.163 , pp. 150-160
    • Whittaker, R.H.1
  • 67
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: phylogenetic analysis by maximum likelihood
    • Yang Z. 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.1
  • 68
    • 0031960185 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous rate variation in nuclear genes of mammals
    • Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution 46: 409–418.
    • (1998) Journal of Molecular Evolution , vol.46 , pp. 409-418
    • Yang, Z.1    Nielsen, R.2
  • 69
    • 70350344794 scopus 로고    scopus 로고
    • Analysis of synonymous codon usage patterns in different plant mitochondrial genomes
    • Zhou M, Li X. 2009. Analysis of synonymous codon usage patterns in different plant mitochondrial genomes. Molecular Biology Reports 36: 2039–2046.
    • (2009) Molecular Biology Reports , vol.36 , pp. 2039-2046
    • Zhou, M.1    Li, X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.