메뉴 건너뛰기




Volumn 30, Issue 3, 2004, Pages 733-742

An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae)

Author keywords

[No Author keywords available]

Indexed keywords

HORDEUM; POACEAE; SECALE; SECALE CEREALE; SECALE STRICTUM; SECALE SYLVESTRE;

EID: 1342268775     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00206-9     Document Type: Article
Times cited : (25)

References (51)
  • 1
    • 0033302755 scopus 로고    scopus 로고
    • Phylogenetic relationships in Lupinus (Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA
    • Aïnouche, A.-K., Bayer, R.J., 1999. Phylogenetic relationships in Lupinus (Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA. Am. J. Bot. 86, 590-607.
    • (1999) Am. J. Bot. , vol.86 , pp. 590-607
    • Aïnouche, A.-K.1    Bayer, R.J.2
  • 2
    • 0026778673 scopus 로고
    • Extensive variation in evolutionary rate of rbcL gene sequences among seed plants
    • Bousquet, J., Strauss, S.H., Doerksen, A.H., Price, R.A., 1992. Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc. Natl. Acad. Sci. USA 89, 7844-7848.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 7844-7848
    • Bousquet, J.1    Strauss, S.H.2    Doerksen, A.H.3    Price, R.A.4
  • 3
    • 0344725546 scopus 로고
    • Numerical chemotaxonomy in the genus Secale
    • Dedio, W., Kaltsikes, J.P., Larter, E.N., 1969. Numerical chemotaxonomy in the genus Secale. Can. J. Bot. 47, 1175-1180.
    • (1969) Can. J. Bot. , vol.47 , pp. 1175-1180
    • Dedio, W.1    Kaltsikes, J.P.2    Larter, E.N.3
  • 4
    • 0343317584 scopus 로고
    • Secale rhodopaeum Delipavlov - A new species of rye from the Rhodope Mountains
    • Delipavlov, D., 1962. Secale rhodopaeum Delipavlov - a new species of rye from the Rhodope Mountains. Dokl. Bulg. Akad. Nauk. 15, 407-411.
    • (1962) Dokl. Bulg. Akad. Nauk. , vol.15 , pp. 407-411
    • Delipavlov, D.1
  • 7
    • 0002594984 scopus 로고
    • A rapid DNA isolation procedure for small quantities of fresh leaf tissue
    • Doyle, J.J., Doyle, J.F., 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15.
    • (1987) Phytochem. Bull. , vol.19 , pp. 11-15
    • Doyle, J.J.1    Doyle, J.F.2
  • 9
    • 0030765855 scopus 로고    scopus 로고
    • Morphometric analyses of Secale L. (Triticeae, Poaceae)
    • Frederiksen, S., Petersen, G., 1997. Morphometric analyses of Secale L. (Triticeae, Poaceae). Nord. J. Bot. 17, 185-198.
    • (1997) Nord. J. Bot. , vol.17 , pp. 185-198
    • Frederiksen, S.1    Petersen, G.2
  • 10
    • 0031732203 scopus 로고    scopus 로고
    • A taxonomic revision of the genus Secale (Triticeae; Poaceae)
    • Frederiksen, S., Petersen, G., 1998. A taxonomic revision of the genus Secale (Triticeae; Poaceae). Nord. J. Bot. 18, 399-420.
    • (1998) Nord. J. Bot. , vol.18 , pp. 399-420
    • Frederiksen, S.1    Petersen, G.2
  • 11
    • 19244375037 scopus 로고
    • Nucleotide sequence of a complete barley alcohol dehydrogenase 1 cDNA
    • Good, A.G., Pelcher, L.E., Crosby, W.L., 1988. Nucleotide sequence of a complete barley alcohol dehydrogenase 1 cDNA. Nucleic Acids Res. 16, 7182.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 7182
    • Good, A.G.1    Pelcher, L.E.2    Crosby, W.L.3
  • 12
    • 0029278663 scopus 로고
    • Phylogenetic relationships of the monogenomic species of the wheat tribe Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences
    • Hsiao, C., Chatterton, N.J., Asay, K.H., Jensen, K.B., 1995. Phylogenetic relationships of the monogenomic species of the wheat tribe Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences. Genome 38, 211-223.
    • (1995) Genome , vol.38 , pp. 211-223
    • Hsiao, C.1    Chatterton, N.J.2    Asay, K.H.3    Jensen, K.B.4
  • 13
    • 1342345756 scopus 로고
    • Chromosomal location of alcohol dehydrogenase gene(s) in rye, using wheat-rye addition lines
    • Irani, B.N., Bhatia, C.R., 1972. Chromosomal location of alcohol dehydrogenase gene(s) in rye, using wheat-rye addition lines. Genetica 43, 195-200.
    • (1972) Genetica , vol.43 , pp. 195-200
    • Irani, B.N.1    Bhatia, C.R.2
  • 14
    • 0345155869 scopus 로고
    • Evolutionary variation of enzymes and phylogenetic relationships in the genus Secale L.
    • Jaaska, V., 1975. Evolutionary variation of enzymes and phylogenetic relationships in the genus Secale L.. Izv. Akad. Nauk Estonsk SSR, ser. Biol 24, 179-198.
    • (1975) Izv. Akad. Nauk Estonsk SSR, Ser. Biol. , vol.24 , pp. 179-198
    • Jaaska, V.1
  • 15
    • 0020352190 scopus 로고
    • The structure, amount and chromosomal localization of defined repeated DNA sequences in species of the genus Secale
    • Jones, J.D.G., Flavell, R.B., 1982. The structure, amount and chromosomal localization of defined repeated DNA sequences in species of the genus Secale. Chromosoma 86, 613-641.
    • (1982) Chromosoma , vol.86 , pp. 613-641
    • Jones, J.D.G.1    Flavell, R.B.2
  • 16
    • 0028946212 scopus 로고
    • Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives
    • Kellogg, E.A., Appels, R., 1995. Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Genetics 140, 325-343.
    • (1995) Genetics , vol.140 , pp. 325-343
    • Kellogg, E.A.1    Appels, R.2
  • 17
    • 0030425120 scopus 로고    scopus 로고
    • When genes tell different stories: The diploid genera of Triticeae (Gramineae)
    • Kellogg, E.A., Appels, R., Mason-Gamer, R.J., 1996. When genes tell different stories: the diploid genera of Triticeae (Gramineae). Syst. Bot. 21, 321-347.
    • (1996) Syst. Bot. , vol.21 , pp. 321-347
    • Kellogg, E.A.1    Appels, R.2    Mason-Gamer, R.J.3
  • 18
    • 0001079372 scopus 로고
    • Cytogenetic and evolutionary studies in Secale. II. Interrelationships of wild species
    • Khush, G.S., 1962. Cytogenetic and evolutionary studies in Secale. II. Interrelationships of wild species. Evolution, 484-496.
    • (1962) Evolution , pp. 484-496
    • Khush, G.S.1
  • 19
    • 12044251313 scopus 로고
    • Missing data versus missing characters in phylogenetic analysis
    • Maddison, W.P., 1993. Missing data versus missing characters in phylogenetic analysis. Syst. Biol. 42, 576-581.
    • (1993) Syst. Biol. , vol.42 , pp. 576-581
    • Maddison, W.P.1
  • 20
    • 0001962774 scopus 로고    scopus 로고
    • Chloroplast DNA analysis of the monogenomic Triticeae: Phylogenetic implications and genome-specific markers
    • Jauhar, P.P. (Ed.), CRC Press, Boca Raton
    • Mason-Gamer, R.J., Kellogg, E.A., 1996. Chloroplast DNA analysis of the monogenomic Triticeae: phylogenetic implications and genome-specific markers. In: Jauhar, P.P. (Ed.), Methods of Genome Analysis in Plants. CRC Press, Boca Raton, pp. 301-325.
    • (1996) Methods of Genome Analysis in Plants , pp. 301-325
    • Mason-Gamer, R.J.1    Kellogg, E.A.2
  • 21
    • 0031796608 scopus 로고    scopus 로고
    • Granule-bound starch synthase: Structure, function, and phylogenetic utility
    • Mason-Gamer, R.J., Weil, C.F., Kellogg, E.A., 1998. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol. Biol. Evol. 15, 1658-1673.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1658-1673
    • Mason-Gamer, R.J.1    Weil, C.F.2    Kellogg, E.A.3
  • 22
    • 0242529224 scopus 로고    scopus 로고
    • Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets
    • Mason-Gamer, R.J., Orme, N.L., Anderson, C.M., 2002. Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets. Genome 45, 991-1002.
    • (2002) Genome , vol.45 , pp. 991-1002
    • Mason-Gamer, R.J.1    Orme, N.L.2    Anderson, C.M.3
  • 23
    • 0024688959 scopus 로고
    • Molecular analysis of an alcohol dehydrogenase (Adh) gene from chromosome 1 of wheat
    • Mitchell, L.E., Dennis, E.S., Peacock, W.J., 1989. Molecular analysis of an alcohol dehydrogenase (Adh) gene from chromosome 1 of wheat. Genome 32, 349-358.
    • (1989) Genome , vol.32 , pp. 349-358
    • Mitchell, L.E.1    Dennis, E.S.2    Peacock, W.J.3
  • 24
    • 84996034859 scopus 로고
    • Studies on the origin of crop species by restriction endonuclease analysis of organellar DNA. III. Chloroplast DNA variation and interspecific relationships in the genus Secale
    • Murai, K., Naiyu, X., Tsunewaki, K., 1989. Studies on the origin of crop species by restriction endonuclease analysis of organellar DNA. III. Chloroplast DNA variation and interspecific relationships in the genus Secale. Jpn. J. Genet. 64, 35-47.
    • (1989) Jpn. J. Genet. , vol.64 , pp. 35-47
    • Murai, K.1    Naiyu, X.2    Tsunewaki, K.3
  • 25
    • 0032801377 scopus 로고    scopus 로고
    • Parsimony analysis of total evidence from extinct and extant taxa and the Cetaceaen-Artiodactyl question (Mammalia, Ungulata)
    • O'Leary, M.A., 1999. Parsimony analysis of total evidence from extinct and extant taxa and the Cetaceaen-Artiodactyl question (Mammalia, Ungulata). Cladistics 15, 315-330.
    • (1999) Cladistics , vol.15 , pp. 315-330
    • O'Leary, M.A.1
  • 26
    • 0027130805 scopus 로고
    • Chloroplast DNA variation in the genus Secale (Poaceae)
    • Petersen, G., Doebley, J.F., 1993. Chloroplast DNA variation in the genus Secale (Poaceae). Plant Syst. Evol. 187, 115-125.
    • (1993) Plant Syst. Evol. , vol.187 , pp. 115-125
    • Petersen, G.1    Doebley, J.F.2
  • 27
    • 0031112130 scopus 로고    scopus 로고
    • Phylogenetic analysis of the Triticeae (Poaceae) based on rpo a sequence data
    • Petersen, G., Seberg, O., 1997. Phylogenetic analysis of the Triticeae (Poaceae) based on rpo A sequence data. Mol. Phylogenet. Evol. 7, 217-230.
    • (1997) Mol. Phylogenet. Evol. , vol.7 , pp. 217-230
    • Petersen, G.1    Seberg, O.2
  • 28
    • 0031864449 scopus 로고    scopus 로고
    • Molecular characterization and sequence polymorphism of the alcohol dehydrogenase 1 gene in Hordeum vulgare L.
    • Petersen, G., Seberg, O., 1998. Molecular characterization and sequence polymorphism of the alcohol dehydrogenase 1 gene in Hordeum vulgare L. Euphytica 102, 57-63.
    • (1998) Euphytica , vol.102 , pp. 57-63
    • Petersen, G.1    Seberg, O.2
  • 29
    • 0033736102 scopus 로고    scopus 로고
    • Phylogenetic evidence for excision of Stowaway miniature inverted-repeat transposable elements in Triticeae (Poaceae)
    • Petersen, G., Seberg, O., 2000. Phylogenetic evidence for excision of Stowaway miniature inverted-repeat transposable elements in Triticeae (Poaceae). Mol. Biol. Evol. 17, 1589-1596.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1589-1596
    • Petersen, G.1    Seberg, O.2
  • 30
    • 0036355297 scopus 로고    scopus 로고
    • Molecular evolution and phylogenetic application of DMCI
    • Petersen, G., Seberg, O., 2002. Molecular evolution and phylogenetic application of DMCI. Mol. Phylogenet. Evol. 22, 43-50.
    • (2002) Mol. Phylogenet. Evol. , vol.22 , pp. 43-50
    • Petersen, G.1    Seberg, O.2
  • 31
    • 0037035485 scopus 로고    scopus 로고
    • The phylogenetic and taxonomic position of Lilaeopsis (Apiaceae), with notes on the applicability of ITS sequence data for phylogenetic reconstruction
    • Petersen, G., Seberg, O., Larsen, S., 2002. The phylogenetic and taxonomic position of Lilaeopsis (Apiaceae), with notes on the applicability of ITS sequence data for phylogenetic reconstruction. Aust. Syst. Bot. 15, 181-191.
    • (2002) Aust. Syst. Bot. , vol.15 , pp. 181-191
    • Petersen, G.1    Seberg, O.2    Larsen, S.3
  • 32
    • 0033775967 scopus 로고    scopus 로고
    • Multiple sequence alignment in phylogenetic analysis
    • Phillips, A., Janies, D., Wheeler, W., 2000. Multiple sequence alignment in phylogenetic analysis. Mol. Phylogenet. Evol. 16, 317-330.
    • (2000) Mol. Phylogenet. Evol. , vol.16 , pp. 317-330
    • Phillips, A.1    Janies, D.2    Wheeler, W.3
  • 33
    • 0029200698 scopus 로고
    • PCR derived molecular markers and phylogenetic relationships in the genus Secale
    • Pozo, J.C. del, Figueiras, A.M., Benito, C., Peña, A. de la., 1995. PCR derived molecular markers and phylogenetic relationships in the genus Secale. Biol. Plantarum 37, 481-489.
    • (1995) Biol. Plantarum , vol.37 , pp. 481-489
    • Del Pozo, J.C.1    Figueiras, A.M.2    Benito, C.3    De La Peña, A.4
  • 34
    • 33751431237 scopus 로고
    • Ribosomal DNA spacer-length variation in Secale spp. (Poaceae)
    • Reddy, P., Appels, R., Baum, B.R., 1990. Ribosomal DNA spacer-length variation in Secale spp. (Poaceae). Plant Syst. Evol. 171, 205-220.
    • (1990) Plant Syst. Evol. , vol.171 , pp. 205-220
    • Reddy, P.1    Appels, R.2    Baum, B.R.3
  • 36
    • 0028239209 scopus 로고
    • Chloroplast and nuclear gene sequences indicate Late Pennsylvanian time for the last common ancestor of extant seed plants
    • Savard, L., Li, P., Strauss, S.H., Chase, M.W., Michaud, M., Bousquet, J., 1994. Chloroplast and nuclear gene sequences indicate Late Pennsylvanian time for the last common ancestor of extant seed plants. Proc. Natl. Acad. Sci. USA 91, 5163-5167.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 5163-5167
    • Savard, L.1    Li, P.2    Strauss, S.H.3    Chase, M.W.4    Michaud, M.5    Bousquet, J.6
  • 37
    • 0036822101 scopus 로고    scopus 로고
    • Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis
    • Schulmeister, S., Wheeler, W.C., Carpenter, J.M., 2002. Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis. Cladistics 18, 455-484.
    • (2002) Cladistics , vol.18 , pp. 455-484
    • Schulmeister, S.1    Wheeler, W.C.2    Carpenter, J.M.3
  • 38
    • 0034954590 scopus 로고    scopus 로고
    • A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology
    • Seberg, O., Frederiksen, S., 2001. A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology. Bot. J. Linn. Soc. 136, 75-97.
    • (2001) Bot. J. Linn. Soc. , vol.136 , pp. 75-97
    • Seberg, O.1    Frederiksen, S.2
  • 40
  • 41
    • 0034350427 scopus 로고    scopus 로고
    • Gaps as characters in sequence-based phylogenetic analyses
    • Simmons, M.P., Ochoterena, H., 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49, 369-381.
    • (2000) Syst. Biol. , vol.49 , pp. 369-381
    • Simmons, M.P.1    Ochoterena, H.2
  • 43
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thomson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thomson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 44
    • 0001628933 scopus 로고
    • Molecular analysis of the alcohol dehydrogenase gene family of barley
    • Trick, M., Dennis, E.S., Edwards, K.J.R., Peacock, W.J., 1988. Molecular analysis of the alcohol dehydrogenase gene family of barley. Plant Mol. Biol. 11, 147-160.
    • (1988) Plant Mol. Biol. , vol.11 , pp. 147-160
    • Trick, M.1    Dennis, E.S.2    Edwards, K.J.R.3    Peacock, W.J.4
  • 45
    • 0001924490 scopus 로고
    • Phylogenetic relationships in Secale (Poaceae): An isozymatic study
    • Vences, F.J., Vaquero, F., Pérez de la Vega, M., 1987. Phylogenetic relationships in Secale (Poaceae): an isozymatic study. Plant Syst. Evol. 157, 33-47.
    • (1987) Plant Syst. Evol. , vol.157 , pp. 33-47
    • Vences, F.J.1    Vaquero, F.2    Pérez De La Vega, M.3
  • 46
    • 0028878618 scopus 로고
    • Sequence alignment, parameter sensitivity and the phylogenetic analysis of molecular data
    • Wheeler, W.C., 1995. Sequence alignment, parameter sensitivity and the phylogenetic analysis of molecular data. Syst. Biol. 44, 321-331.
    • (1995) Syst. Biol. , vol.44 , pp. 321-331
    • Wheeler, W.C.1
  • 47
    • 0001857390 scopus 로고    scopus 로고
    • Optimization alignment: The end of multiple sequence alignment in phylogenetics
    • Wheeler, W.C., 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics. Cladistics 12, 1-9.
    • (1996) Cladistics , vol.12 , pp. 1-9
    • Wheeler, W.C.1
  • 48
    • 0000910719 scopus 로고    scopus 로고
    • The phylogeny of the extant chelicerate orders
    • Wheeler, W.C., Hayashi, C.Y., 1998. The phylogeny of the extant chelicerate orders. Cladistics 14, 173-192.
    • (1998) Cladistics , vol.14 , pp. 173-192
    • Wheeler, W.C.1    Hayashi, C.Y.2
  • 51
    • 0024698890 scopus 로고
    • Rice alcohol dehydrogenase genes: Anaerobic induction, organ specific expression and characterization of cDNA clones
    • Xie, Y., Wu, R., 1989. Rice alcohol dehydrogenase genes: anaerobic induction, organ specific expression and characterization of cDNA clones. Pl. Mol. Biol. 13, 53-68.
    • (1989) Pl. Mol. Biol. , vol.13 , pp. 53-68
    • Xie, Y.1    Wu, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.