1994
DOI: 10.2307/2399898
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Progress and Prospects in Reconstructing Plant Phylogeny

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Cited by 68 publications
(40 citation statements)
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“…Ceratophyllum is the longest branch near the base of the tree, with 44 steps shown on its branch and 22 more along the branch subtending the rest of the angiosperms. This observation has suggested the possibility that the Ceratophyllum rooting is an artifact of long branch attraction (Donoghue, 1994). Similarly, in the analysis of 18S rRNA, 45 character changes are shown on the angiosperm branch, and 14 more on the sister branch subtending the gymnosperms (which form a clade in this analysis), for a total of 59 differences separating angiosperms from other seed plants their Fig.…”
Section: The Root Of Angiospermssupporting
confidence: 54%
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“…Ceratophyllum is the longest branch near the base of the tree, with 44 steps shown on its branch and 22 more along the branch subtending the rest of the angiosperms. This observation has suggested the possibility that the Ceratophyllum rooting is an artifact of long branch attraction (Donoghue, 1994). Similarly, in the analysis of 18S rRNA, 45 character changes are shown on the angiosperm branch, and 14 more on the sister branch subtending the gymnosperms (which form a clade in this analysis), for a total of 59 differences separating angiosperms from other seed plants their Fig.…”
Section: The Root Of Angiospermssupporting
confidence: 54%
“…Over the past decade our understanding of the phylogeny of green plants has progressed a great deal (Donoghue, 1994;Crane et al, 1995;Kenrick and Crane, 1997). However, despite considerable attention, some significant issues remain unresolved.…”
Section: Introductionmentioning
confidence: 99%
“…(Bowe et al 2000;Chaw et al 2000). The strong resemblance of Gnetum to certain angiosperms helped inspire the hypothesis that the angiosperms were derived from gymnosperms via Gnetales (Doyle and Donoghue 1986;Donoghue 1994). Molecular data do not support that hypothesis, however, indicating that the gymnosperms as a whole are sister to the angiosperms and that Gnetales arose from within the conifers (Bowe et al 2000;Chaw et al 2000;Soltis et al 2002; but see Rydin et al 2002).…”
Section: Concerted Convergencementioning
confidence: 99%
“…The poor resolution among the Peperomia and other angiosperm coxI sequences is not unexpected, both because relationships among the major lineages of angiosperms are still poorly understood (Donoghue 1994) and because of the limited number of changes among the angiosperm sequences• The intron phylogenetic analyses included those introns that showed the highest similarity with the related coxI introns from Peperomia and Marchantia in Blast searches and which also contain a (related) endonuclease ORF, regardless of the intron's genic position• CoxI intron aI2a from Schizosaccharomyces pombe (Trinkl and Wolf 1986) is inserted at the same position as the Peperomia intron, but was excluded because it lacks an ORF. Phylogenetic analysis of the entire intron nucleotide sequence resolved the nine plant and fungal group I introns into three major groups, each with moderateto-high bootstrap support with all three methods (Fig, 5A).…”
Section: Quences Again With 100% Bootstrap Support• That Thementioning
confidence: 99%
“…Based on current sampling and phylogenetic concepts (Donoghue 1994), this would require a minimum of at least six and more likely ten independent losses, one each from the ten groups of vascular plants shown in Fig. 4 I IIIIII I I II I II III III I lllll IIIIIII I IIIIIII a14 GCAUUAGAAGAUGAAAUAGCUUUAAAAGAAAUUCAAAAUAAAUUUGBUGGUUCUAUUAAAUUAAGAUCAGG 250 300 PEP UGCUAAASCUUAUCGUUAUCSACUACAUAAUCAACUUSGUAUGAUUAAACUAAUUAAUUGUAUUAAUGGUA I IIIIII I I III II III I II II llllll IIIIII IIIIIIII IIIIIIIII aI4 UGUAAAAGCUAUUAGAUAUAGAUUACUUAAUAAAACUBGUAUAAUUAAAUUAAUUAAUGCAGUUAAUGGUA 321 371 PEP ~UAUUCGACAUUCABCACBACUACUUCAACUACAUCBUGUCUGUCAABUACUBBAUAACCCUUUAAUUCUA IIII II II I I II II I II I II II III I I I II III III aI4 AUAUUABAAAUACUAAAABAUUAGUACAAUUUAAUAAAGUUUGUAUUUUAUUAGGUAUUGAUUUUAUUUAU 392 442 PEP CCUAAUACACUUUCAGCUCAAUCCAAUUGGUUUGCAGGAUUCUUUGAUBCUGABGBUACUAUUGGUAUCGC I I II I I I I I II IIII IIIII IIIIII IIII IIIII III I I aI4 CCAAUUAAAUUAACUAAAGAUAAUAGUUGAUUUGUUGGAUUUUUUGAUGCUGAUGGUACAAUUAAUUAUUC 463 513 PEP UAUGAAGCAUCGACUACCUCAACUAAGUAUUCBAGUAAAUAAUCAACUUCUACAAGAUGUUGAGUCUUAUA I II II I IIIIII Ill IIII IIII II Illlllllll I Illl aI4 AUUUAAAAAUAAUCAUCCUCAAUUAACAAAAACUGUAACUAAUAAAUAUUUACAABAUGUACAAGAAUAUA 534 584 PEP AGGUCGUAUUUGGAGGAAAUAUCUACUUUUCUAGUAGUCAAAAUGGUUACUAUCAAUGGUCUGUACAAAGU l I II II II IIIII II II II IIIIIIIIII III IIII II I III aI4 AAAAUAUUUUAGGUGGUAAUAUUUAUUUUSAUAAAU~ACAAAAUGGUUAUUAUAAAUGAUCCAUUCAAUCA 605 655 PEP CGAAAABAUGUUAUCA.…”
Section: The Peperomia Group I Intron Originated By Horizontal Transfermentioning
confidence: 99%