Progress and Prospects in Reconstructing Plant Phylogeny

Donoghue, Michael J.

doi:10.2307/2399898

Cited by 68 publications

(40 citation statements)

References 127 publications

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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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Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

Donoghue

Mathews

1998

Molecular Phylogenetics and Evolution

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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%

Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

Donoghue

Mathews

1998

Molecular Phylogenetics and Evolution

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“…(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%

Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

Givnish¹,

Pires²,

Graham³

et al. 2006

aliso

103

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We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 monocot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales-Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve-and thus undergo concerted convergence-in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P < I0-9 ) and are each even more strongly associated with shaded habitats (P < I0-10 to I0-23 ); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia.

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“…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%

Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric coxI gene of Peperomia

et al. 1995

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We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene arose recently by horizontal transfer from a fungal donor species. A 1,716-bp fragment of the mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the polymerase chain reaction and sequenced. Comparison to other coxI genes revealed a 966-bp group I intron, which, based on homology with the related yeast coxI intron aI4, potentially encodes a 279-amino-acid site-specific DNA endonuclease. This intron, which is believed to function as a ribozyme during its own splicing, is not present in any of 19 coxI genes examined from other diverse vascular plant species. Phylogenetic analysis of intron origin was carried out using three different tree-generating algorithms, and on a variety of nucleotide and amino acid data sets from the intron and its flanking exon sequences. These analyses show that the Peperomia coxI gene intron and exon sequences are of fundamentally different evolutionary origin. The Peperomia intron is more closely related to several fungal mitochondrial introns, two of which are located at identical positions in coxI, than to identically located coxI introns from the land plant Marchantia and the green alga Prototheca. Conversely, the exon sequence of this gene is, as expected, most closely related to other angiosperm coxI genes. These results, together with evidence suggestive of co-conversion of exonic markers immediately flanking the intron insertion site, lead us to conclude that the Peperomia coxI intron probably arose by horizontal transfer from a fungal donor, using the double-strand-break repair pathway. The donor species may have been one of the symbiotic mycorrhizal fungi that live in close obligate association with most plants.

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Progress and Prospects in Reconstructing Plant Phylogeny

Cited by 68 publications

References 127 publications

Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

Duplicate Genes and the Root of Angiosperms, with an Example Using Phytochrome Sequences

Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric coxI gene of Peperomia

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