Angiosperm Phylogeny Inferred from 18S Ribosomal DNA Sequences (original) (raw)
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Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences
Annals of the Missouri …, 1997
A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18s rDNA (1855 bp), rbcl. (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early-branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schisandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well-supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well-supported eudicot clade, the early-diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise * Correspondence to 0. E. Soltis.
Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences
Botanical Journal of …, 2000
A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18s rDNA (1855 bp), rbcl. (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early-branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schisandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well-supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well-supported eudicot clade, the early-diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise * Correspondence to 0. E. Soltis.
Angiosperm phylogeny: 17 genes, 640 taxa
American Journal of Botany, 2011
Premise of the study : Recent analyses employing up to fi ve genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses.
Phylogenetics of sees plants: An analysis of nucleotide sequences from the plastid gene rbcL
1993
We present the results of two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups. The data are exclusively from the chloroplast gene rbcL, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO or RuBPCase). We used two different state-transformation assumptions resulting in two sets of cladograms: (i) equal-weighting for the 499-taxon analysis; and (ii) a procedure that differentially weights transversions over transitions within characters and codon positions among characters for the 475-taxon analysis. The degree of congruence between these results and other molecular, as well as morphological, cladistic studies indicates that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Because the topologies presented are necessarily approximate and cannot be evaluated adequately for internal support, these results should be assessed from the perspective of their predictive value and used to direct future studies, both molecular and morphological. In both analyses, the three genera of Gnetales are placed together as the sister group of the flowering plants, and the anomalous aquatic Ceratophyllum (Ceratophyllaceae) is sister to all other flowering plants. Several major lineages identified correspond well with at least some recent taxonomic schemes for angiosperms, particularly those of Dahlgren and Thorne. The basalmost clades within the angiosperms are orders of the apparently polyphyletic subclass Magnoliidae sensu Cronquist. The most conspicuous feature of the topology is that the major division is not monocot versus dicot, but rather one correlated with general pollen type: uniaperturate versus triaperturate. The Dilleniidae and Hamamelidae are the only subclasses that are grossly polyphyletic; an examination of the latter is presented as an example of the use of these broad analyses to focus more restricted studies. A broadly circumscribed Rosidae is paraphyletic to Asteridae and Dilleniidae. Subclass Caryophyllidae is monophyletic and derived from within Rosidae in the 475-taxon analysis but is sister to a group composed of broadly delineated Asteridae and Rosidae in the 499-taxon study.
Molecular phylogenies in angiosperm evolution
Molecular biology and evolution, 1993
We have cloned and sequenced cDNAs for the glyceraldehyde-3-phosphate dehydrogenase of glycolysis, gapC, from a bryophyte, a gymnosperm, and three angiosperms. Phylogenetic analyses are presented for these data in the context of other gapC sequences and in parallel with published nucleotide sequences for the chloroplast encoded gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL). Relative-rate tests were performed for these genes in order to assess variation in substitution rate for coding regions, along individual plant lineages studied. The results of both gene analyses suggest that the deepest dichotomy within the angiosperms separates not magnoliids from remaining angiosperms, but monocotyledons from dicotyledons, in sharp contrast to prediction from the Euanthial theory for angiosperm evolution. Furthermore, these chloroplast and nuclear sequence data taken together suggest that the separation of monocotyledonous and dicotyledonous lineages took...
Evolution and Diversification of Land Plants, 1997
Although the phylogenetic relationship of Western Palearctic brown frogs has been repeatedly studied, the taxonomic status and phylogenetic relationship of Anatolian-Hyrcanian brown frogs is still not fully resolved. Here, we assess the phylogenetic status of these species among Western Palearctic brown frogs with special emphasize on Iranian populations based on two partial mitochondrial DNA sequences (16S rRNA and cytochrome b genes) and the application of a molecular clock. Our results clearly show that Western Palearctic brown frogs underwent a basal radiation in to two main monophyletic clades, the European brown frogs plus the Asian R. asiatica and the Anatolian-Hyrcanian brown frogs, during Early Miocene ca. 20.2 mya. The Hyrcanian (R. pseudodalmatina) and the Anatolian lineage diverged approximately 16.6 mya. The further diverged into two subclades, R. tavasensis and R. macrocnemis, during the Middle Miocene, 14.5 mya. Our results suggest that diversification within these lineages may be closely linked to the formation of Neotethys and Paratethys and the subsequent uplift of the Turkish-Iranian plateau during the Early Miocene which led to restricted gene flow among brown frogs in these regions. Contrary to previous studies, we conclude that the Plio-Pleistocene epoch seems to be not associated to further significant speciation events within Anatolian-Hyrcanian brown frogs.
Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL
Annals of the Missouri …, 1993
We present the results of two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups. The data are exclusively from the chloroplast gene rbcL, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO or RuBPCase). We used two different state-transformation assumptions resulting in two sets of cladograms: (i) equal-weighting for the 499-taxon analysis; and (ii) a procedure that differentially weights transversions over transitions within characters and codon positions among characters for the 475-taxon analysis. The degree of congruence between these results and other molecular, as well as morphological, cladistic studies indicates that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Because the topologies presented are necessarily approximate and cannot be evaluated adequately for internal support, these results should be assessed from the perspective of their predictive value and used to direct future studies, both molecular and morphological. In both analyses, the three genera of Gnetales are placed together as the sister group of the flowering plants, and the anomalous aquatic Ceratophyllum (Ceratophyllaceae) is sister to all other flowering plants. Several major lineages identified correspond well with at least some recent taxonomic schemes for angiosperms, particularly those of Dahlgren and Thorne. The basalmost clades within the angiosperms are orders of the apparently polyphyletic subclass Magnoliidae sensu Cronquist. The most conspicuous feature of the topology is that the major division is not monocot versus dicot, but rather one correlated with general pollen type: uniaperturate versus triaperturate. The Dilleniidae and Hamamelidae are the only subclasses that are grossly polyphyletic; an examination of the latter is presented as an example of the use of these broad analyses to focus more restricted studies. A broadly circumscribed Rosidae is paraphyletic to Asteridae and Dilleniidae. Subclass Caryophyllidae is monophyletic and derived from within Rosidae in the 475-taxon analysis but is sister to a group composed of broadly delineated Asteridae and Rosidae in the 499-taxon study.
The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?
1999
Previous studies of the phylogeny of land plants based on analysis of 18S ribosomal DNA (rDNA) sequences have generally found weak support for the relationships recovered and at least some obviously spurious relationships, resulting in equivocal inferences of land plant phylogeny. We hypothesized that greater sampling of both characters and taxa would improve inferences of land plant phylogeny based on 18S rDNA sequences. We therefore conducted a phylogenetic analysis of complete (or nearly complete) 18S rDNA sequences for 93 species of land plants and 7 green algal relatives. Parsimony analyses with equal weighting of characters and character state changes and parsimony analyses weighting (1) stem bases half as much as loop bases and (2) transitions half as much as transversions did not produce substantially different topologies. Although the general structure of the shortest trees is consistent with most hypotheses of land plant phylogeny, several relationships, particularly among major groups of land plants, appear spurious. Increased character and taxon sampling did not substantially improve the performance of 18S rDNA in phylogenetic analyses of land plants, nor did analyses designed to accommodate variation in evolutionary rates among sites. The rate and pattern of 18S rDNA evolution across land plants may limit the usefulness of this gene for phylogeny reconstruction at deep levels of plant phylogeny. We conclude that the mosaic structure of 18S rDNA, consisting of highly conserved and highly variable regions, may contain historical signal at two levels. Rapidly evolving regions are informative for relatively recent divergences (e.g., within angiosperms, seed plants, and ferns), but homoplasy at these sites makes it difficult to resolve relationships among these groups. At deeper levels, changes in the highly conserved regions of small-subunit rDNAs provide signal across all of life. Because constraints imposed by the secondary structure of the rRNA may affect the phylogenetic information content of 18S rDNA, we suggest that 18S rDNA sequences be combined with other data and that methods of analysis be employed to accommodate these differences in evolutionary patterns, particularly across deep divergences in the tree of life.
Molecular Phylogenetics and Evolution, 2007
We have determined the complete chloroplast genome sequences of four early-diverging lineages of angiosperms, Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae), to examine the organization and evolution of plastid genomes and to estimate phylogenetic relationships among angiosperms. For the most part, the organization of these plastid genomes is quite similar to the ancestral angiosperm plastid genome with a few notable exceptions. Dioscorea has lost one protein-coding gene, rps16; this gene loss has also happened independently in four other land plant lineages, liverworts, conifers, Populus, and legumes. There has also been a small expansion of the inverted repeat (IR) in Dioscorea that has duplicated trnH-GUG. This event has also occurred multiple times in angiosperms, including in monocots, and in the two basal angiosperms Nuphar and Drimys. The Illicium chloroplast genome is unusual by having a 10 kb contraction of the IR. The four taxa sequenced represent key groups in resolving phylogenetic relationships among angiosperms. Illicium is one of the basal angiosperms in the Austrobaileyales, Chloranthus (Chloranthales) remains unplaced in angiosperm classifications, and Buxus and Dioscorea are early-diverging eudicots and monocots, respectively. We have used sequences for 61 shared protein-coding genes from these four genomes and combined them with sequences from 35 other genomes to estimate phylogenetic relationships using parsimony, likelihood, and Bayesian methods. There is strong congruence among the trees generated by the three methods, and most nodes have high levels of support. The results indicate that Amborella alone is sister to the remaining angiosperms; the Nymphaeales represent the next-diverging clade followed by Illicium; Chloranthus is sister to the magnoliids and together this group is sister to a large clade that includes eudicots and monocots; and Dioscorea represents an early-diverging lineage of monocots just internal to Acorus. Published by Elsevier Inc.
The prevailing view in molecular phylogenetics is that relationships at deeper levels, for example among major angiosperm lineages, should be inferred using rather conserved genes. Rapidly evolving DNA has been deemed unsuitable because of putative high levels of homoplasy caused by multiple substitutions and frequent microstructural mutations resulting in their non-alignability. Recent analyses of rapidly evolving spacers and introns in the chloroplast genome from basal angiosperms show that extreme sequence variability is confined to certain mutational hotspots. These hotspots correlate with structural elements (stem loops), where selective pressure is low. Phylogenetic trees of basal angiosperms inferred from rapidly evolving genomic regions are well resolved and highly supported statistically. Reasons are not only greater amounts of informative sites in rapidly evolving DNA, but also differing levels of homoplasy that can result in better phylogenetic signal per informative site. Based on these findings, perspectives for further utilizing non-coding DNA in angiosperm phylogenetic studies are explored. Zusammenfassung Nach vorherrschenden Konzepten werden zur Phylogenie-Rekonstruktion von Verwandtschaftsverhältnissen auf tieferer Ebene, z. B. zwischen den Hauptgruppen der Angiospermen, vorwiegend konservierte Gene eingesetzt. Schnell evolvierende DNA wurde als ungeeignet angesehen, weil von starken Homoplasie-Effekten durch Saturierung (multiple Nukleotid-Substitutionen) sowie fehlender Alignbarkeit durch häufige mikrostrukturelle Mutationen ausgegangen wurde. Neuere Analysen schnell evolvierender Spacer und Introns des Chloroplastengenoms bei basalen Angiospermen zeigen aber, daß extreme Sequenzvariabilität auf bestimmte Mutations-Hotspots konzentriert ist. Diese korrelieren mit Strukturelementen (z. B. Stem-Loops), die geringen selektiven Zwängen unterliegen. Stammbaumhypothesen basaler Angiospermen, basierend auf schnell evolvierenden Genomabschnitten, sind gut aufgelöst und hoch statistisch gestützt. Gründe dafür liegen nicht nur in der größeren Zahl informativer Positionen in schnell evolvierender DNA, sondern auch in anderen Homoplasieverhältnissen, die ein stärkeres phylogenetisches Signal pro informativer Position bedeuten können. Anhand der vorliegenden Daten werden Perspektiven für die weitergehende Anwendung von nicht-codierender DNA in der Evolutionsforschung bei Angiospermen erörtert.