Phylogeny of Basal Angiosperms: Analyses of Five Genes from Three Genomes

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620

601

Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (Ϸ42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae ؉ magnoliids as sister to a well supported clade of monocots ؉ (Ceratophyllum ؉ eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 ؎ 4.8 and 140.3 ؎ 4.8 Mya.

Section: Discussionmentioning

confidence: 99%

Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms

Moore

Bell²,

Soltis³

et al. 2007

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620

601

“…This model provides a compromise between model complexity and computational time (42). The phylogenetic tree was arranged with Amborellaceae as sister to the rest of the angiosperms (27,28,(43)(44)(45). To correct for variation in substitution rate among lineages, we used nonparametric rate smoothing (46), as implemented in TREEEDIT V1.0 A10 (http:͞͞evolve.zoo.…”

Section: Methodsmentioning

confidence: 99%

Darwin's abominable mystery: Insights from a supertree of the angiosperms

Davies

Barraclough

Chase

et al. 2004

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545

554

Angiosperms are among the major terrestrial radiations of life and a model group for studying patterns and processes of diversification. As a tool for future comparative studies, we compiled a supertree of angiosperm families from published phylogenetic studies. Sequence data from the plastid rbcL gene were used to estimate relative timing of branching events, calibrated by using robust fossil dates. The frequency of shifts in diversification rate is largely constant among time windows but with an apparent increase in diversification rates within the more recent time frames. Analyses of species numbers among families revealed that diversification rate is a labile attribute of lineages at all levels of the tree. An examination of the top 10 major shifts in diversification rates indicates they cannot easily be attributed to the action of a few key innovations but instead are consistent with a more complex process of diversification, reflecting the interactive effects of biological traits and the environment.

“…However, despite considerable support for Amborella as sister to all other angiosperms, some reservations regarding this placement have been expressed. Parkinson et al (2) and Qiu et al (7) could not reject, using the Kishino-Hasegawa (KH) test (8), the hypothesis that Nymphaeales are sister to all other flowering plants or that Amborella and Nymphaeales form a clade sister to all remaining angiosperms. In addition, a maximum likelihood (ML) analysis of basal angiosperms with a subset of the taxa analyzed in larger parsimony analyses found a clade of Amborella ϩ Nymphaeales to be the sister to all other flowering plants (9).…”

mentioning

confidence: 98%

The root of the angiosperms revisited

Zanis

Soltis²,

Soltis³

et al. 2002

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241

257

Most recent phylogenetic analyses of basal angiosperms have converged on the placement of Amborella as sister to all other extant angiosperms. However, certain recent studies suggest that Amborella and Nymphaeales (water lilies) form a clade sister to all remaining angiosperms or that Nymphaeales alone are the sister to the remaining angiosperms. We report here (i) maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses of 11 genes (>15,000 bp per taxon) for 16 taxa, (ii) maximum parsimony analysis for a subset of these genes for 104 taxa, and (iii) tests of alternative rootings with the nonparametric bootstrap and the likelihood ratio test with the parametric bootstrap. In addition, we use simulation analyses to examine the amount of bias that may be present in our methods of phylogeny estimation. Amborella continues to receive strong bootstrap support as the sister to all other extant angiosperms, and three of four tests reject alternative hypotheses of the angiosperm root. Although we cannot conclusively choose between Amborella vs. Amborella ؉ Nymphaeales as sister to all other angiosperms, most analyses favor the former rooting.W ithin the past few years, phylogenetic relationships among the major lineages of angiosperms have largely been clarified (1-5). Understanding the major branching patterns in the angiosperms is critical for character reconstruction in the earliest angiosperms and for understanding subsequent patterns of diversification. A particularly noteworthy development has been the general agreement, based on maximum parsimony (MP) analyses of DNA sequences from all three genomes (nuclear, chloroplast, and mitochondrial), on the placement of the root of the angiosperms-the monotypic Amborella is sister to all other extant flowering plants, followed by Nymphaeales (water lilies), and a clade of Austrobaileyaceae, Trimeniaceae, Illiciaceae, and Schisandraceae as successive sisters to the remaining lineages of flowering plants (1-3, 6). When multiple gene sequences were combined, high internal support, as measured by the bootstrap or jackknife, was obtained for these basal branches, with values above 90% attained in some analyses (1-3, 6). However, despite considerable support for Amborella as sister to all other angiosperms, some reservations regarding this placement have been expressed. Parkinson et al. (2) and Qiu et al. (7) could not reject, using the Kishino-Hasegawa (KH) test (8), the hypothesis that Nymphaeales are sister to all other flowering plants or that Amborella and Nymphaeales form a clade sister to all remaining angiosperms. In addition, a maximum likelihood (ML) analysis of basal angiosperms with a subset of the taxa analyzed in larger parsimony analyses found a clade of Amborella ϩ Nymphaeales to be the sister to all other flowering plants (9). Similarly, Mathews and Donoghue (10) could not reject alternative rootings at Amborella ϩ Nymphaeales or at Nymphaeales alone with Templeton's significantly less parsimonious test (SLP T ) in an expanded analysis of phyt...