Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils

Soltis, Pamela S.; Soltis, Douglas E.; Savolainen, Vincent; Crane, Peter R.; Barraclough, Timothy G.

doi:10.1073/pnas.032087199

Cited by 232 publications

(174 citation statements)

References 34 publications

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“…As has been noted elsewhere, however, the age estimates for all of these basal angiosperm divergences antedate the earliest unambiguous fossil angiosperms, which are of Hauterivian Age, Ϸ136-130 Mya (53)(54)(55)(56). A number of causes have been advanced to explain this discrepancy, ranging from missing fossil histories to the problems inherent in molecular-based dating techniques (51,52,(57)(58)(59). Our dating analyses rely on a large and apparently internally consistent data set (as judged by the similar phylogenetic results among the various partitions under ML) and consequently should be less susceptible to phylogenetic sources of error (52,57).…”

Section: Discussionmentioning

confidence: 84%

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

Moore

Bell²,

Soltis³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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614

601

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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.

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Section: Discussionmentioning

confidence: 84%

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

Moore

Bell²,

Soltis³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

614

601

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show abstract

“…There remains active debate over methods for calibrating phylogenetic trees (42,47,59), but many alternative methods are not applicable to such large data sets. The alternative calibration point, the origin of the eudicots, produced slightly younger estimates of divergence times, dating the split between Fagales and Cucurbitales Ϸ10 my younger than that suggested by the fossil record and leading to, on average, 89% younger dates than for the alternative calibration.…”

Section: Resultsmentioning

confidence: 99%

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

Davies

Barraclough

Chase

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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541

554

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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.

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“…The LRX phylogeny suggests that the origin and initial expansion of the LRX family predate the divergence of monocots and eudicots 160 to 240 million years ago (Wolfe et al, 1989;Goremykin et al, 1997;Soltis et al, 2002). The first step in the diversification of the LRX gene family possibly occurred by the duplication of a unique ancestral gene resulting in the two clades observed in modern angiosperms.…”

Section: Discussionmentioning

confidence: 99%

“…Both Arabidopsis and rice contain large duplicated segments, suggesting that they have undergone one or several polyploidization events during their evolutionary history. Monocots and eudicots diverged 180 to 240 million years ago (Wolfe et al, 1989;Goremykin et al, 1997;Soltis et al, 2002), and the main polyploidization or large duplication events still detectable in the genome of Arabidopsis and rice are estimated to have occurred around 112 million years and 40 to 50 million years ago, respectively Goff et al, 2002). Combined with local tandem duplications, polyploidization is a mechanism that generates multigene families and is a major source of evolutionary novelty.…”

mentioning

confidence: 99%

Whole-Genome Comparison of Leucine-Rich Repeat Extensins in Arabidopsis and Rice. A Conserved Family of Cell Wall Proteins Form a Vegetative and a Reproductive Clade,

et al. 2003

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We have searched the Arabidopsis and rice (Oryza sativa) genomes for homologs of LRX1, an Arabidopsis gene encoding a novel type of cell wall protein containing a leucine-rich repeat (LRR) and an extensin domain. Eleven and eight LRX (LRR/EXTENSIN) genes have been identified in these two plant species, respectively. The LRX gene family encodes proteins characterized by a short N-terminal domain, a domain with 10 LRRs, a cysteine-rich motif, and a variable C-terminal extensin-like domain. Phylogenetic analysis performed on the conserved domains indicates the existence of two major clades of LRX proteins that arose before the eudicot/monocot divergence and then diversified independently in each lineage. In Arabidopsis, gene expression studies by northern hybridization and promoter::uidA fusions showed that the two phylogenetic clades represent a specialization into "reproductive" and "vegetative" LRXs. The four Arabidopsis genes of the "reproductive" clade are specifically expressed in pollen, whereas the seven "vegetative" genes are predominantly expressed in various sporophytic tissues. This separation into two expression classes is also supported by previous studies on maize (Zea mays) and tomato (Lycopersicon esculentum) LRX homologs and by information on available rice ESTs. The strong conservation of the amino acids responsible for the putative recognition specificity of the LRR domain throughout the family suggests that the LRX proteins interact with similar ligands.With the completion of the Arabidopsis genome sequence, it became clear that many Arabidopsis genes are members of multigene families. Although this had already been suggested by the analysis of expressed sequence tag (EST) databases and by classical gene searches, the availability of the full gene set of a plant provides the unique opportunity to get a complete inventory of all the members of a gene family. Among the 25,500 genes predicted in the Arabidopsis genome, 65% are members of a multigene family and 37% belong to families of more than five members (Arabidopsis Genome Initiative, 2000). Although the predicted total gene number of Arabidopsis is significantly larger than that of other sequenced multicellular eukaryotes such as Caenorhabditis elegans (19,000; C. elegans Sequencing Consortium, 1998) or Drosophila melanogaster (13,600; Adams et al., 2000), the absolute number of gene families and singletons (11,601 in Arabidopsis) is comparable in all these organisms (Arabidopsis Genome Initiative, 2000). This indicates that frequent gene duplications and consequently large gene families are a distinctive feature of the Arabidopsis genome, and possibly of all plant genomes. With the recent publication of a high-quality draft from two different subspecies, rice (Oryza sativa) is the second plant whose genome can be comprehensively investigated. Depending on the stringency applied in gene prediction, the rice genome contains between 32,277 and 61,668 genes (Goff et al., 2002;Yu et al., 2002). With 77% of the genes distributed in about 15,000 m...

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Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils

Cited by 232 publications

References 34 publications

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

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

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

Whole-Genome Comparison of Leucine-Rich Repeat Extensins in Arabidopsis and Rice. A Conserved Family of Cell Wall Proteins Form a Vegetative and a Reproductive Clade,

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