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, 104 (49), 19363-8

Using Plastid Genome-Scale Data to Resolve Enigmatic Relationships Among Basal Angiosperms

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Using Plastid Genome-Scale Data to Resolve Enigmatic Relationships Among Basal Angiosperms

Michael J Moore et al. Proc Natl Acad Sci U S A.

Abstract

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 ( approximately 42,000 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.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Comparison of simplified tree topologies among different partitions and phylogenetic optimization criteria. Numbers associated with branches in MP trees are MP BS support values >50%, whereas numbers associated with branches in ML trees are ML BS support values >50%/Bayesian posterior probabilities >0.5. Codon 1 + 2 refers to the combined first and second codon positions of the 61-gene combined analyses. The asterisk at the node uniting Amborella and Nymphaeales in the 61 genes/codons 1 and 2 ML/Bayes tree indicates that the GARLI ML BS analysis weakly favors a topology where Amborella is sister to all remaining angiosperms (BS = 54%).
Fig. 2.
Fig. 2.
Phylogram of the best ML tree as determined by GARLI (−ln L = 460,654.151) for the 61-gene combined data set. Numbers associated with branches are ML BS values >50%/Bayesian posterior probabilities >0.5. The number in parentheses is the branch length separating outgroups from angiosperms.

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