Identifying the Basal Angiosperm Node in Chloroplast GenomePhylogenies: Sampling One's Way Out of the Felsenstein Zone

Journal Article · Fri May 27 04:00:00 EDT 2005 · Molecular Biology and Evolution

DOI:https://doi.org/10.1093/molbev/msi191· OSTI ID:860913

Leebens-Mack, Jim; Raubeson, Linda A; Cui, Liying; Kuehl, Jennifer V; Fourcade, Matthew H; Chumley, Timothy W; Boore, JeffreyL; Jansen, Robert K; dePamphilis, Claude W

While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca and Typha), a water lily (Nuphar), a ranunculid(Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein datasets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiospermphylogeny. However, their relative positions proved to be dependent on method of analysis, with parsimony favoring Amborella as sister to all other angiosperms, and maximum likelihood and neighbor-joining methods favoring an Amborella + Nympheales clade as sister. The maximum likelihood phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single gene phylogenies, estimated divergence dates and conflicting in del characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiospermphylogeny. Molecular dating analyses provided median age estimates of 161 mya for the most recent common ancestor of all extant angiosperms and 145 mya for the most recent common ancestor of monocots, magnoliids andeudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction can mislead genome-scale phylogenetic analyses.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director. Office of Science. Office of Biological andEnvironmental Research; National Science Foundation Grants DEB-0120709and DBI-0115684
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 860913
• Report Number(s): LBNL--58174; BnR: KP1103010
• Journal Information: Molecular Biology and Evolution, Journal Name: Molecular Biology and Evolution Journal Issue: 10 Vol. 22
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
AGE ESTIMATION
Angiosperm phylogeny phylogenomics parametricbootstrap
CHLOROPLASTS
DNA
GENES
HYPOTHESIS
MAGNOLIOPHYTA
PINOPHYTA
PROTEINS
RESOLUTION
SAMPLING
WATER