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Comparative Chloroplast Genomics

Leebens-Mack, Jim [1], dePamphilis, Claude W. [2], Raubeson, Linda A. [3], Boore, Jeffrey L. [4], Jansen, Robert K. [5].

The Use of Whole Chloroplast Genome Sequences for Phylogeny Reconstruction in Angiosperms.

Recent phylogenetic analyses of large numbers of genes extracted from chloroplast genome sequences provide breakthroughs and illustrate possible pitfalls that we may encounter in the emerging field of phylogenomics. Poor taxon sampling has been identified as a source of error even in some genome-scale analyses. However, the precise sources of errors associated with sparse taxon sampling are typically not discussed. Long branch attraction can occur even when substitution rates and character state transition probabilities are constant across all lineages when taxon sampling is sparse and uneven. Variation in substitution rates or transition probabilities across a phylogeny can result in increased susceptibility to long-branch attraction, especially when these processes lead to convergent biases in nucleotide, codon, or amino acid usage. Analyses of chloroplast genome sequences show how these sources of error can be diagnosed using parametric bootstrap analyses. Moreover, simulations can be used to test the efficacy of taxon sampling for reducing susceptibility to long-branch attraction. The results of these analyses suggest that with proper taxon sampling, chloroplast genome sequences can provide a very powerful and efficient means of resolving relationships among angiosperm lineages. Specifically, phylogenetic analyses of concatenated plastid gene sequences reveals strong support Amborellales and Nymphaeales as the most basal angiosperm lineages and, within the eudicots, the Caryophyllales is supported as sister to the asterids. More sampling will be necessary to resolve the relationships of the magnoliids, monocots and eudicots.

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1 - Pennsylvanian State University, Department of Biology, University Park, Pennsylvania, 16802, USA
2 - Pennsylvania State University, Department of Biology and Institute of Molecular Evolutionary Genetics, University Park, Pennsylvania, 16801, USA
3 - Central Washington State University, Department of Biological Sciences, Ellensburg, Washington, 98926-7537, USA
4 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA
5 - University of Texas Austin, Section of Integrative Biology, 1 University Station, A6700, Austin, Texas, 78712-7640, USA

Chloroplast genome.

Presentation Type: Symposium or Colloquium Presentation
Session: 19-4
Location: Salon K - Austin Grand Ballroom/Hilton
Date: Monday, August 15th, 2005
Time: 4:00 PM
Abstract ID:182

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