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Methods and theory of phylogenetic inference

Soltis, Douglas E. [2], Soltis, Pamela S. [1], Albert, Victor A. [3], Kim, Sangtae [2].

The use of ESTs in phylogenetic analyses .

Numerous expressed sequence tags (ESTs) are now available, representing a diverse array of plants and providing a rich genetic resource. These ESTs afford the opportunity to address a large number of conspicuous evolutionary genomic questions, including genome-wide duplication history, gene lineage-specific duplication and functional divergence, and analyses of adaptive molecular evolution. Recently funded initiatives have provided new genomic resources comprising cDNA libraries and EST sequences for a suite of phylogenetically pivotal angiosperms specifically selected to bridge the gaps between model plants such as Arabidopsis, Antirrhinum, Zea, and Oryza. These ESTs can play important roles in phylogenetic analyses, permitting taxonomically broad samples of gene families that would not be possible using only complete sequences. For example, our initial comparisons illustrate the utility of EST data toward discovery of the basic floral transcriptome. We provide examples from our own work on various floral gene families (e.g., MADS, AP2, Shaggy-like kinases) in which ESTs have been included in large phylogenetic analyses to obtain novel insights into the evolution of these gene families. These studies have revealed, for example, that basal angiosperms already possessed a diverse tool kit of floral genes, with many of the genes present in Arabidopsis and rice also present in basal angiosperms. In addition, within many clades, relationships often roughly track organismal phylogeny, with ESTs from basal angiosperms appearing near the base of lineages. Inclusion of ESTs also presents challenges in phylogenetic analysis, including large amounts of missing data. Another challenge is the sheer size of the data sets that can be compiled. Unlike distance matrix methods, which ignore sites with missing data, rapid parsimony search approaches (such as jackknifing) provide an informative and rapid means by which such phylogenetic analyses including ESTs can be conducted and internal support for clades assessed.

1 - University of Florida, Department of Natural History, Florida Museum of Natural History, P.O. Box 117800, Gainesville, Florida, 32611-7800, USA
2 - University of Florida, Department of Botany, 220 Bartram Hall, P.O. Box 118526, Gainesville, Florida, 32611-8526, USA
3 - University of Oslo, Botanical Garden, Natural History Museums and Botanical Garden, P.O. Box 1172 Blindern, Oslo, NO-0318, Norway

expressed sequence tags
phylogeny reconstruction
genomic resources.

Presentation Type: Symposium
Session: 31-5
Location: Alpine A (Snowbird Center)
Date: Tuesday, August 3rd, 2004
Time: 10:45 AM
Abstract ID:432

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