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Resolving the green branch of life: Current progress and future challenges

Driskell, Amy [2], Kelch, Dean [1], Mishler, Brent [1], Sanderson, MJ [2].

Non-traditional approaches to resolving the green plant tree of life.

Ancient divergence events, which are often represented in modern phylogenies as relatively short internodes of interest subtending long terminal branches, are notoriously difficult to resolve with conventional molecular phylogenetic methods. Here we describe a number of non-traditional approaches to the resolution of deep nodes and broad phylogenetic questions in green plants. First, we apply comparative genomics and take advantage of the increasing availability of complete chloroplast genomes. We coded phylogenetic characters from gene rearrangements and gene and intron presence/absence data to reconstruct basal relationships among land plants. This character set has very low homoplasy and provides good support for a sister relationship between liverworts and all other land plants. Our approach will facilitate the analysis of the additional whole chloroplast and mitochondrion genomes to be completed by the NSF-funded Green Plant Tree of Life project. We also apply a variety of compartmentalization approaches to the problem of resolving relationships among liverworts, hornworts, mosses and tracheophytes. We analyze a number of different taxon-dense or character-dense data matrices and use results of local analyses within compartments as constraints to improve the behavior of global parsimony analyses. Lastly, we have examined the phylogenetic information content of all of the green plant protein data in GenBank with the goal of determining their utility for reconstructing the green plant tree of life. We parse the database into complete multi-gene supermatrices (bicliques) and sets of input trees for supertree construction (groves) and discuss the potential phylogenetic depth and breadth encompassed by each of these methods. Only a small fraction of the database is potentially phylogenetically informative, but this fraction contains a high proportion of green plant biodiversity.

1 - University of California, Berkeley, Integrative Biology, University and Jepson Herbaria, 1001 Valley Life Sciences Building, Berkeley, California, 94720-2465, USA
2 - University of California, Davis, Section of Evolution and Ecology, One Shields Ave., Davis, California, 95616, USA

phylogenetic methods
Tree of Life.

Presentation Type: Symposium
Session: 46-2
Location: Ballroom 3 (Cliff Lodge)
Date: Wednesday, August 4th, 2004
Time: 8:30 AM
Abstract ID:767

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