Colloquium: Assembling the Tree of Life Colloquium
Crawley, Sunny S , Hilu, Khidir W. .
Caryophyllales: gene choices, signal, and phylogenetic structure.
Efforts toward reconstructing phylogeny of the Caryophyllales has relied on using from two to numerous genomic regions that range in characters from around 3,000 to 46,000 base pairs. Topology, resolution, and support for the internal structure of the order have varied, but show improvement with increased number of genes/characters. We explore in this study the impact of gene choices and degree of missing data on tree topology and support in the Caryophyllales. The order is moderate in size, comprised of 29 families (APG II) making it a good study group for exploring these issues both at deep and shallow evolutionary histories. We selected two rapidly evolving genomic regions (matK and surrounding trnK intron), two slowly evolving regions (atpB and rbcL) and one with an intermediate rate of evolution (ndhF). We supplemented new matK/trnK sequences with complete and partial sequences from GenBank for all genomic regions. The 130 species used in this study were analyzed using maximum parsimony and maximum likelihood methods with six basal eudicot species as outgroup. Several different partitions were analyzed with varying degrees of missing data. The phylogenetic structure of the order recovered with rapidly evolving genes was for the most part comparable to that obtained with the three other genes. With increased numbers of genes from two to five, topology remained stable but support improved. The topology and support based on combined analysis of the five genes was remarkably similar to those obtained using much larger numbers of genes/characters; this was achieved despite having about 46% missing data in the five gene data set. Combining genes of different mode of evolution and inclusion of partial sequences resulted in both increased taxon representation and improved overall phylogenetic structure.
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1 - Virginia Tech, Biological Sciences, 2119 Derring Hall, Blacksburg, VA, 24061, USA
2 - Virginia Polytechnic Institute and State University, Department of Biology, Blacksburg, Virginia, 24061, USA
Presentation Type: Symposium or Colloquium Presentation
Location: Cottonwood C/Snowbird Center
Date: Tuesday, July 28th, 2009
Time: 2:30 PM