The Challenges Posed by Large Data Sets in Assembling the Plant and Fungal Trees of Life
Moore, Michael , Soltis, Douglas E. , Soltis, Pamela S. , Bell, Charles , Piedrahita, Ana , Hassan, Nasr , Brockington, Samuel F , Ramdial, Jeremy , Alexandre, Roolse , Dhingra, Amit .
Chloroplast phylogenomics and the Angiosperm Tree of Life.
Vast improvements in DNA sequencing technologies in recent years have led to an explosion of plastid genome sequencing projects. Over 120 complete plastid genome sequences are now available for angiosperms, with many more on the way. Large sequence data matrices constructed from these genome sequences have shown great promise in resolving difficult regions of the Angiosperm Tree of Life. For example, several recent studies based upon plastid genome-scale data sets (up to ~67,000 aligned bases) have resolved the positions of Amborella and Nymphaeales as successively sister to other angiosperms, have provided strong support for a clade of monocots, Ceratophyllum, and eudicots, and have resolved the Pentapetalae into 2 large clades: (1) a “super-rosid” clade of Dilleniaceae, Vitaceae, Saxifragales, and rosids, and (2) a “super-asterid” clade of Santalales, Berberidopsidales, Caryophyllales, and asterids. We review the recent progress in plastid phylogenomics and discuss its promise for resolving other difficult areas of angiosperm phylogeny, particularly eudicots. We also examine the utility of the chloroplast inverted repeat (IR) region as a phylogenetic tool for angiosperms. The IR in angiosperms is a region of ~25 kb that is characterized by a relatively slow rate of evolution. Recent IR-based phylogenies of Saxifragales and rosids suggest that this region may provide an ideal source of characters for deeper-level angiosperm phylogenetics. By combining all publicly available IR sequences with over 100 new sequences, we created a comprehensive IR alignment for over 200 angiosperms, including multiple representatives of all major clades. Phylogenetic results from this data set are compared with those of other large-scale plastid data sets to compare the topological effects of (1) including much improved taxon sampling compared to other genome-scale analyses (> 200 in the IR, vs. < 100 in other analyses), and (2) using a slow-evolving plastid region (IR) vs. complete genome coverage.
Log in to add this item to your schedule
1 - Oberlin College, Biology Department, 119 Woodland Street, Science Center K111, Oberlin, Ohio, 44074-1097, USA
2 - University of Florida, Botany, PO Box 117800, Gainesville, FL, 32611, USA
3 - Florida Museum of Natural History, Dickinson Hall, P.O. Box 117800, Gainesville, Florida, 32611, USA
4 - University of New Orleans, Department of Biological Sciences, New Orleans, LA, 70148, USA
5 - University of Florida, Dept. of Botany, PO Box 117800, Gainesville, FL, 32611, USA
6 - University of Florida, Department of Botany, Florida Museum of Natural History, P.O. Box 117800, Gainesville, Florida, 32611-7800, USA
7 - University of Florida, Department of Botany, Florida Museum of Natural History, P.O. Box 117800, Gainesville, Florida, University of Florid, USA
8 - Washington State University, Department of Horticulture and Landscape Architecture, PO Box 646414, Pullman, WA, 99164-6414, USA
Angiosperm Tree of Life
large data sets
Presentation Type: Symposium or Colloquium Presentation
Location: Ballroom 2/Cliff Lodge - Level B
Date: Tuesday, July 28th, 2009
Time: 11:15 AM