Abstract Detail

Botany 2015 Colloquium: Phylogenomics and the 1000 plants (1KP) initiative 

Puzey, Joshua [1], Zhan, Shing Hei [2], Chen, Tao [3], Deyholos, Michael [4], Leebens-Mack, James [5], Stevenson, Dennis [6], Thomas, Philip [7], Wong, Gane Ka-Shu [8], Graham, Sean W. [9], Mathews, Sarah [10].

Nuclear phylogenomics of the seed plants.

The living seed plants – angiosperms, cycads, gnetophytes, Ginkgo biloba, Pinaceae, and cupressophyte conifers – comprise six disparate clades that represent a small proportion of the major lineages that have existed through time. Reconstructing the history of seed plants accurately remains challenging due to extinction and the divergence ages of living taxa. Phylogenomics approaches, to address relationships among living seed plants, yield trees with strong backbone support, but analyses of nuclear and plastid phylogenomic matrices yield trees that conflict with respect to the position of the gnetophytes, Ephedra, Gnetum, and Welwitschia. Nuclear data place them with Pinaceae, plastid data with cupressophytes. It is unclear whether this indicates different histories of nuclear and plastid genes, whether one tree is erroneous, or whether both are. We are exploring the phylogenetic signals in a nuclear phylogenomics matrix of 502 putatively orthologous regions mined from gymnosperm transcriptome assemblies produced by the 1KP project and from published angiosperm genomes. To explore signal and conflict among partitions, we are using a variety of approaches, including tree- and character-based tests for incongruence among data partitions and the comparison of different partitioning and modeling approaches.

1 - College of William and Mary, Biology, Williamsburg, VA, 23187
2 - University of British Columbia, Vancouver, BC
3 - Fairy Lake Botanical Garden, Shenzen, China
4 - University of Alberta, Edmonton, AL, Canada
5 - University of Georgia, Department of Plant Biology, Athens, GA, USA
6 - The NY Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
7 - Royal Botanic Garden Edinburgh, Edinburgh, UK
8 - University of Alberta, Biological Sciences; Medicine (Gastroenterology), CW405 Biological Sciences, Edmonton, AB, T6G 2E9, Canada
9 - University of British Columbia, Department of Botany, Vancouver, BC, V6T 1Z4, Canada
10 - CSIRO National Research Collections Australia, The Australian National Herbarium, Canberra, ACT, 2601, Australia

Keywords:
seed plant
gymnosperm
Phylogeny
species tree
Transcriptome
phylogenomics.

Presentation Type: Colloquium Presentations
Session: C1
Location: Salon 4/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 9:45 AM
Number: C1008
Abstract ID:1028
Candidate for Awards:None