Phyloinformatics Research
Integrating local and distributed data on the Tree of Life
AToL has employed the first of the "next generation sequencers", the 454 Life Sciences
GS20/FLX platform, to sequence 36 flowering plant plastid genomes (Moore et. al. 2007). The 454 sequencer
produces highly accurate and complete plastid genome sequence at great savings of time and money over
traditional shotgun sequencing (Moore et. al. 2006). With genome-scale data, the most difficult
relationships among major groups of angiosperms can now be addressed, resulting in a new era of
great promise for resolving the remaining thorny nodes in the angiosperm branch of the Tree of Life.
The angiosperm AToL group, along with other Tree of Life groups, collaborates in TOLKIN, an informative management
and analytical web application for phylodiversity and biodiversity research. This application allows
collaborators in different locations to access shared data on voucher specimens, taxonomy, bibliography,
morphology and DNA samples and sequences.
TOLKIN generates external data to resources such as International Plant Names Index, Global
Biodiversity Information Facility, Tropicos, GenBank, Index Nominum Genicorum, TreeBASE and BioGeomancer,
where users are able to see a summary of sequencing activities.
Tolkin also provides a workbench functionality for analysis of sequence data by automating the assemblage
of Fasta files, BLASTing capability, multiple sequence alignments, output of Nexus Files, and automating
deposit of digital data to repositories such as GenBank.
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Outreach
Use of the AToL Grant has enabled the following activities
Public education through the new family-friendly exhibit, Travels in the Great Tree of Life (Peabody
Museum of Natural History, Yale University), and through First Flower, part of the PBS television
series NOVA (April 2007)
Training for postdocs, graduate, and undergraduate students, especially underrepresented groups, that focus on
interdisciplinary training, combining phylogenetic, genomic, and evolutionary biology
AToL experience gained by PIs is used in their academic courses and to update the widely used
book, Plant Systematics: A Phylogenetic Approach
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