Cranston Evolution 2013
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Transcript of Cranston Evolution 2013
Karen CranstonNational Evolutionary Synthesis Center
@kcranstn / @opentreeoflifehttp://www.slideshare.net/kcranstn
opentreeoflife.org
Gordon BurleighKeith CrandallKaren Cranston
Karl GudeDavid HibbettMark Holder
Laura KatzRick Ree
Stephen SmithDoug Soltis
Tiffani Williams
What does it mean to “have” the tree of life?
complete & dynamic
browse, download, query
use for research questions
implies digital access
Open Tree of Life
Taxonomy + Source trees
•filter / weight input trees• combine into synthetic tree
• feedback • input new data sets
~ 4% of all published phylogenetic trees
Stoltzfus et al 2012
Inputs: Phylogenetic data
Archiving sequence data is a community norm
Heroic data collection effortsSurveyed >7000 phylogenetic studies in plants, fungi and animals, unicellular organisms
Result: data for >2300 studies, >4800 trees
Poster P133003 tonight!
Inputs: Taxonomies
Large fraction of species not represented in phylogenies
taxonomy provides backbone & coverage at tips
2,644,685 names: NCBI (structure) + GBIF (completeness)
https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-Taxonomy
Synthesis process
Source trees(Phylografter) Data storage &
synthesis(treemachine)
OpenTree: visualize, comment, search,
downloadTaxonomies
(taxamachine)
Source tree management
phylografter.opentreeoflife.org
Synthesizing trees and taxonomies
Graph database for phylogenies (treemachine) and taxonomy (taxomachine)
Allows for extremely efficient storage and retrieval
Rules to extract binary tree from highly conflicting graph
More details? Stephen Smith 8:30 am Monday!
OpenTree browser
dev.opentreeoflife.org/opentree
Public tree of life
publictreeoflife.com/tree
“Open” Tree of Life
Collaborations
providing images and text for public tree
developing methods for subtree extraction
summer student providing links to ToLWeb pages
treeviz project from U Indiana MOOC, GNOME summer intern
partner for data archiving / harvest
August 2013 release
Year 2 & 3 goalsRefine draft tree based on user feedback / new data
Research into phylogenetic synthesis
User features
How does my tree compare with others?
Synthesis on demand
Quantifying / visualizing conflict
Suggestions?
Gordon BurleighKeith CrandallKaren Cranston
Karl GudeDavid HibbettMark Holder
Laura KatzRick Ree
Stephen SmithDoug Soltis
Tiffani Williams