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