5 to 100 million species of organisms on Earth

All organisms on Earth are genetically related

“Tree of Life”

Bacteria

Archaea

Eukaryotes

All organisms are genetically related

PHYLOGENY

History of lineages changing through time

NSF Assembling the Tree of Life (ATOL) Program

http://atol.sdsc.edu

“Increased knowledge of phylogenetic relationships will improve human health, push the frontiers of comparative developmental biology, meet threats to agriculture and forestry from invasive species and pests, and improve management of our natural resources.”

http://tolweb.org

Scientific Core Content

> 6000

web pages with scientific content

> 500 scientific contributors

Most pages are still under construction…

> 6000

web pages with scientific content

Some content is provided by amateur contributors

> 6000

web pages with scientific content

> 200

treehouses (learning materials)

> 20,000

images, videos, audio files

The structure of the Tree of Life web site

illustrates phylogenetic relationshipsLife on Earth

Rosa davuricaBembidion zephyrum

Eukaryotes

Insects

Branch pages

Leaf pages

http://tolweb.org

HomoplasyThe Scourge of Phylogentic Biologists!

Homoplasy in Sequence Data:Long Branch Attraction

A

B C

D D

CB

A

Reconstructed TreeTrue Tree

many informative changes

fewinformative changes

How to avoid long branch attraction?

• Exclude long-branch taxa

• Exclude characters that show evidence of excessive homoplasy

• Use other inference methods that take branch lengths into account

• Split long branches by adding more taxa