IF THIS IS THE FUTURE, WHERE IS MY TREE OF LIFE?

Karen CranstonNational Evolutionary Synthesis Center (NESCent)

@kcranstnhttp://www.slideshare.net/kcranstn

• ~2 million named species

• Millions more unnamed / undiscovered

Tree of life

0"

2000"

4000"

6000"

8000"

10000"

12000"

1978"1979"1980"1981"1982"1983"1984"1985"1986"1987"1988"1989"1990"1991"1992"1993"1994"1995"1996"1997"1998"1999"2000"2001"2002"2003"2004"2005"2006"2007"2008"

Num

ber'o

f'pap

ers'p

ublishe

d'

Year'

Phylogeny'papers,'1978;2008'

Source:"ISI"Web"of"Science""

Rapid"increase"in"applica?ons"of"phylogeny,"beginning"in"early"1990s"

graph from David Hillis

What does it mean to “have” the tree of life?

~4% of all published phylogenetic trees

Archiving sequence data is a community norm

Stoltzfus et al 2012

thermore, a paraphyletic relationship of phorids and syrphidswould support the hypothesis that their shared special mode ofextraembryonic development (dorsal amnion closure) (26)evolved in the stem lineage of Cyclorrhapha and preceded theorigin of the schizophoran amnioserosa.

To test this hypothesis, we used a relatively recent phylogenomicmarker: small, noncoding, regulatory micro-RNAs (miRNAs).miRNAs exhibit a striking phylogenetic pattern of conservationacross the metazoan tree of life, suggesting the accumulation andmaintenance ofmiRNA families throughout organismal evolution

Fig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (!lnL =344155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im-proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Colored squares on terminal branches indicate the presence, in at least one species of a family, of ecological traits as shown to lower left. The numberof origins of each trait was estimated with reference to the phylogeny, the distribution of each trait among genera within a family, and the known biology ofthe organisms.

Wiegmann et al. PNAS Early Edition | 3 of 6

EVOLU

TION

Weigmann et al. PNAS, 2011

“Publishing a tree” = picture in a PDF

Lander et al. Nature 2001

Rod asks: Why do we need a database of trees?

thermore, a paraphyletic relationship of phorids and syrphidswould support the hypothesis that their shared special mode ofextraembryonic development (dorsal amnion closure) (26)evolved in the stem lineage of Cyclorrhapha and preceded theorigin of the schizophoran amnioserosa.

To test this hypothesis, we used a relatively recent phylogenomicmarker: small, noncoding, regulatory micro-RNAs (miRNAs).miRNAs exhibit a striking phylogenetic pattern of conservationacross the metazoan tree of life, suggesting the accumulation andmaintenance ofmiRNA families throughout organismal evolution

Fig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (!lnL =344155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im-proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Colored squares on terminal branches indicate the presence, in at least one species of a family, of ecological traits as shown to lower left. The numberof origins of each trait was estimated with reference to the phylogeny, the distribution of each trait among genera within a family, and the known biology ofthe organisms.

Wiegmann et al. PNAS Early Edition | 3 of 6

EVOLU

TION

assemblyalignmentinference

expertisetime$$$

thermore, a paraphyletic relationship of phorids and syrphidswould support the hypothesis that their shared special mode ofextraembryonic development (dorsal amnion closure) (26)evolved in the stem lineage of Cyclorrhapha and preceded theorigin of the schizophoran amnioserosa.

To test this hypothesis, we used a relatively recent phylogenomicmarker: small, noncoding, regulatory micro-RNAs (miRNAs).miRNAs exhibit a striking phylogenetic pattern of conservationacross the metazoan tree of life, suggesting the accumulation andmaintenance ofmiRNA families throughout organismal evolution

Fig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (!lnL =344155.6169) calculated in RAxML. Circles indicate bootstrap support >80% (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Nodes with im-proved bootstrap values resulting from postanalysis pruning of unstable taxa are marked by stars (black/bp = 95–100%, gray/bp = 88–94%, white/bp = 80–88%). Colored squares on terminal branches indicate the presence, in at least one species of a family, of ecological traits as shown to lower left. The numberof origins of each trait was estimated with reference to the phylogeny, the distribution of each trait among genera within a family, and the known biology ofthe organisms.

Wiegmann et al. PNAS Early Edition | 3 of 6

EVOLU

TION

NSF IDEAS LAB

i. Pre-proposal / application

ii. 5 day highly facilitated workshop

iii. Self-assembly into groups

iv. Pitch high risk proposal ideas at end

v. NSF invited full proposals

• Community assembly of the tree of life (Open Tree of Life)

• Next generation Phenomics (PI O’Leary)

• Arbor: Comparative Analysis Workflows (PI Harmon)

opentreeoflife.org

Karen Cranston, lead PI (Duke)

Gordon Burleigh (Florida)

Keith Crandall (BYU)

Karl Gude (MSU)

David Hibbett (Clark)

Mark Holder (Kansas)

Laura Katz (Smith)

Rick Ree (FMNH)

Stephen Smith (Michigan)

Doug Soltis (Florida)

Tiffani Williams (TAMU)

AVAToL: Assembling, Visualizing and Analysis of the Tree of Life

1. Synthesize a complete draft tree of life from existing phylogenetic trees

1. Synthesize a complete draft tree of life from existing phylogenetic trees

2. Release with:

a. ability to add annotations and upload new data sets

b. areas of uncertainty / conflict

c. links to source data and analysis methods

d. utilities to download whole tree and subtrees

Graph database holding thousands of input trees with

millions of nodes• filter / weight input trees• build synthetic trees

• compare to alternate trees• input new data sets

Dipsicales graphtaxonomy data (578 taxa) +Soltis et al APG III phylogeny (30 taxa)

Dipsicales graph Synthesized tree (favouring phylogenetic branches); contains all 578 taxa

AUTOMATIC UPDATING

update trees with new

sequence data

detect and synthesize newly published trees

• Open Data

• increasing availability of digital data associated with phylogeny publications

• synthetic tree open to community annotation and new data submission

• whole tree / subtrees available for download

?

• Open Science

• project wiki: http://opentree.wikispaces.com/

• open source software: https://github.com/OpenTreeOfLife

• public mailing list, meeting notes, management tools

?

• source / storage of underlying data

• provide complete phylogenetic framework

• link to biodiversity and systematics content

• API for downloading subtrees to analysis tools

opentreeoflife.org

• We’ve only just started (June 1 2012)

• Open to input, feedback and participation:

• join the mailing list & wiki

• add publications to the Mendeley group

• vote / comment on plans on the development boards

• participate in virtual data curation sprint in 2013

opentreeoflife.org

Karen Cranston, lead PI (Duke)

Gordon Burleigh (Florida)

Keith Crandall (BYU)

Karl Gude (MSU)

David Hibbett (Clark)

Mark Holder (Kansas)

Laura Katz (Smith)

Rick Ree (FMNH)

Stephen Smith (Michigan)

Doug Soltis (Florida)

Tiffani Williams (TAMU)

AVAToL: Assembling, Visualizing and Analysis of the Tree of Life