Towards inferring the history of life in the presence of lateral gene transfers. Evolution 2014.

Towards inferring the history of life in the presence of lateral gene transfers

Bastien Boussau

LBBE, CNRS, Université de Lyon

Collaborators

–Gergely Szöllősi (Budapest), –Eric Tannier (LBBE, Lyon), –Nicolas Lartillot (LBBE, Lyon), –Vincent Daubin (LBBE, Lyon)

Gene trees provide confusing signals about species relationships

Boussau, Gueguen, Gouy, BMC Evol. Biol. 2008HOGENOM database

Gene transfers and the quixotic pursuit of the TOL

Doolittle WF,

Science 1999

Gene transfers and the quixotic pursuit of the TOL

Doolittle WF,

Science 1999

Gene transfers and the quixotic pursuit of the TOL

Doolittle WF,

Science 1999

“The monistic concept of a single universal tree appears […] increasingly obsolete. […][It is] no longer the most scientifically productive position to hold[…][It] accounts for only a minority of observations from genomes.”

Bapteste, O’Malley, Beiko, Ereshefsky, Gogarten, Franklin-Hall, Lapointe, Dupré, Dagan, Boucher, Martin, Biology Direct 2009.

Gene transfers and the quixotic pursuit of the TOL

Doolittle WF,

Science 1999

“The monistic concept of a single universal tree appears […] increasingly obsolete. […][It is] no longer the most scientifically productive position to hold[…][It] accounts for only a minority of observations from genomes.”

Bapteste, O’Malley, Beiko, Ereshefsky, Gogarten, Franklin-Hall, Lapointe, Dupré, Dagan, Boucher, Martin, Biology Direct 2009.

“Bien parece, respondió Don Quijote, que no estás cursado en esto de las aventuras”

!"Obviously," replied Don Quijote,

"you don't know much about adventures” Don Quijote, VIII

Can we extract some signal from the noise?Huge amounts of gene tree incongruence in genomic

data

1. What proportion of it is biological (=signal) and what proportion of it comes from our failure to correctly infer gene trees (=noise)?

2. Amid the signal, is there trace of a tree of life?

1-Removing the noise in gene trees

Usual approach

ALE+DTL

RF d

ista

nce

to re

al tr

ee

Szöllősi et al., Syst. Biol. 2013

1-Removing the noise in gene trees

Usual approach

ALE+DTL

Tran

sfer

eve

nts

per f

amily

Usual approach

ALE+DTL

RF d

ista

nce

to re

al tr

ee

Szöllősi et al., Syst. Biol. 2013

2-Amid the signal, is there trace of a tree of life?

• STRALE: • A Bayesian probabilistic method that can interpret thousands of

gene trees in terms of: • speciation events • duplication events (D) • transfer events (T) • loss events (L)

• A method able to estimate the DTL rates • A method able to reconstruct the species tree • A method able to order the nodes of the species tree

Using transfers to date clades

?T IM E

Using transfers to date clades

?T IM E

Using transfers to date clades

?T IM E

Using transfers to date clades

?T IM E

Using transfers to date clades

?T IM E

Because we can identify gene transfers, we have information for ordering the nodes of a species tree

Simulation to test the species tree reconstruction• 20 species • 200 gene families

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Simulated Inferred

Can we recover DTL rate heterogeneity among families?

• Simulation: • 10 species ; 100 gene families per rate category • 4 rate categories drawn from a Gamma distribution

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Rate category

Rat

e

Simulated DTL rate

Infe

rred

DTL

rat

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Application to 36 Cyanobacteria

PROM3

SYNE7

TRIEI

CYAA5

ACAM1

NOSP7

PROM9

PROM5

CYAP4

SYNPX

SYNP6

CYAP8

SYNS9

ANAVT

SYNPW

PROMS

SYNY3

SYNS3

SYNSC

GLVIO1

SYNR3

SYNJA

THEEB

PROM2

CYAP7

PROM0

PROMT

MICAN

SYNJB

PRMAR1

PROMM

PROM4

SYNP2

PROMP

ANASP

PROM1

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Szöllősi et al., PNAS 2012

1099 gene families

Conclusion, perspectives

• STRALE: • A Bayesian probabilistic method that can interpret thousands of

gene trees with DTL events and reconstruct a time-ordered species tree

• Currently undergoing tests • Can run on thousands of gene families (parallel architecture) • Will be open access • Can run on dozens of species

Postdocs wanted!

Thank you!

• Organizers of Evolution 2014!

• LBBE collaborators (Lyon and Budapest):

–Gergely Szöllősi, –Eric Tannier, –Nicolas Lartillot –Vincent Daubin,

Postdocs wanted!