Neontology & Paleontology

A uniﬁed framework for inferring phylogenies with fossils

joint work with Tracy Heath & John Huelsenbeck

Tanja Stadler Computational Evolution group — Department of Biosystems Science and Engineering [email protected] Combining molecular and fossil data

ACACACCC Species1 ACACACCC Classic Species2 TCACACCT TCACACCT phylo- Species3 AAAGACTT AAAGACTT genetics Species4 ACAGACTT ACAGACTT

2 Combining molecular and fossil data

ACACACCC Species1 ACACACCC Classic Species2 TCACACCT TCACACCT phylo- Species3 AAAGACTT AAAGACTT genetics Species4 ACAGACTT ACAGACTT

Prior for each fossil calibration point Fossil Yang & Rannala (MBE, 2006) calibration Heath (Syst. Biol., 2010) Time

3 Combining molecular and fossil data

ACACACCC Species1 ACACACCC Classic Species2 TCACACCT TCACACCT phylo- Species3 AAAGACTT AAAGACTT genetics Species4 ACAGACTT ACAGACTT

Prior for each fossil calibration point Fossil Yang & Rannala (MBE, 2006) calibration Heath (Syst. Biol., 2010) Time

Non-mechanistic models for speciation-extinction-fossilization

Limitation Prior for each fossil to deﬁne Speciation and extinction rates cannot be estimated from trees with fossils 3 The birth-death model as a model for speciation, extinction and fossilization

• stem age of a clade t λ μ • speciation rate λ Species • extinction rate μ Birth-death • fossil-observation rate ψ model • sampling probability ρ ψ

Stadler (JTB, 2010) 4 The birth-death model as a model for speciation, extinction and fossilization

• stem age of a clade t λ μ • speciation rate λ Species • extinction rate μ Birth-death • fossil-observation rate ψ model • sampling probability ρ ψ

Phylo- genetic trees

complete phylogeny Stadler (JTB, 2010) 4 The birth-death model as a model for speciation, extinction and fossilization

• stem age of a clade t λ μ • speciation rate λ Species • extinction rate μ Birth-death • fossil-observation rate ψ model • sampling probability ρ ψ

Phylo- genetic trees

complete phylogeny reconstructed phylogeny Stadler (JTB, 2010) 4 The birth-death model as a model for speciation, extinction and fossilization

• stem age of a clade t λ μ • speciation rate λ Species • extinction rate μ Birth-death • fossil-observation rate ψ model • sampling probability ρ ψ

t Lik ( ) Phylo- genetic trees

complete phylogeny reconstructed phylogeny Stadler (JTB, 2010) 4 Combining molecular and fossil data: Likelihood of the phylogeny

1 4λρ 4λρ p(y )q(y ) If ψ 2λ f f Lik ( ) = λ(1 − p0(x0)) q(x0) q(xi) q(zf ) i∈V f∈F

Stadler (JTB, 2010) 5 Calibrating molecular phylogenies using the fossilized birth-death (FBD) model

Heath, Huelsenbeck, Stadler (PNAS, 2014) 6 Calibrating molecular phylogenies using the fossilized birth-death (FBD) model

We sample all fossil attachments and λ, μ, ψ in an MCMC using our likelihood function (ρ=1)

Heath, Huelsenbeck, Stadler (PNAS, 2014) 6 Simulation study

Trees on 25 extant species were simulated with: Turnover: μ/λ = 0.5 Net diversiﬁcation rate: λ-μ = 0.01 Fossilization rate: 0.1, Observation: 10% ψ = 0.01

Heath, Huelsenbeck, Stadler (PNAS, 2014) 7 Simulation results

Heath, Huelsenbeck, Stadler (PNAS, 2014) 8 Simulation results

Heath, Huelsenbeck, Stadler (PNAS, 2014) 8 More fossils yield smaller credible intervals

Observation

Heath, Huelsenbeck, Stadler (PNAS, 2014) 9 What about model violations in fossilization / observation?

Heath, Huelsenbeck, Stadler (PNAS, 2014) 10 Biased fossil sampling

Heath, Huelsenbeck, Stadler (PNAS, 2014) 11 Stratographic fossil sampling

Heath, Huelsenbeck, Stadler (PNAS, 2014) 12 What about model violations in extant species sampling?

Outgroup collapsed

Deep nodes (young speciation events pruned)

Heath, Huelsenbeck, Stadler (PNAS, 2014) 13 What about model violations in extant species sampling?

Outgroup collapsed

Deep nodes (young speciation events pruned)

Heath, Huelsenbeck, Stadler (PNAS, 2014) 13 Data analysis: Dating the phylogeny of bears

Heath, Huelsenbeck, Stadler (PNAS, 2014) 14 Summary

All fossils can be used Calibrating No arbitrary priors for each calibration node phylogenies Very robust towards model misspeciﬁcation (biased fossil and extant species sampling)

15 Summary

All fossils can be used Calibrating No arbitrary priors for each calibration node phylogenies Very robust towards model misspeciﬁcation (biased fossil and extant species sampling)

Add Work in progress morpho- RevBayes logical Beast v2.0 information

15 Summary

All fossils can be used Calibrating No arbitrary priors for each calibration node phylogenies Very robust towards model misspeciﬁcation (biased fossil and extant species sampling)

Add Work in progress morpho- RevBayes logical Beast v2.0 information

Model unifying processes leading to paleontological and Fossilized neontological data birth-death Allows to estimate speciation and extinction rates from model phylogenies with fossils 15 Phylogeny of Acknowledgements

Paper: Heath, Huelsenbeck, Stadler (PNAS, 2014)

DPPDiv: github.com/trayc7/FDPPDIV BEAST2: beast2.cs.auckland.ac.nz/ RevBayes: to come soon!

A. Gavryushkina T. Heath A. Drummond J. Huelsenbeck