Tip-­‐da'ng  with  fossils  in  Beast2,    using  R  to  convert  NEXUS  data  

files  to  XML  input

Nicholas  J.  Matzke Na1onal  Ins1tute  of  

Mathema1cal  and  Biological  Synthesis

(NIMBioS,  www.nimbios.org)

BEASTmasteR:

SSB2015.  1:30  pm,  session  C,  Michigan  Union,  Pendleton  room.

Thanks  to:  April  Wright,  Brian  O’Meara,  Jeremy  Beaulieu,  Remco  Boukaerrt,  Alex  Pyron,  Michael  Lee

BEASTmasteR: big picture

Fossils

BEASTmasteR: big picture

Dated phylogenies

Fossils

BEASTmasteR: big picture

Dated phylogenies

Fossils

BEASTmasteR: big picture

Dated phylogenies

Tip-dating: your optionsMrBayes Beast1 Beast2

Setup easy hard hard*

Tree models uniform, BDSS, SABD

BDSSonly BDSS, SABD

New features some no many

flexible no sorta yes

Works? sorta yes yes

Fossils

BEASTmasteR: setup

Dated phylogenies

Characters101110110101110110122

Settingsmodels, priors, settings

XML

BEAST requires XML input

BEAST requires XML inputXML

BEAST requires XML inputThe Matrix

Fossils

BEAST2: BEAUTi

Dated phylogenies

NEXUS101110110101110110122

Beautimodels, priors, settings

XML

Fossils

BEAST2: BEAUTi

Dated phylogenies

NEXUS101110110101110110122

Beautimodels, priors, settings

XML

1. Importing NEXUS morphology

2. Tip dates, tip-date priors

3. Clade constraints and node age priors

4. Saving. Re-loading. Changing stuff.

5. Remembering everything.

6. Not making mistakes. Not crashing.

Things that are hard in BEAUTi (* although it’s always being updated)

Fossils

BEAST2: BEAUTi

Dated phylogenies

NEXUS101110110101110110122

Beautimodels, priors, settings

XML

Fossils

BEASTmasteR: setup

Dated phylogenies

NEXUS101110110101110110122

Excelmodels, priors, settings

XML

Fossils

BEASTmasteR: things that are easy

Dated phylogenies

NEXUS101110110101110110122

Excelmodels, priors, settings

XML

1. Importing NEXUS morphology (discrete or continuous)

2. Tip dates, tip-date priors 3. Clade constraints and node age priors 3a. Changing priors, e.g. to Normal

4. BDSS, Sampled Ancestors, Skyline setup

5. Relative priors

6. Saving/loading/changing

BEASTmasteR: test

Example: Can we reproduce the

expert phylogeny of North American fossil Canidae?

Wang, X.T., Richard H. 2008 Dogs: Their Fossil Relatives and Evolutionary History. New York, Columbia University Press.

BEASTmasteR: test

Example: Can we reproduce the

expert phylogeny of North American fossil Canidae?

Wang, X.T., Richard H. 2008 Dogs: Their Fossil Relatives and Evolutionary History. New York, Columbia University Press.

BEASTmasteR: test

Example: Can we reproduce the

expert phylogeny of North American fossil Canidae?

Wang, X.T., Richard H.; Taylor, Beryl E. 1999 Phylogenetic systematics of the Borophaginae. Bulletin of the ANMH 243, ! 1-391.

BEASTmasteR: test

Example: Can we reproduce the

expert phylogeny of North American fossil Canidae?

Wang, X. 1994 Phylogenetic systematics of the ! Hesperocyoninae(Carnivora, Canidae). Bulletin of the AMNH 221, 1-207.!Wang, X.T., Richard H.; Taylor, Beryl E. 1999 Phylogenetic ! systematics of the Borophaginae. Bulletin of the ANMH 243, ! 1-391.!Tedford, R.H.W., Xiaoming; Taylor, Beryl E. 2009 Phylogenetic ! systematics of the North American fossil Caninae (Carnivora, ! Canidae). Bulletin of the AMNH 325, 1-218.!

Digitized using TreeRogue, from:

“Ground truth”

BEASTmasteR: test

Example: Can we reproduce the

expert phylogeny of North American fossil Canidae?

Slater, G.J. 2015 Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution. Proceedings of the National Academy of Sciences 112, 4897-4902.

Character data from Slater (2015):

“Ground truth”

Slater (2015) mb-uniform, node- calibrations

“Ground truth”

02040Mya: 02040

“Ground truth”

mb3.2.5uniform, flat priors

02040Mya: 02040

“Ground truth”

BEASTmasteR Beast2 BDSS, flat priors

02040Mya: 02040

“Ground truth”

BEASTmasteR Beast2 SABD, flat priors

02040Mya: 02040

“Ground truth”

mb3.2.5BDSS (fossilized BD) flat priors

02040Mya: 02040

“Ground truth”

mb3.2.5SABD (fossilized BD) flat priors

02040Mya: 02040

“Ground truth”

mb3.2.5SABD (fossilized BD) flat priors

02040Mya: 02040

“Ground truth”

mb3.2.5SABD (fossilized BD) flat priors

02040Mya: 02040

Uh-oh! Wild dogs in the extinct Borophagines!

Try  it  at:phylo.wikidot.com  

/beastmaster

Conclusions1. Makes tip-dating easier. 2. Helps customize 3. R graphics 4. Think critically about models!!! (esp. mb-unif, SABD)