2015-05-21 matzke ssb2015 beastmaster v2phylo.wdfiles.com/.../2015-05-21_matzke_ssb2015... ·...
TRANSCRIPT
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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
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BEASTmasteR: big picture
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Fossils
BEASTmasteR: big picture
Dated phylogenies
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Fossils
BEASTmasteR: big picture
Dated phylogenies
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Fossils
BEASTmasteR: big picture
Dated phylogenies
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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
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Fossils
BEASTmasteR: setup
Dated phylogenies
Characters101110110101110110122
Settingsmodels, priors, settings
XML
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BEAST requires XML input
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BEAST requires XML inputXML
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BEAST requires XML inputThe Matrix
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Fossils
BEAST2: BEAUTi
Dated phylogenies
NEXUS101110110101110110122
Beautimodels, priors, settings
XML
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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)
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Fossils
BEAST2: BEAUTi
Dated phylogenies
NEXUS101110110101110110122
Beautimodels, priors, settings
XML
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Fossils
BEASTmasteR: setup
Dated phylogenies
NEXUS101110110101110110122
Excelmodels, priors, settings
XML
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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
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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.
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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.
![Page 18: 2015-05-21 Matzke SSB2015 BEASTmasteR v2phylo.wdfiles.com/.../2015-05-21_Matzke_SSB2015... · Fossil Relatives and Evolutionary History. New York, Columbia University Press. ... reproduce](https://reader034.vdocuments.site/reader034/viewer/2022042219/5ec5489a776f3670184d8ccb/html5/thumbnails/18.jpg)
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.
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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”
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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”
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Slater (2015) mb-uniform, node- calibrations
“Ground truth”
02040Mya: 02040
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“Ground truth”
mb3.2.5uniform, flat priors
02040Mya: 02040
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“Ground truth”
BEASTmasteR Beast2 BDSS, flat priors
02040Mya: 02040
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“Ground truth”
BEASTmasteR Beast2 SABD, flat priors
02040Mya: 02040
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“Ground truth”
mb3.2.5BDSS (fossilized BD) flat priors
02040Mya: 02040
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“Ground truth”
mb3.2.5SABD (fossilized BD) flat priors
02040Mya: 02040
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“Ground truth”
mb3.2.5SABD (fossilized BD) flat priors
02040Mya: 02040
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“Ground truth”
mb3.2.5SABD (fossilized BD) flat priors
02040Mya: 02040
Uh-oh! Wild dogs in the extinct Borophagines!
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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)