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BEASTmasteR Workshop Description
Workshop Title: BEASTmasteR: An R package for designing phylogenetic dating analyses in Beast2, including dated fossils as tips
Workshop Summary: This workshop will introduce participants to new computational methods that allow joint inference of phylogenetic relationships and divergence times. In older dating methods, fossil relationships were estimated with an undated cladistic or Bayesian analysis, and then these fossils were converted, usually subjectively, into prior probability distributions on the dates of certain nodes. These calibrations were then used in molecular clock analyses to date molecular trees. This procedure essentially “threw away” hard-won fossil data (and any living morphology data as well) once the dating calibration was produced.
However, recently, several programs have become available that allow "tip-dating" — the addition of fossil and living morphology, as well as fossil dates, to dating analyses (e.g., MrBayes, original BEAST, and Beast2). In these methods, the phylogenetic relationships of the fossils and living taxa are estimated simultaneously with the dating of the tree. These methods have the potential to revolutionary for paleontologists as well as neontologists with access to fossil data. First, because character and dating data from fossil specimens are a requirement for the method, paleontologists and morphologists will have an increased role to play in future divergence time analyses, previously the domain of molecular biologists. Second, the joint estimation of fossil relationships and the divergence times of fossil taxa is of intrinsic interest, and many phylogenetic comparative methods can be applied to fossil data once statistically-estimated, time-scaled trees of fossil taxa are available.
As tip-dating methods are still in development, they are less easy to set up and run than traditional phylogenetic analyses. This workshop focuses on Beast2, which has the most options and flexibility for implementing new tree models (e.g., the Birth-Death Serial Sampling Skyline Model, BDSKY; and the Sampled Ancestor Birth-Death Serial Sampling Skyline Model, SABDSKY), as well as models for relaxed morphological clocks, implementation of user-specified priors for including relative dating information, and future extensibility in the form of Beast2 packages.
Beast2 analyses are set up with a complex XML file, and recoding fossil data for this format is virtually impossible by hand. I have written an R package, BEASTmasteR, to automate the conversion of NEXUS data files into Beast2 XML, as well as to implement default settings most useful for fossil tip-dating analyses.
This workshop will guide participants through a BEASTmasteR analysis, and introduce the fundamentals of Bayesian tip-dating analyses, and Beast2 XML. At the end of the workshop, I can help participants with their own data files run the analyses.
We will cover: Basics of Bayesian analysis, introduction to the key models (character/DNA site models, clock models, and tree models), Beast2 XML format, and BEASTmasteR logic, inputs, and analysis.
Requirements: Previous experience with R is helpful, but NOT required. Attendees may wish to bring their own NEXUS data file (and dates or date ranges for each fossil) and run it at the end of the workshop. I have written a short "Intro to R" tutorial which those new to R may work through beforehand.
Equipment: A laptop or desktop computer (people may share; this may be particularly helpful for newbies).
Setup: Setup is not difficult, but is non-trivial and should be attempted before the workshop. In summary, you need to have installed Beast2, Beast2 packages, R, R packages, and Python. Macs come with Python installed, but Windows machines do not. If you hit errors (especially e.g. Windows, or the newest Mac OS X: 10.10), make sure to google the error message. These are all widespread programs, so all of the common installation errors have been encountered by many other people before you, and there is usually an easy solution.
Detailed instructions for BEASTmasteR workshop setup are at: http://phylo.wikidot.com/beastmaster#setup
Links
Special Symposium on Tip-dating: Annual Meeting of the Society for Vertebrate Paleontology, November 2014: Abstracts For Putting Fossils In Trees Symposium
BEASTmasteR website: http://phylo.wikidot.com/beastmaster
References
Alexandrou MA, Swartz BA, Matzke NJ and Oakley TH (2013). "Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae." Molecular Phylogenetics and Evolution 69(3): 514-523. http://dx.doi.org/http://dx.doi.org/10.1016/j.ympev.2013.07.026
Atterholt J and Matzke NJ (2011). "Evolution of life history traits using a dated phylogeny derived from combined-analysis dataset of dinosaurs and birds." Journal of Vertebrate Paleontology 31(3 suppl.): Program and Abstracts, Society of Vertebrate Paleontology Annual Meeting, November 2011, Las Vegas.
Gorscak E and O'Connor P (2013). "Integrating temporal data within a phylogenetic analysis: a Bayesian approach for characterizing divergence estimates in an extinct clade." Journal of Vertebrate Paleontology 33(Society of Vertebrate Paleontology 73rd Annual Meeting Program and Abstracts): 135-136.
Matzke NJ, Wright A, and Bapst D (2014). "Incorporation of Absolute and Relative Fossil Dating Information In Bayesian Tip-Dating Analyses Using the R Package BeastmasteR: Examples From Assassin Spiders, Salmonids, and Hominids." Journal of Vertebrate Paleontology, Program and Abstracts, Society of Vertebrate Paleontology Annual Meeting, November 2014, Berlin. pp. 182-183. http://phylo.wikidot.com/abstracts-for-putting-fossils-in-trees-symposium#talk1
Pyron RA (2011). "Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia." Systematic Biology 60(4): 466-481. http://dx.doi.org/10.1093/sysbio/syr047
Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL and Rasnitsyn AP (2012). "A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera." Systematic Biology 61(6): 973-999. http://dx.doi.org/10.1093/sysbio/sys058
Turner A, Pritchard A, and Matzke NJ (2014). "'Tip-Dating' When All You Have Are Fossils: Comparing Traditional and Bayesian Approaches To Fossil Divergence Times." Journal of Vertebrate Paleontology, Program and Abstracts, Society of Vertebrate Paleontology Annual Meeting, November 2014, Berlin. pp. 242-243. http://phylo.wikidot.com/abstracts-for-putting-fossils-in-trees-symposium#talk12
Wood HM, Matzke NJ, Gillespie RG and Griswold CE (2013). "Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders." Systematic Biology 62(2): 264-284. http://dx.doi.org/10.1093/sysbio/sys092
Wright A, Lloyd G, and Matzke NJ (2014). "Fossils-Only Tip-Dating of Deinonychosaurian Theropods: a Comparison of Methods and Models." Journal of Vertebrate Paleontology, Program and Abstracts, Society of Vertebrate Paleontology Annual Meeting, November 2014, Berlin. p. 258. http://phylo.wikidot.com/abstracts-for-putting-fossils-in-trees-symposium#talk13
BEASTmasteR workshop: Thursday, January 22, 2015, Ludwig Maximilian University of Munich
I am visiting the Ludwig Maximilian University of Munich from Jan. 20-Jan. 24. I am giving this BEASTmasteR workshop, as well as a less formal "pre-workshop" the day before, and visiting with researchers.
Title: BEASTmasteR: An R package for designing phylogenetic dating analyses in Beast2, including dated fossils as tips
Date: Thursday, January 22, 2015
Time: TBA
Building/room: TBA
Location: Department für Geo- und Umweltwissenschaften, Paläontologie & Geobiologie, Ludwig-Maximilians-Universität München
Requirements: R experience helpful but not required
Equipment: Have a computer or share with someone.
Host: Bettina Reichenbacher, Paläontologie & Geobiologie, Ludwig-Maximilians-Universität München
Description and Setup: see BEASTmasteR workshop description
BEASTmasteR workshop: Wednesday, January 14, 2015, University of Helsinki, Finland
I am visiting the University of Helsinki from Jan. 13-Jan. 20. I am giving this BEASTmasteR workshop, a lecture, and then a BioGeoBEARS workshop.
Title: BEASTmasteR: An R package for designing phylogenetic dating analyses in Beast2, including dated fossils as tips
Date: Wednesday, January 14, 2015
Time: 10 a.m. - 4 p.m.
Building/room: TBA
Location: University of Helsinki, Finland
Requirements: R experience helpful but not required
Equipment: Have a computer or share with someone.
Host: Laura K Säilä, Department of Geosciences and Geography / Geosciences Graduate Program / LUOVA , University of Helsinki, Finland
Description and Setup: see BEASTmasteR workshop description
SVP 2014, Berlin: Tip-Dating: Estimating Dated Phylogenies Using Fossils as Terminal Taxa
Note: See the BEASTmasteR code and example scripts!
Tip-Dating: Estimating Dated Phylogenies Using Fossils as Terminal Taxa - FULL
This workshop will introduce participants to new computational methods that allow joint inference of phylogenetic relationships and divergence times. In older dating methods, fossil relationships were estimated with an undated cladistic or Bayesian analysis, and then these fossils were converted, usually subjectively, into prior probability distributions on the dates of certain nodes. These calibrations were then used in molecular clock analyses to date molecular trees. This procedure essentially “threw away” hard-won fossil data (and any living morphology data as well) once the dating calibration was produced.
However, in the last two years, several methods have become available that allow the addition of fossil and living morphology, as well as fossil dates, to dating analyses. In these methods, the phylogenetic relationships of the fossils and living taxa are estimated simultaneously with the dating of the tree. These methods have the potential to revolutionary for paleontologists. First, because character and dating data from fossil specimens are a requirement for the method, paleontologists and morphologists will have an increased role to play in future divergence time analyses, previously the domain of molecular biologists. Second, the joint estimation of fossil relationships and the divergence times of fossil taxa is of intrinsic interest, and many phylogenetic comparative methods can be applied to fossil data once statistically-estimated, time-scaled trees of fossil taxa are available.
The two main methods in use currently are BEAST (Pyron 2011; Wood, Matzke et al. 2013; Alexandrous et al. 2013) and MrBayes 3.3 (Ronquist et al. 2012). Both take more skill and background than traditional phylogeny-estimation and dating methods. Therefore we will guide participants through tutorials and then help them to set up analyses of their own data.
Date: Tuesday, November 4
Time: 10:00am - 4:00pm
Location: The Leibniz Headquarters (Chausseestr. 111, 150 meters away from the Museum für Naturkunde and next to the UBahn station Naturkundemuseum)
Cost: Free (FULL!)
Minimum Number of Participants: 10
Maximum Number of Participants: 40
Leaders:
Nicholas J. Matzke
National Institute for Mathematical and Biological Synthesis
University of Tennessee
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April Wright
University of Texas, Austin
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