PS 2019 Short Course: QUANTITATIVE METHODS IN PHYLOGENETIC PALEOBIOLOGY

There has been considerable development of Bayesian and likelihood methods for assessing phylogenetic relationships in recent years. This includes advances in probabilistic models of anatomical character evolution and models of assessing tree probabilities given diversification and sampling rates. The 2019 Paleontological Society Short Course will be a day-long workshop-style short course that will feature not just lectures about methodological advances, but also hands-on exercises for the audience members to perform on their laptop computers. The work shop is being organized and run by David Bapst, Sandy Carlson, Laura Soul, Peter Wagner, Rachel Warnock, April Wright & David Wright.

We are designing the short course so that novices can learn not only about the current methods for modeling character change and divergence times, but also can learn tactics for recognizing characters and delimiting character states on fossils. The short course also should provide a "refresher" course for more experienced workers who have conducted phylogenetic analyses with parsimony and other methods. Moreover, we intend the short course to be useful for paleontologists who do not do phylogenetics themselves, but who mentor students or collaborate with colleagues that do.

 Exercises will be conducted using RevBayes; the relevant workshop materials & tutorials are all developed online (http://revbayes.com). We strongly encourage participants to download these materials before the short course: although there will be Internet access at the convention center, we cannot guarantee that it will be fast enough for people to download files on site.

 The workshop will take place at the Sheraton Grand Phoenix Hotel (two blocks from the Convention Center) on Saturday the 21st of September 8:00 - 17:00 (with several short breaks and a lunch break). A short workshop for installing relevant software will be held Friday late afternoon to early evening at the Convention center, with the exact times and location to be announced. We emphasize that because this short course is being conducted as a workshop rather than a day-long symposium, attendees will get the most out of the course by attending the entire session.

Organizers and presenters:  David Bapst, Sandra Carlson, Laura Soul, Peter Wagner, Rachel Warnock, April Wright, and David Wright.

Schedule:

  • 08:00 AM - Module 1 - Introduction: Tree-Thinking:  Sandy Carlson and Pete Wagner
  • 08:15 AM - Module 2 - Meet Our Data: Smith and Zamora, 2009:  Davey Wright
  • 08:25 AM - Module 3 - Morphological Character Coding:  Davey Wright, Pete Wagner
  • 09:00 AM - Module 4 - Intro to RevBayes, Graphical Modeling:  April Wright
  • 09:45 AM - BREAK (15 min)
  • 10:00 AM - Module 5 - Tripartite Model 1: Morphological Character Change Models: April Wright and Pete Wagner
  • 12:00 PM - LUNCH (1.5 hour)
  • 01:30 PM - Module 6 - Tripartite Model 2: Clock Models for Character Change:  Davey Wright
  • 02:00 PM - Module 7 - Tripartite Model 3: Fossilized Birth Death:  Dave Bapst
  • 03:30 PM - BREAK (15 min)
  • 03:45 PM - Module 8 - Worked Example with Phylogenetic Comparative Methods:  Laura Soul and Davey Wright (see https://revbayes.github.io/tutorials/chromo/)
  • End-of-Day Summary

Readings:  Attendees will be asked to read three overviews of the field beforehand:
Holder, M., and P. O. Lewis. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat    Rev Genet 4(4):275-284.
Wright, A. M. 2019. A Systematist’s Guide to Estimating Bayesian Phylogenies From Morphological Data. Insect Systematics and Diversity 3(3)
https://academic.oup.com/isd/article/3/3/2/5519658 Preprint Here: https://paleorxiv.org/jupva
Wright, D. F. 2017. Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata). Journal of Paleontology 91(4):799-814.

Elements of Paleontology contributions resulting from the 2019 Short Course:

• Understanding the Tripartite Approach to Bayesian Divergence Time Estimation
Rachel C. M. Warnock  and April M. Wright
https://www.cambridge.org/core/elements/abs/understanding-the-tripartite-approach-to-bayesian-divergence-time-estimation/BE50345449E2EC8A1EBAB7CFB1D74400

• Phylogenetic Comparative Methods: A User's Guide for Paleontologists
Laura C. Soul and David F. Wright
https://www.cambridge.org/core/elements/abs/phylogenetic-comparative-methods-a-users-guide-for-paleontologists/973B90CCB6F4B9E07CE23793F1E4D1AD

• Testing Character Evolution Models in Phylogenetic Paleobiology. A case study with Cambrian echinoderms
April M. Wright, Peter J. Wagner, and David F. Wright
https://www.cambridge.org/core/elements/abs/testing-character-evolution-models-in-phylogenetic-paleobiology/BE1C4EE27EAFAA3FD1025191892FCC87