Lecture/Exercise 5.3 →
Applying all of this to your data
Marguerite Butler, Brian O’Meara, Samantha Price, Josef Uyeda, Steve Arnold, and Joe Felsenstein
This session consisted of small group discussions about individual topics chosen by the participants, about methods applicable to their data.
Lecture/Exercise 5.2 →
Phylogenetic natural history: uniting data-driven and hypothesis testing frameworks
Format: PPT, PDF, DPS
Lecture/Exercise 5.1 →
Making sense of your output: assessing confidence in model selection and parameters
Some thoughts on development and limitations on applying the OU models, and some recommendations on how to interpret results.
Testing Adaptation with Evolutionary Models
Massive Simulation Take Aways
A Few References
Ané C. 2008. Analysis of comparative data with hierarchical autocorrelation. Ann. Appl. Stat. 2:1078–1102.
Boettiger C., Coop G., Ralph P. 2012. Is your phylogeny informative? Measuring the power of comparative methods. Evolution 66: 2240–2251.
Bonine K.E., Gleeson T.T., and Garland T. 1999. Sprint performance of phrynosomatid lizards, measured on a high-speed treadmill, correlates with hindlimb length. J. Zool. 40: 1–18.
Cressler C., Butler M.A., and King A. A. 2015. Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model. Sys. Bio. 64(6):953-968. DOI: 10.1093/sysbio/syv043
Ho L.S.T., Ané C. 2013. Asymptotic theory with hierarchical autocorrelation: Ornstein-Uhlenbeck tree models. Ann. Stat. 41:
Scales J.A., King A.A., and Butler M.A. 2009. Running for your life or running for your dinner: What drives fiber type evolution in lizard locomotor muscles? Am. Nat. 173: 543–553.
Lecture/Exercise 4.6 →
Measurement error, identifiability, and model adequacy
Presentation: PDF and Powerpoint
You may need to install the following packages:
install.packages(c(“OUwie”, “plyr”, “knitr”, “ggplot2”, “rmarkdown”))
You can create the object using the knit button in an Rstudio window or rmarkdown::render(“MeasurementError.Rmd”) in R.
Lecture/Exercise 4.5 →
Accounting for sexual radiation with coevolutionary models & OUwie
Stevan J. Arnold
Arnold & Houck 2016
Arnold & Houck 2016 Suppl Figs
Lecture/Exercise 4.3 →
Morphometrics and phylogenies
Lecture/Exercise 4.2 →
Long-term and short-term evolution
Lecture/Exercise 4.1 →
OU processes on phylogenies and their interpretation
Marguerite Butler and Brian O’Meara
Butler: Testing Hypotheses of Evolution by Varying the Model
- Gain appreciation for how models can be used to test evolutionary hypotheses
- Building intuition about BM and OU processes by making your own simulations
- adding stochastic components to trait values through discrete time (sigma)
- adding trends toward optimal values (theta and alpha)
- adding branching
- changing the parameters along the tree
Notes: R_BM_OUCH_minitutorial.pdf chapter 3
ou2drgl.R (optional, extra)
- Understand connection between OU methods
- Be able to compare models
- Understand potential problems with your particular analysis (more on this tomorrow)
- Parameter estimation for the win!
OUwie: install.packages(“OUwie”) or bleeding edge remotes::install_github(“thej022214/OUwie”).
Presentation: PDF and PowerPoint
O’Meara: Exercise and Answers
Lecture/Exercise 3.3 →
Brownian motion, contrasts and comparative methods
Samantha Price and Joe Felsenstein
First part of Joe Felsenstein’s lecture: Lecture3-2a.pdf
First part of Samantha Price’s lecture: Lecture3-2b.pdf
Second part of Joe Felsenstein’s lecture: Lecture3-2c.pdf
Second part of Samantha Price’s lecture: Lecture3-2d.pdf
For contrasts part of exercise:
Text file of R exercise: constrasts.R
Other functions that this needs: plotmeans.R
Data sets: fishes.1 fishes.2 fishes.3 fishes.4 fishes.5 fishes.6 fishes.7 fishes.8 fishes.9 fishes.10
Trees: intree.1 intree.2 intree.3 intree.4 intree.5 intree.6 intree.7 intree.8 intree.9 intree.10
For Brownian motion on phylogenies exercise:
Text file of R exercise: PhyloBrownian.R
Other functions that this needs: you need the R libraries ape, geiger, phytools and OUwie
Data sets: CetaceaLH.txt