BYUDepartment
of Biology 
Biology 559R: Introduction to Phylogenetic Comparative
Methods
Instructor 
Juan C. Santos, Postdoctoral Fellow Office: LSB 4136 Phone: 8014224398 email: infraguttatus@gmail.com Office Hours: by appointment 
Term 
Winter (2015) 
Times 
TTh,
2:00 – 2:50 p.m. 
Room 
2142 LSB (2nd floor LSB) 
Credits 
2 credits 


Prerequisites 
A graduatelevel course in ÔPhylogenetic SystematicsÕ and basic knowledge of R scripting (recommended) 
Course Description
This course is a Ôhands onÕ practice and
application of phylogenetic comparative methods. For this purpose, I will
introduce different statistical and quantitative methods for analyzing
character evolution and ecological and evolutionary processes along
phylogenetic trees. We will use different R packages and other freely
available software that allow us to analyze and retrieve data from online
repositories, but students are also encouraged to use their own research data
for this purpose. The statistical and theoretical foundations of techniques
will be discussed, but the emphasis of this course is on the analysis,
visualization and implementation of the current comparative methodologies.
The main topics include: (1) brief introduction to R scripting and
environment, (2) data retrieval from online databases for the construction of
phylogenetic trees, (3) sequence alignment and phylogenetic inference, (4)
tree manipulation and visualization, (5) ancestral state reconstruction, (6)
diversification analyses and trait evolution inferences, (7) tree and data
simulations, and (8) multivariate comparative methods. The list of R packages
and software that we will review and implement are provided below. Students
will conduct a course project based on their own datasets and prepare a final
report and presentation. 
Course Format
The course will consist of lab sessions during each class with an
introduction of the methodologies and a brief discussion of relevant key
literature. During the first nine classes, students will develop and present
a work plan for their course projects using their own data. Subsequent
meetings will cover additional topics with the opportunity for the students
to request practice of specific methodologies in support of their projects.
For suggestions about methods, you are encouraged to visit the CRAN Task
View: Phylogenetics, Especially Comparative Methods
(http://cran.rproject.org/web/views/Phylogenetics.html). The final evaluation will be studentled presentations of
their projects and a written report in manuscript format.

*2142 LSB
(computer room) is equipped with PC computers, but most of software runs at
its best in MAC OS systems. Students are encouraged to bring their own
computer to the lab. 
Prerequisites
Students should have had at least one upperlevel course in Evolutionary Biology or ÔPhylogenetic SystematicsÕ. It is also recommended some basic univariate statistics methods and knowledge of statistical inference, but these latter components are not a requirement. The instructorÕs consent is required after discussing possible course projects, as students need to have a suitable dataset for their final projects. 
Textbooks
There are no required textbooks and all course material will be
provided as pdf files. Students are encouraged to
read the manuals of each software or R package. However, the following
reference may be useful for the course:

Emmanuel Paradis (2012) Analysis of Phylogenetics and Evolution with R. Second Edition.
Springer. ISBN 9781461417422*

*This book is available to download at the Harold B. Lee Library 
Grading

Total Grade (%) 
Due Date 
Participation (showing up in class, asking
questions, participating in the discussions) 
20 

Project Proposal (510 minute presentation) 
10 
Feb5 
Final Presentation (1015 minute
presentation) 
20 
Apr 9
and Apr 14 
Final Project Report 
50 
Day of
presentation 
Course Topics and Schedule 
Date 
Topic 
Software and R packages 
Presentation 
Data 
References 
Jan 6 
Introduction to R and comparative methods 

Jan 8 
Introduction to R basic functions 

Jan 13 
Getting sequences from GenBank (manually)
and BLAST 


Jan 15 
Getting sequences from GenBank into R 


Jan 20 
Alignment: Simultaneous alignment
and tree estimation 

Jan 22 
Alignment visualization and
manipulation 


Jan 27 
Statistical estimation of models of sequence evolution 

Jan 29 
Implementation of models of
sequence evolution and phylogenetic inference 

Feb 3 
Chronogram estimation: Penalized Likelihood Approach 

Feb 5 
Project proposal
presentation 
 
 
 
 
Feb 10 
Chronogram estimation: BEAST 

Feb 12

Tree visualization, plotting 
R_commands 


Feb 17 
NO CLASS  
Feb 19 
Data retrieval, supertrees and data concordance 

Feb 24 
Ancestral
state reconstruction (discrete)

'ape’

data1, data2, data3, data4


Feb 26 
Ancestral state
reconstruction (continuous)

'ape’

data1, data2, data3, data4


Mar 3 
Tree simulations

'ape’



Mar 5 
Ancestral state
reconstruction (Threshold models)

data1, data2, data3, data4,


Mar 10 
Diversification
analysis: BiSSE (MLE) based models


Mar 12 
Diversification
analysis: BiSSE (Bayesian) based models


Mar 17 
Trait
evolution: Correlation analyses (discrete traits)

'phytools', 'corHMM', 
data1, data2, data3, data4, R_commands


Mar 19 
Trait
evolution: Correlation analyses (continuous traits)

‘caper’


Mar 24 
Trait
evolution: Correlation analyses (discrete with continuous traits)

‘caper’,

data1, data2


Mar 26 
Open Class: Project Preparation in class 








Mar 31 
Taxonomy, geographic records, and multivariate methods (e.g., PPCA) 
'ape’



Apr 2 








Apr 7 
Cluster fun:
Running programs and jobs


Apr 9 
Student presentations of
final project 
 
 
 
 
Apr 14 
Student presentations of
final project 
 
 
 
 
Printable version of this
syllabus: PDF