BYU-Department of Biology

 

 

Biology 559R: Introduction to Phylogenetic Comparative Methods

 

Instructor

Juan C. Santos, Postdoctoral Fellow

Office: LSB 4136

Phone: 801-422-4398

e-mail: infraguttatus@gmail.com

Office Hours: by appointment

 

Term

Winter (2015)

 

Times

T-Th, 2:00 – 2:50 p.m.

 

Room

2142 LSB (2nd floor LSB)

 

Credits

2 credits

 

 

 

Prerequisites

A graduate-level course in ‘Phylogenetic Systematics’ and basic knowledge of R scripting (recommended)

 

Course Description

 

This course is a ‘hands on’ 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.r-project.org/web/views/Phylogenetics.html). The final evaluation will be student-led 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 upper-level course in Evolutionary Biology or Phylogenetic Systematics’. It is also recommended some basic univariate statistics methods and knowledge of statistical inference, but these latter components are not a requirement. The instructor’s 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 978-1-4614-1742-2*

 

*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 (5-10 minute presentation)

10

Feb-5

Final Presentation (10-15 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

R webpage

PDF

ref1, ref2

Jan 8

Introduction to R basic functions

plyr’, ‘reshape’, ‘ggplot2’

PDF

data1, data2, data3, R_commands

ref1, ref_card

Jan 13

Getting sequences from GenBank (manually) and BLAST

NCBI-taxonomy

PDF

 

Jan 15

Getting sequences from GenBank into R

ape’, seqinr, rentrez

PDF

data1, data2, data3, R_commands

 

Jan 20

Alignment: Simultaneous alignment and tree estimation

‘Sate-II’

PDF

data1, data2

ref1

Jan 22

Alignment visualization and manipulation

‘Mesquite’

PDF

data1, data2, data3

 

Jan 27

Statistical estimation of models of sequence evolution

'jmodeltest'

PDF

data1, data2, data3, data4

ref1

Jan 29

Implementation of models of sequence evolution and phylogenetic inference

‘Garli-2.0’,'Garli GUI''RAxML',

'RAxML GUI',

'FigTree'

PDF

data1, data2

ref1, ref2 , ref3

Feb 3

Chronogram estimation: Penalized Likelihood Approach

ape’

PDF

data1, data2, data3 R_commands

ref1, ref2

Feb 5

Project proposal presentation

--

--

--

--

Feb 10

Chronogram estimation: BEAST

‘BEAST’

PDF

data4, data5, data6, data7, data8,

ref1

Feb 12

Tree visualization, plotting

'FigTree', ape’ , 'phytools'

PDF

data1, data2 ,

R_commands

Feb 17

NO CLASS        

Feb 19

Data retrieval, supertrees and data concordance

'ape’ , 'geiger', rOpenSci

PDF

data1, data2, data3, data4, data5, R_commands

ref1

Feb 24

Ancestral state reconstruction (discrete)

'ape’ , 'phytools' , 'geiger'

PDF

data1, data2, data3, data4 , R_commands

ref1, ref2

Feb 26

Ancestral state reconstruction (continuous)

'ape’ , 'phytools' , 'geiger'

PDF

data1, data2, data3, data4 , R_commands

ref1

Mar 3

Tree simulations

'ape’ , 'phytools' , 'geiger' , 'TreeSim', 'phyclust'

PDF

data1, data2, data3, data4, R_commands_1, R_commands_2

 

Mar 5

Ancestral state reconstruction (Threshold models)

'phytools', 'Threshml'

PDF

data1, data2, data3, data4, R_commands

ref1, ref2, ref3

Mar 10

Diversification analysis: BiSSE (MLE) based models

diversitytree

PDF

data1, data2, R_commands

ref1, ref2, ref3

Mar 12

Diversification analysis: BiSSE (Bayesian) based models

diversitytree

PDF

R_commands

ref1, ref2, ref3

Mar 17

Trait evolution: Correlation analyses (discrete traits)

'phytools', 'corHMM',

'BayesTraits'

PDF

data1, data2, data3, data4, R_commands

ref1, ref2

Mar 19

Trait evolution: Correlation analyses (continuous traits)

caper

PDF

R_commands

ref1, ref2, ref3

Mar 24

Trait evolution: Correlation analyses (discrete with continuous traits)

caper’, 'phytools', 'MCMCglmm'

PDF

data1, data2 , R_commands

ref1, ref2

Mar 26

Open Class: Project Preparation in class

--

--

--

--

Mar 31

Taxonomy, geographic records, and multivariate methods (e.g., PPCA)

'ape’ , 'phytools' , 'geiger' , 'taxize', 'rgbif', 'psych', 'GPArotation'

PDF

data1, data2, data3, R_commands

 

Apr 2

Open Class: Project Preparation in class

--

--

--

--

Apr 7

Cluster fun: Running programs and jobs

  'FSL' , 'Slurm',

'BYU-Cluser videos' , 'Evolution author guidelines'

PDF

data1

ref1

Apr 9

Student presentations of final project

--

--

--

--

Apr 14

Student presentations of final project

--

--

--

--

 

Printable version of this syllabus: PDF