Biology 550D

Morphometrics for Biologists

Autumn, 2016

Who:

Fred L. Bookstein (Department of Statistics) and Joe Felsenstein (Department of Genome Sciences and Department of Biology)

How much:

3 credits

When:

Tuesdays and Thursdays

10:30-11:50am

Where:

Hitchcock 312

Description:

This course will be a general introduction to morphometric methods and their use in developmental and evolutionary biology. Bookstein is a world leader in morphometrics, and he and Felsenstein are working actively on methods for applying morphometrics to phylogenetic questions. The course is intended for graduate students in the biological sciences. Use of morphometric methods to describe 2- and 3-dimensional shapes and differences between shapes is increasing rapidly. The class will give students an overview of methods in this field, along with the mathematical and statistical methods needed to use them. The syllabus will combine techniques for analysis of "extents" -- measures like length or area that it makes sense to take logarithms of -- with techniques for analysis of shape (the tools usually called "geometric morphometrics").

Classes, 80 minutes long, will be a combination of lectures and in-class exercises using R packages and other free software. Many of the lectures will be drawn from a new Bookstein book manuscript that attempts to rebuild today's morphometric toolkit on a new, firmer foundation of biological reasoning.

Please note that in the Time Schedule the class is BIOL 550D (the D is important). There are four "sections" of Biology 550, which is listed as "Evolution and Systematics Seminar". The sections are actually separate courses. Only the fourth, section D, is this course. The schedule line number is 22546.


News about the course


Course email mailing list

The course now has an email mailing list, to which all registered students have been subscribed. You can view past mailings here). To send mail to the whole mailing list, email to  bio550d_au16@u.washington.edu"  Everyone on the list can email to the whole list. I will also post announcements about the course and answer questions there. If people email me questions at my own email address about the course, if they are of general interest I will often use the mailing list to answer them, after anonymizing who asked the question.


Where is the lecture room?

Directions to the lecture room: Most of you are familiar with Hitchcock Hall and where room 312 is. For those who are not:

From upper campus use the overpass near Kincaid Hall. At the south end of the overpass continue on the same level -- there is a walkway to the third floor of Hitchcock Hall on the right. Enter the building and turn left at the first hallway. The room is the last room on the right.

From UW Medical Center, walk along the sidewalk on the south (medical center) side of Pacific Street. When you reach the second pedestrian bridge over Pacific Avenue, turn left and follow the walkway until you come to the stairway that leads up to the bridge. Go up one floor and turn left. Then you are at the south end of that overpass, and can follow the instructions in the previous paragraph.

If climbing stairs is a problem, instead proceed past the stairs toward the building, turn left, and follow the walkway entering the second floor of Hitchcock Hall. Proceed ahead to the elevators, which can be taken to the 3rd floor. Coming out of the elevator, turn right at the second corridor and proceed to the far end. The room is on the right.

Here is a campus map showing the location.


Lecture projections and audio recordings

Here we will have links to lecture projections. The ones marked “(old)” are from the 2014 course; they will be replaced by the lecture dates in 2016 by ones which are similar but which will have some more material added.

Joe will be making audio recordings of the lectures. They will be posted here in two forms, as WMA files and as MP3 files. They will be recorded at a medium quality (to reduce file size) and should be about 18-20 Megabytes each. Watch for them here. Their names indicate the date of the lecture: thus the lecture for February 13th would be files 20160213.WMA and 20160213.mp3. The 4-digit year is followed by the 2-digit month and the 2-digit day.

The audio recordings are organized according to the topic being covered at the beginning of the talk (so to find a given topic you may need to start in the last recording of the previous group).

WeekDate   Lecture projections (PDFs)   Lecture recordings   
      (WMA format)
      
   Lecture recordings   
      (MP3 format)
      
  Week 1     9/29  
   Joe: course summary    20160929.WMA       20160929.mp3   
  Week 2    10/4  
  10/6  
   Fred: summary of Chapter 2   
   Fred: summary of Chapter 3   
   20161004.WMA   
 (no recording made*) 
   20161004.mp3   
 (no recording made*) 
  Week 3     10/11  
  10/13  
   Joe: quantitative genetics   
   Joe: Brownian motion and comparative methods   
   20161011.WMA   
   20161013.WMA   
   20161011.mp3   
   20161013.mp3   
  Week 4   10/18  
  10/20  
   Fred: Introduction to GMM: how to keep your place in an anatomy. (Chapter 5.1)   
   Methods for landmarks three at a time. Tensors; uniform term. (Chapter 5.2)   
   20161018.WMA   
   20161020.WMA   
   20161018.mp3   
   20161020.mp3   
  Week 5   10/25  
  10/27  
   Fred: Chapter 4 ("Transition to Multivariate Analysis")
   Student discussion   
   20161025.WMA   
(not recorded)
   20161025.mp3   
(not recorded)
  Week 6   11/01  
  11/03  
   Paul Sampson: more of Chapter 4   
   Joe: comparative methods   
(Lecture not recorded)
   20161103.WMA   
(Lecture not recorded)
   20161103.mp3   
  Week 7  11/08  
  11/10  
   Fred: Chapter 4 material, continued
   Fred: Chapter 5 material  
   20161108.WMA   
   20161110.WMA   
   20161108.mp3   
   20161110.mp3   
  Week 8  11/15  
  11/17  
   Fred: chapter 5 material
   Fred: remainder of chapter 5 (thin plate splines)
   20161115.WMA   
   20161117.WMA   
   20161115.mp3   
   20161117.mp3   
  Week 9  11/22  
  11/24  
   Joe: using morphometrics; OU methods   
   Holiday   
   20161122.WMA   
   Holiday   
   20161122.mp3   
   Holiday   
  Week 10  11/29  
  12/1  
   Joe: Ornstein-Uhlenbeck processes and selective optima   
   Student presentations  
   20161129.WMA   
   20161201.WMA   
   20161129.mp3   
   20161201.mp3   
  Week 11  12/06  
  12/08  
   One student presentation; Joe: 3D issues, migration between populations
   Joe: R migration example; Morphometric consensus; Sampling variation
   20161206.WMA   
   20161208.WMA   
   20161206.mp3   
   20161208.mp3   
* Owing to a brain malfunction on 10/6, Joe did not record that lecture.  


R exercises