Studying Evolution with Bioinformatics

DATES: June 12-14, 2006

TIME:  9:00-4:00 pm

COURSE LOCATION: University of Texas, Austin, TX

Instructor Info | Resources | Articles
Course description:

Students in this course will learn how bioinformatics resources can be applied to the study of evolution on a molecular level. Course topics include thefollowing: generating multiple sequence alignments for phylogenetic studies, issues to consider when choosing sequences for phylogenetic studies, a comparison of methods for creating phylogenetic trees (neighbor joining, parsimony, maximum likelihood), orthology, paralogy, homology, homoplasy, and comparative genomics. Case studies where phylogenetic trees have been tested experimentally will also be discussed.

This course will include a significant hands-on component. Participants will learn how to obtain a set of DNA sequences, generate a multiple alignment, and produce a phylogenetic tree. Participants will also use free tools for viewing protein structures. Three dimensional structures from related proteins will be compared with information from phylogenetic trees will to determine if structural features are due to homology or homoplasy.

Lastly, participants will have time to discuss and explore how bioinformatics resources can be used in their courses.

Tentative Schedule

HIV and drug resistance
Identify the active site – where are the mutations?
- ClustalX and Cn3D
* Colonno – signature mutation in HIV protease
*Watkins - changes in a population of virus over time, sequence key

June 12, Day 1
9:00 am Introduction and overview

Discuss: how can we use bioinformatics to address Darwin's ideas?

* Species originate from a common ancestor

* Speciation occurs through natural selection

  • variation in a population
  • inheritance of traits
  • change over time
How can we use evolutionary studies in the classroom?
noon lunch

1:00 pm -4pm

Mechanisms of evolution

Natural selection and point mutations

Evidence for a common ancestor - UCSC genome browser
June 14, Day 2
9:00 am

Watching populations change over time and detecting signatures of evolution

Other resources:

  1. Genetic code web site: www.evolvingcode.net
  2. Mitochondrial DNA database: www.mitomap.org
  3. Phylip site - over 100 phylogeny programs
  4. Tutorial on using trees in HIV evolution studies - from Los Alamos National Laboratory
  5. Making a data set.pdf
  6. Power point presentation on making phylogenetic trees
noon lunch

1:00 pm -4pm


Can we find evidence for other mechanisms of evolution - i.e. gene duplication, horizontal transfer, mobile elements, etc.?

June 15, Day 3
9:00 am How does evolution explain some of the things that we see?
noon lunch
1:00 pm-4pm


Other activities, special topics

Chautauqua courses 2006 | Geospiza education | Geospiza home
Last modified June 2nd, 2006