BIOCHEM 4/6Y03 - Genomes and Evolution
Paul Higgs
Schedule for
Winter 2014: Mon 11.30-13.20, Wed - 11.30-12.20 - KTH B132
This
course will focus on key issues in molecular evolution, and will introduce the
bioinformatics methods that are necessary to answer these questions. Now that
hundreds of complete genomes are available, what have we learned? Which genes
are shared between organisms? How do we build evolutionary trees? Is there a
molecular clock? What are the evolutionary relationships between bacteria? How
often does horizontal gene transfer occur? What are the origins of organelles
and their genomes? How does the human genome compare with other species? What
do microarray and proteomics experiments tells us about how organisms work at
the whole genome level?
Prerequisites:
BIOCHEM 2B03 or 3G03
Antirequisite:
BIOLOGY 4DD3
Recommended text:
Lectures will be based on material included in the
book ‘Bioinformatics and Molecular Evolution’ by P.G.Higgs
and T.K.Attwood.
Lecture Contents
1.
What is bioinformatics? Data explosions. The relationship between molecular
evolution and bioinformatics. The relevance of bioinformatics for genomics,
microarrays and proteomics.
Read:
Chapter 1
2.
Molecular Evolution and Population Genetics. Sequence variation within and
between populations. Random drift and fixation. Neutral evolution and
selection.
Read:
Chapter 3
Examples
related to Human evolution - mitochondria and Y chromosomes: Adam and Eve
3.
Models for nucleic acid sequence evolution. Synonymous and non-synonymous
substitutions. Models for protein sequence evolution. Scoring systems for
sequence alignment.
Read: Chapter 4 and Chapter 2, sections 2.4-2.6.
4. Methods of molecular phylogenetics.
Comparison of distance matrix, parsimony, maximum likelihood and Bayesian
methods. Biological examples and controversies in phylogenetics.
Mammalian orders. Animal Phyla. Major Eukaryotic groups. Molecular Clocks.
Read: Chapter 8 and Lecture notes: phylogenynotes.ppt
5. Codon Usage and Base frequency variation among genomes
Lecture Notes: CodonsAndMitochondria.ppt
Useful papers for details:
Sharp - Table of RSCU
values in various organisms
Duret
- tRNAs and codon usage in C. elegans
Akashi - codon usage in
yeast as a function of gene expression level
Ran and Higgs -
Variation of codon usage with tRNA content in
bacteria
Jia
and Higgs - Context-dependent mutation in mitochondria
Xu et al
- Variations in mitochondrial gene order
6. Evolution of the Genetic Code
Notes: GeneticCodeLectures.ppt
Useful papers:
Sengupta
et al - Codon reassignment in mitochondrial genomes
7. Sequence alignment. Database searching.
Read: Chapter 6 and Chapter 7
8. Bacterial genome evolution. Horizontal transfer.
Read: Chapter 12
Notes: BacterialGenomes.ppt
Two views of the Tree of Life:
Bacterial Genomes:
Assessment
Three written
assignments - each worth 15%
Midterm test -
worth 15%
Final Exam -
worth 40%
Additional work
for graduate students - Graduate students will complete a literature review on
a chosen topic. This will be worth 30% and the other parts of the course will
be scaled down to 70%.
Download
Assignment 1 - Assignment1.doc . Please hand
in on Mon 27th Jan. You will need the following paper for this assignment: Ingman.pdf
Download
Assignment 2 - Assignment2.doc . Please hand
in on Mon 24th Feb. You will need the following papers: Subramanian , Sharp
, Yang
Midterm - in
class on Wed March 12th. Topics will be points 2,3,4,5 on the lecture list
above.
Download
Assignment 3 - Assignment3.doc . Please hand
in on Mon 31st March. You will need the following papers: Hao & Golding , McCutcheon (and the Sengupta paper in no. 6 above may be useful)
EXAM HINTS: For the exam, please focus on the following topics -
·
Sequence
alignment methods & PAM matrices
·
Bacterial genome
evolution
·
Horizontal gene
transfer
·
Evolution of
the genetic code
Reminder on
university policies regarding academic dishonesty
=========================================================================
Academic dishonesty consists of misrepresentation by deception or by
other fraudulent means and can result in serious consequences, e.g. the
grade of zero on an assignment, loss of credit with a notation on the
transcript (notation reads "Grade of F assigned for academic
dishonesty"), and/or suspension or expulsion from the university.
It is your responsibility to understand what constitutes academic
dishonesty. For information on the various kinds of academic dishonesty
please refer to the Academic Integrity Policy, specifically Appendix 3,
located at http://www.mcmaster.ca/senate/academic/ac_integrity.htm
The following illustrates only three forms of academic dishonesty:
1. Plagiarism, e.g. the submission of work that is not one's own or for
which credit has been obtained.
2. Improper collaboration in group work.
3. Copying or using unauthorized aids in tests and examinations.
=========================================================================