Genomes and Evolution (Biochem 4Y03/6Y03) - 2008

Dr Paul Higgs

Course Outline to download -   DOC

Schedule for Winter 2008: Mon, Wed, Thur 10.30 ABB 271

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

Lecture Contents

Lectures will be based on material included in the book "Bioinformatics and Molecular Evolution" by P.G.Higgs and T.K.Attwood. Chapter references below refer to this book. Other papers will be added to this website to download.

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

3. Models for nucleic acid sequence evolution. Synonymous and non-synonymous substitutions.

READ Section 4.1

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 Section 11.3

Phylogeny notes - PPT

5. Models for protein sequence evolution. Scoring systems for sequence alignment. Codon usage.

READ Sections 2.4 and 2.5

READ Sections 4.2 and 4.3

6. Sequence alignment. Database searching.

READ Chapter 6 and Section 7.1

EVERYTHING UP TO HERE WILL BE ON THE MIDTERM

7. Bacterial genome evolution. Horizontal transfer. The tree of life.

READ Section 12.1

8. Organellar genomes. The origin of mitochondria and chloroplasts. Gene transfer between nuclear and organellar genomes.

READ Section 12.2

Lecture notes on evolution in mitochondrial genomes - PPT

9. Eukaryotic genomes. Introns. Mobile Elements. Comparison of human genome with other species.
10. The transcriptome and the proteome. Microarray experiments and data analysis. Proteomics techniques. Protein-protein interaction networks.

READ Chapter 13

Assignments

Assignment 1 (worth 15%) Due by Wed 30th Jan. - DOC

You will also need this paper for Assignment 1. Ingman et al. (2000) - PDF

Assignment 2 (worth 15%) Due by Mon Feb 25th. - DOC

You will also need these papers for Assignment 2. Nei and Gojobori (1986) - PDF ---- Notes from class on dN and dS - DOC ---- Subramanian and Kumar (2006) - PDF

Mid-term test (worth 15%) In lecture on Thur March 6th. This is last year's paper as an example of what to expect. - PDF

Assignment 3 (worth 15%) Due by Wed April 2nd. - DOC

You will also need these papers for Assignment 3. Hao and Golding (2006) - PDF ---- Blomme et al. (2006) - PDF

Final exam (worth 40%)