Microsoft word - 203.761 0902 i pnak.doc

Provisional –to be approved by Programme Director M A S S E Y U N I V E R S I T Y
COLLEGE OF SCIENCES
Paper Outline 2009

Paper Number and Title: 203.761 Molecular Evolution

Credits value:
Semester: 2
Mode: Internal

Calendar Prescription: Analysis of the evolution of DNA, RNA and proteins. Analysis of theories and
experiments on the origin of life, especially the transition from the RNA to the protein/DNA world. Use of
molecular 'fossils' in living cells to infer ancient processes. Analysis of DNA from extinct organisms.
Human genetic diversity and evolution. Problems in molecular evolution.

Pre- and Co-requisites: Graduate Status and Permission AD

Restrictions: None
E-Learning Category: web supported

Paper Coordinator: David Penny, [email protected]

Other Contributing Staff: Dr Lesley Collins, IMBS , Room D5.31, e-mail [email protected]
Aim:
A synthesis of evolutionary theory with the evolution of macromolecules. An aim of the course is to
integrate basic biological questions with molecular and genetic knowledge in order to give an improved
understanding of dynamic biological processes. A good background in molecular biology is expected, and
testing of evolutionary hypotheses will be emphasized
Learning Outcomes:
On successful completion a student will be able to:
1. critically evaluate published papers
2. synthesize scientific knowledge
3. summarize information
4. understand the importance of testing hypotheses

Assessment:

Alignment of Assessment to Learning outcomes.
Assessment Description
Learning Outcomes Assessed
Contribution to Paper
The final examination is to answer either, one question (pre-circulated), or three questions out of six.
Deadlines and Penalties:
Assessment
Due Date / Deadline
Provisional –to be approved by Programme Director Summaries
Before next class, or by negotiation
Draft 2nd Oct.; Final 16th Oct, or by N/A
negotiation

Requirements to Successfully Complete the Paper:
To pass the paper with a C grade, an aggregate of 50% of the total assessment is required.

Learning Program and Schedule:
The lectures are in a discussion format where students evaluate the main points of papers that they have read
before the session
Student Time Budget:
Lectures/Discussion 2 hrs per week, 12 weeks
Total: 187.5 hours

Timetable:
Lectures: Suggested time (negotiable) 10.00am-12noon (Tuesday)

Tutorials:
Laboratories:

Proposed Feedback and Support for Student Learning:
Feedback is immediate during each session, and comes from the other students as well. Summaries of the
lecture notes are evaluated in the week they are submitted. The “Report” is a major component, and students
submit a draft report that is evaluated and commented on, before the final Report is submitted. There is
opportunity for a student to focus on one particular aspect of the course4.
Textbook and Other Recommended Reading:
N/A (papers supplied, see later)

Conditions for Aegrotat Pass and Impaired Performance:
If you are prevented by illness, injury or serious crisis from attending an examination (or completing an
element of assessment by the due date), or if you consider that your performance has been seriously
impaired by such circumstances, you may apply for aegrotat or impaired performance consideration. You
must apply on the form available from the Examinations Office, the Student Health Service or the Student
Counseling Service.
(a)
To qualify for an aegrotat pass on the final examination, you must have attempted at least 40% of the
total formal assessment and your performance must be well above the minimum pass standard, so that
the examiners can be confident that you would have passed the paper if you had completed the final
examination.

Plagiarism:
Massey University, College of Sciences, has taken a firm stance on plagiarism and any form of cheating.
Plagiarism is the copying or paraphrasing of another person’s work, whether published or unpublished,
without clearly acknowledging it. It includes copying the work of other students. Plagiarism will be
penalized; it is likely to lead to loss of marks for that item of assessment and may lead to an automatic
failing grade for the paper and/or exclusion from reenrollment at the University.

Grievance Procedures:
A student who claims that he/she has sustained academic disadvantage as a result of the actions of a
University staff member should use the University Grievance Procedures. Students, whenever practicable,
should in the first instance approach the University staff member concerned. If the grievance is unresolved
with the staff member concerned, the student should then contact the College of Sciences office on his/her
campus for further information on the procedures, or read the procedures in the University Calendar.
Paper Outline submitted by
Provisional –to be approved by Programme Director Reading list (2008)
Note: Where this symbol ➼ appears, the paper is available as a .pdf file on the course website:
You will need Adobe acrobat reader 3.0 or higher to view these. Acrobat is available for free and can be
downloaded from the web at www.adobe.com for both Mac and PC.
Note also: readings will be updated if appropriate newer papers appear.
Topic 1. Principles of molecular evolution
Background Reading in evolution
➼D Penny, Lectures 2 and 3. Evolution course notes.
➼F Jacob (1977) Evolution and tinkering. Science 196: 1161-1166.
Neutral evolution
➼M Kimura and T. Ohta (1974) On some principles governing molecular evolution. Proc. Natl. Acad.
Müller's ratchet
➼Blanchard JL and Lynch M (2000) Organellar genes: why do they end up in the nucleus? Trends
➼Sallstrom, B and Siv GE Andersson (2005) Genome reduction in the a-Proteobacteria. Current Opinion ➼Nilsson, A.I. S. Koskiniemi, S. Eriksson, E. Kugelberg, J. C. D. Hinton, and D. I. Andersson (2005) Bacterial genome size reduction by experimental evolution. PNAS 102, 12112–12116. ➼Patrick J Keeling and Claudio H Slamovits. (2005) Causes and effects of nuclear genome reduction. Current Opinion in Genetics & Development 15, 601–608. Mutation rate and error catastrophe
➼M Eigen (1993) The origin of genetic information: viruses as models. Gene 135: 37-47.
➼J.W. Drake, A. Bebenek, G.E. Kissling, and S. Peddada, (2005) Clusters of mutations from transient
hypermutability. PNAS. 102, 12849–12854.
Topic 2. RNA Viruses as models of evolution
a) Evolution in real time
➼G.J.D. Smith, et al. (2006) Evolution and adaptation of H5N1 influenza virus in avian and human hosts
in Indonesia and Vietnam. Virology 350 258–268. ➼L Campitelli et al. (2006) H5N1 influenza virus evolution: a comparison of different epidemics in birds and humans (1997–2004). J. General Virology, 87, 955–960 ➼D H Bamford, J M Grimes and D I Stuart 2005 What does structure tell us about virus evolution? Current Opinion in Structural Biology 15: 655–663. ➼L. D. Sims, et al. Origin and evolution of highly pathogenic H5N1 avian influenza in Asia. Veterinary
b) Illustrating principles of evolution
➼Keese PK and Gibbs A (1992) Origins of genes: big bang or continuous creation? Proc Natl Acad Sci.
USA 89:9489-9493.
➼Crotty S, Cameron CE, Andino P (2001) RNA virus error catastrophe: direct molecular test by using ribavirin. Proc Natl Acad Sci. USA 98: 6895-6900. ➼ Bush RM, Bender CA, Subbarao K, Cox NJ, Fitch WM (1999) Predicting the evolution of human influenza A. Science 286 :1921-5. (Hillis, ibid. 1866-7.) ➼P E Turner and L Chao (1999) Prisoners Dilemma in an RNA virus. Nature 398: 441-443. (Nowak & Sigmund, ibid. 367-368) (or, ➼P E Turner and L Chao. 2003. Escape from Prisoner’s dilemma. Amer. Nat. 161; 497-505)
Topic 3. Origin of life
a) Early
➼ Penny, D. 2005. An Interpretive Review of the Origin of Life Research. Biology and Philosophy 20:
➼Schuster P. 2000. Taming combinatorial explosion. Proc. Natl. Acad. Sci. USA 97: 7678-7680. Provisional –to be approved by Programme Director ➼Chen, I.A., Roberts, R.W. and Szostak, J.W. 2004. The emergence of competition between model protocells. Science 305: 1474-1476. ➼Levy, M and Miller, S.L. 1998. The stability of the RNA bases: Implications for the origin of life. Proc. Natl. Acad. Sci. U.S.A. 95: 7933-7938. ➼ Mossel, E and M. Steel. 2005. Random biochemical networks: the probability of self-sustaining autocatalysis. J. Theor. Biol. 233: 327–336. b) The RNA World
➼Cech TR (2000) Structural biology. The ribosome is a ribozyme. Science 289: 878-9.
➼Chaput, J.C. and J.W Szostak. 2003. TNA synthesis by DNA polymerases. J Am. Chem Soc. 125,

Topic 4. Origins of prokaryotes and eukaryotes:
a) The tree of life & the LUCA.
b) Eukaryotes origin

Topic 5. General molecular evolution
a) Splicing, alternative splicing.
b) Evolution of cancer.

Topic 6. Human origins.
a) Out of Africa
Höss M. 2000. Neanderthal population genetics. Nature 404, 453-454.
Ovchinnikov I.V. et al. 2000. Molecular analysis of Neanderthal DNA from the northern Caucasus.
Ingman M. et al. 2000. Mitochondrial genome variation and the origin of modern humans. Nature 408, Ke Y, et al. 2001. African Origin of Modern Humans in East Asia: A Tale of 12,000 Y Chromosomes. Stringer, C. 2000. Coasting out of Africa. Nature 405, 24-25.
b) Polynesia – and language evolution
➼ Murray-McIntosh R P, Scrimshaw BJ, Hatfield PJ & Penny D (1998) Testing migration patterns and
estimating foundation population size in Polynesia by using human mtDNA sequences. Proc. Natl. Acad.
Sci. USA 95:9407-9052.
➼Hurles, ME, Matisoo-Smith E, Gray, RD and Penny D. (2003) Untangling Pacific settlement: the edge
of the knowable. TREE 18: 531-538.
➼Gray R & Jordan FM (2000) Language trees support the express-train sequence of Austronesian
expansion. Nature 405:1052-1055.

Source: http://science.massey.ac.nz/outlines/2009/pdf/203761_PN_I_S2_2009.pdf