Genome Evolution Course – 2009-2010

Clockwork Evolution: Molecular Clocks

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Presentation: (PPT or PDF)

Essay version

Topics

• The biological concept of homology
• Orthologs and paralogs
• Inparalogs and outparalogs
• Molecular clocks
• Zuckerkandl and Pauling christen the molecular clock
• Local clocks
• Testing the molecular clock hypothesis with relative rate tests
• Deviations from the molecular clock
• Estimating evolutionary distance between biological
• Simulation of the accumulation of mutations to a sequence
• Correcting for multiple hits
• How many millions of years separate us from the apes?

Suggested readings

• Kumar and Hedges. A molecular timescale for vertebrate evolution. (1998) Nature 372 917-920
• Sonnhammer and Koonin. Orthology, paralogy, and proposed classification for paralog subtypes. (2002) TIGs 18 619-620.
• Zuckerkandl and Pauling. Evolutionary Divergence and Convergence in Proteins. (1965) In: Evolving genes and proteins (Bruson, V., Vogel, H.J., eds.), pp. 97-166, Academic Press, New York.
• Graur and Li. Chapter 3 and 4 of "Fundamentals of Molecular Evolution".
• “Initial sequence of the chimpanzee genome and comparison with the human genome”. Nature (2005) 437: 69
• Kumar. Molecular clocks: four decades of evolution” Nature Reviews Genetics. (2005) 6:654

Assignment

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Back to the Genome Evolution Course.

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Itai Yanai, yanai@technion.ac.il