Return to course overview

1. T Jan 18.
Introduction to course business. Central concepts: evolution, natural selection, phylogeny.

• Recommended reading: Futuyma, ch. 1; review Graur and Li, ch. 1.

2. Th Jan 20.
The Neo-Darwinian Synthesis / Evolution of genes in populations. Hardy-Weinberg equilibrium; mutation.

• Selection without life: LE Orgel. Selection in vitro. Proc. R. Soc. Lond. B 205:435-442, 1979. ** (instructor)
• Graur and Li, ch. 2.
• Recommended: Futuyma, pp. 24-28, 231-239, 267-283.

Population genetics continued: Natural selection.

• Graur and Li, ch. 2, cont.
• Recommended: Futuyma, ch. 13.

Population genetics, continued: Genetic drift; population structure (inbreeding and gene flow); measures of genetic diversity.

• Graur and Li, ch. 2, cont.
• Recommended: Futuyma, ch. 11.
• Exercises on population genetics.

Aligning DNA and protein sequences.

• Demonstration of alignment software (instructor)
• Exercise on alignment
• Graur and Li, ch. 3.

Calculating evolutionary distances among sequences; corrections and models.

• Graur and Li, ch. 3, cont.
• Exercise on distance calculations

Selection at the molecular level: variations in substitution rates and their causes in nuclear, organellar, and viral DNA; tests of selection.

• Graur and Li, ch. 4.

The neutral and nearly-neutral theories of molecular evolution.

• Graur and Li, ch. 4, cont.
• T. Ohta. The current significance and standing of neutral and nearly neutral theories. Bioessays 18:673, 1996.
• M Kreitman. The neutral theory is dead; long live the neutral theory. Bioessays 18:678, 1996.
• Recommended: Page and Holmes, ch. 7.

9. T Feb 15.
Molecular clocks.

• Lahn BT, Page DC. Four evolution strata on the human X chromosome. Science 286:964-967, 1999.**
• Ayala FJ. Molecular clock mirages. Bioessays 21:71-75, 1999.

10. Th Feb 17.
Dating major evolutionary events. The Cambrian explosion and the K-T radiation.

• Hedges SB, Parker PH, Sibley CG, Kumar S. Continental breakup and theordinal diversification ofbirds and mammals. Nature 381:226-9, 1996. (See also Benton MJ. Early origins of modern birds and mammals: molecules vs. morphology. Bioessays 21:1043-1051, 1999.) **
• Wray GA, Levinton JS, Shapiro LH. Molecular evidence for deep precambrian divergences among metazoan phyla. Science 274:568-573, 1996. (See also Ayala FJ et al. Proc. Natl Acad. Sci 95:606-611, 1998.) **

Concepts: kinds of trees, rooting, clades, reconstructing character evolution, consensus trees, phylogeny as hypothesis.

• Graur, ch. 5
• Highly recommended: Page and Holmes, ch. 2

Phylogenetic methods: parsimony.

• Highly recommended: Page and Holmes, ch. 6, Futuyma, ch. 5.

Methods, distance and likelihood-based phylogenetics.

• Exercise on phylogenetic inference

Examples of phylogenetic studies

• Relationship of humans and African apes: Miyamoto MM et al. Molecular systematics ofhigher primates: genealogical relations and classification. Proc. Natl. Acad. Sci. USA 85:7627-7631, 1988. **
• Two major superphyla of animals: Aguinaldo AMA et al. Evidence for a clade of netmatodes, arthropods, and other moulting animals. Nature 387:489-493, 1997.**

Review and overflow

16. Th Mar 9

MIDTERM EXAM

(Mar 13-17 = break)

17. T Mar 21.
Endosymbiosis and lateral gene transfer.

• Graur and Li, pp. 245-246, 359-365,
• Nelson KE et al. Evidence for lateral gene transfer between Archae and Bacteria from genome sequence of Thermotoga maritima. Nature 399:323-330, 1999. **
• Doolittle WF. Phylogenetic classification and the universal tree. Science 284:2124-2128, 1999.

18. Th Mar 23.
Transposition, retroposition, and junk DNA.

• Lahn BT, Page DC. Retroposition of autosomal mRNA yielded testis-specific gene family on human Y chromosome. Nature Genetics 21:429-433, 1999. **
• Graur and Li, ch. 7.

19. T Mar 28.

Chromosomal evolution: genome projects and comparative mapping.

• Graur and Li, pp. 402-411.

20. Th Mar 30.

Genome duplications.

• Postlethwait JH, et al. Vertebrate genome evolution and the zebrafish gene map. Nature Genetics 18(4):345-9, 1998 ** (see also Smith NGC, Knight R, Hurst LD. Vertebrate genome evolution: a slow shuffle or a big bang? Bioessays 21:697-703, 1999.)
• Graur and Li, pp. 375-384.

21. T April 4.

The origin of introns.

• Gilbert W, Glynias M. On the ancient nature of introns. Gene 135:137-144, 1994.** (See also Hurst LD, McVean GT. A difficult phase for introns early. Current Biology 6:533-536, 1996.)

21. Th April 6.

Orthology and paralogy. Embedded trees. Inferring gene duplication and losses. Rooting the tree of life with gene families. Reconstructing the evolution of function.

• Exercise on gene family phylogeny.
• Highly recommended: Page and Holmes, pp. 286-293.

23. T April 11.
Domain shuffling and concerted evolution.

• Graur and Li, ch. 6.

24. Th April 13.
The evolution of gene function. Neofunctionalization and subfunctionalization; role of gene family evolution in morphological innovations.

• Swanson WJ, Vacquier VD. Concerted evolution in an egg receptor a rapidly evolving abalone sperm protein. Science 281:710-712, 1998. **
• Fryxell KJ. The coevolution of gene family trees. Trends in Genetics 12:364-369, 1996.

25. T April 18.

The evolution of function: examples.

• Reconstructing the evolution of function: Yokoyama S, Radlwimmer FBH. The molecular genetics of red and green color vision in mammals. Genetics 153:919-932, 1999.**
• Reconstructing the evolution of function: Fitch WM, Upper K. The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harbor Sym. Quant. Biol. 52:759-67, 1987. **

26. Th April 20.
Changes in expression of developmental control genes as the cause of morphological change; homology concepts.

• Cohn MJ, Tickle C. Developmental basis of limblessness and axial patterning in snakes. Nature 399:474-479, 1999. **
• Tomarev SL, Callaerts P, Kos L, Zinovieva R, Halder G, Gehring W, Piatigorsky J. Squid Pax-6 and eye development. Proceedings of the National Academy of Sciences USA 94:2421-2426, 1997. **
• Wray GA, Abouheif E. When is homology not homology. Current Opinion in Genetics and Development 8:6750680, 1998.
• Recommended: Futuyma, ch. 23.

27. T April 25.
Complexity and canalization in development.

• Rutherford SL, Lindquist S. Hsp90 as a capacitor for morphological evolution. Nature 396:336-342, 1998. **

28. Th April 27.
Review.