Spring 2008

The Molecular Basis of Adaptation

IB 249 – Seminar on Evolutionary Genetics

1 credit units (S/U only)

The first two weeks the instructor will provide lectures to bring all students up to speed on the statistical and computational methodologies used to detect adaptation at the molecular level. Knowledge of evolutionary and molecular biology at the level expected of graduate students in MCB and IB will be assumed.

During each meeting, except for the first two weeks, one (or sometimes two) students give a presentation. These presentations should provide sufficient background on the subject being covered, review the current state of knowledge in the area, and then critically analyze, in detail, the assigned paper. All students in the class are expected to read the specific paper that will be presented at each session. Additional readings and background materials will be assigned for the presenter but are optional for other participants. In addition, regular attendance and active participation in discussions is required of all students in the seminar in order to receive a passing grade.

Course Control Number: 43599

Instructor: R. Nielsen

NEW TIME AND PLACE! Mondays 11 AM, 2063 VLSB NEW TIME AND PLACE!

NB! I have added names to each date and corrected the dates. Please notify me regarding any spelling errors or other errors.

1/25/2008 Organizational meeting and Introductory Lecture (I) (click for ppt file).

1/28/2008 Introductory Lecture (II) (click for ppt file).

* Nielsen, R. 2005. Molecular signatures of natural selection. Ann. Rev. Genet. 39:197-218.

2/4/2008 Adaptive gene transposition in Drosophila (Weiwei Zhai, Jonathan Fong).

* Aminetzach, Y. T. et al. 2005 Pesticide Resistance via Transposition-Mediated Adaptive Gene Truncation in Drosophila. Science 309: 764 – 767.

Schlenke, T. A. and D. J. Begun 2004. Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc. Natl. Acad. Sci. 101: 1626–1631.

2/11/2008. Adaptation and selection in reproductive proteins (Colin Brown).

* Swanson, W. J. et al. 2001. Positive Darwinian selection drives the evolution of

several female reproductive proteins in mammals. Proc. Natl. Acad. Sci. 98: 2509–2514.

Clark, N. L. et al. 2006. Evolution of reproductive proteins from animals and plants. Reproduction 131: 11-22.

2/18/2008 President’s day

2/25/2008 Human Adaptation: Lactase (Rebecca Welch).

*Tishkoff, S.A. et al. 2007. Convergent adaptation of human lactase persistence in Africa and Europe. Nature Genetics 39: 31 – 40.

Bersaglieri, T. et al. 2004. Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet. 74, 1111–1120.

3/3/2008 Human Adaptation: FOXP2 (Andrew Rush, Leonid Teytelman).

*Enard et al. 2002. Molecular evolution of FOXP2, a gene involved in speech and language', Nature 418: 869 – 872.

Krause J. et al. 2007. The derived FoxP2 variant of modern humans was shared with Neandertals. Curr Biol 17:1-5.

3/10/2008 Human Adaptation: ASPM (Philip Johnson, Molly Orton).

*Nitzan Mekel-Bobrov et al. 2005. Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens. Science 309 (5741): 1720–1722.

Mathias Currat et al. 2006. Comment on "Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens". Science 313 (5784): 172.

Mekel-Bobrov, N., et al. 2007. The ongoing adaptive evolution of ASPM and Microcephalin is not explained by increased intelligence". Hum. Mol. Genet.: adv. access. doi:10.1093/hmg/ddl487

3/17/2008 Human adaptation: Skin color (Katherine Brown, Guin Wogan).

*Lamason, R. L. et al. 2005. SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans. Science 310: 1782 – 1786.

McEvoy, B. et al. 2006. The genetic architecture of normal variation in human pigmentation: an evolutionary perspective and model. Human Molecular Genetics 15: R176-R181.

3/24/2008 Spring break

3/31/2008 Genome wide scans for molecular adaptation in humans (Roberta Damascerno, Shobi Lawalata).

*Voight B. F. et al. 2006. A Map of Recent Positive Selection in the Human Genome. PLoS Biol 4(3): e72 doi:10.1371/journal.pbio.0040072.

Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nat. Rev Genet. 8:857-68.

4/7/2008 Genome wide comparisons of humans and chimps (Veronica Morris).

*Bakewell M. A, Shi P, and Zhang J. 2007. More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci USA 104:7489-7494 doi:10.1073/pnas.0701705104

Nielsen, R. et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biology 3(6): e170.

4/14/2008 Molecular adaptation of antiviral factors (Caroline Lee).

*Sawyer S. L. 2005. Positive selection of primate TRIM5&alpha identifies a critical species-specific retroviral restriction domain. Proc Natl Acad Sci U S A. 102: 2832–2837.

Zhang, J. and D. M. Webb. 2004. Rapid evolution of primate antiviral enzyme APOBEC3G. Human Molecular Genetics 13: 1785–1791.

4/21/2008 Opsins and vision (Sean Schoville, Luqman Hodkinson).

*Frentiu, F. D. et al. 2007. Adaptive evolution of color vision as seen through the eyes of butterflies. Proc. Natl. Acad. Sci. 104: 8634–8640.

Fernald, R. D. 2006. Casting a Genetic Light on the Evolution of Eyes. Science 313: 1914-1918.

4/28/2008 Molecular evolution of the HIV (Malaspinas Anna, Caroline Uhler).

*Ross, H. A. and A. G. Rodrigo. 2002. Immune-Mediated Positive Selection Drives Human Immunodeficiency Virus Type 1 Molecular Variation and Predicts Disease Duration. J. Virol. 76: 11715–11720.

Rambaut et al. (2004). The .causes and consequences of HIV evolution. Nature Review Genetics 52-61.

5/5/2008 Molecular adaptation of the Influenza virus (Sonal Singhal, Stephen Fairclough).

*Bush, R. M. et al. 1999. Predicting the Evolution of Human Influenza A. Science 286: 1921 – 1925.

Zhai et al. 2007. Exploring Variation in the dN/dS Ratio Among Sites and Lineages Using Mutational Mappings: Applications to the Influenza Virus. J. Mol. Evol. 65: 340-348.

5/12/2008 Evolution of centromers (Mansi Srivastana).

*Malik H.S., Henikoff S. 2001. Adaptive evolution of Cid, a centromere-specific histone in Drosophila. Genetics. 157: 1293-1298,

Malik HS, Henikoff S. (2002) Conflict begets complexity: the evolution of centromeres.

Curr. Op. Genet. Dev. 12: 711-718.

*Only papers marked with a star are mandatory reading.