BIO 498/545 – Population and Evolutionary Genetics

Spring 2017

Instructor: Dr. Jay Taylor, office: PSA 447; phone: 965-2641; e-mail: jetaylo6@asu.edu
Time: Tuesdays and Thursdays 4:30-5:45
Location: LSC L1-14
Office Hours: Wednesdays 11:00-1:00 in PSA 447.
Text: Most readings will come from the primary literature and are provided below as linked PDF's. For an introductory book-length treatment, John Gillespie's primer 'Population Genetics: A Concise Guide' (Johns Hopkins 2004, 2nd ed.) is recommended. Although more advanced, John Wakeley's text 'Coalescent Theory: An Introduction' (Roberts and Co., 2009) is the best book-length treatment of population genetics from the genealogical perspective. 'The Phylogenetic Handbook' (Cambridge, 2009), edited by P. Lemey et al., also has chapters discussing genealogies and their role in population genetical inference.

Course Description: This course will cover both pure and applied population genetics, with an emphasis on genealogies and coalescent-based methods for analyzing sequence data. Roughly speaking, the first half of the semester will focus on neutral population genetics and demographic inference, while the second half will focus on the population genetics of selected alleles and its implications for molecular evolution and adaptation.

Grading: There are no formal requirements, but please attend class regularly, participate and read the assigned papers.

Exercises: These will be posted on the course web page at the following link, along with their solutions. Although not mandatory, I encourage you to attempt the problem sets and turn in your solutions so that I can correct them. You are also welcome to work in groups.


Date

Topic

Reading

10 Jan

Overview; Hardy-Weinberg equilibrium
Crow (1987)

12 Jan

Probability review

detailed notes; brief summary

17 Jan
Genetic drift: the Wright-Fisher and Moran models Gillespie pp. 21-29; slides
19 Jan
Genealogies and Kingman's coalescent Hudson (1990); slides

24 Jan

Effective population size

Charlesworth (2009); slides

26 Jan

Mutation-drift balance

slides

31 Jan
Bayesian inference in population genetics

Beaumont & Rannala (2004); slides

2 Feb
Bayesian inference in population genetics

7 Feb
Skyline plots and demographic inference
Ho & Shapiro (2011); slides
9 Feb
BEAST tutorial: skyline plots and calibration
tutorial; Dengue4_PR.nex; Plasmodium_mtDNA.nex; starting_tree.txt

14 Feb

Population structure and differentiation

Holsinger & Weir (2009); slides

16 Feb
Structured coalescents
Hey (2010); slides; migrate output

21 Feb

The multispecies coalescent and phylogenomic inference

Liu & Pearl (2007); slides

23 Feb
The site frequency spectrum and demographic inference

Gutenkunst et al. (2009); slides

28 Feb
Selection in finite populations

Orr (2010); slides

2 March

Selection and genealogies

Williamson (2002); Barton & Etheridge (2004)

7 March

Spring Break


9 March

Spring Break


14 March
Balancing selection

Takahata & Nei (1990); Azevedo et al. (2015); slides

16 March

Fluctuating selection

Bell (2010)

21 March
Neutrality tests

Nielsen (2001); slides

23 March
Linkage disequilibrium

Pritchard & Przeworski (2001); slides

28 March
The ancestral recombination graph

Rasmussen et al. (2014); slides

30 March

Admixture

Schraiber & Akey (2015)

4 April

Genetic hitchhiking and interference

Barton (2010); slides

6 April
Selective sweeps and genomic signatures of selection

Vitti et al. (2013); slides

11 April

Genetic draft

Gillespie (2001)

13 April
Background selection

Charlesworth (2013); slides

18 April

Genetics of adaptation

Barrick & Lenski (2013)

20 April
Gene duplication and the evolution of gene families
Innan & Kondrashov (2010)

25 April

Local adaptation and gene flow

Tigano & Friesen (2016)

27 April

Neutral theory and selectionism

Ohta (1996); Hahn (2008)