EEOB 881.04: Seminar in
Analysis of Population Genetic Data |
During Fall Quarter 2007, a one-hour seminar in the analysis of population genetic data will be organized by Prof. Lisle Gibbs, Laura Kubatko, and Paul Fuerst. The seminar will focus on developing an understanding of the statistical methods used in analyzing population genetic data in two settings. The first involves the estimation of effective population size and population growth rate using genetic data such as nucloetide sequences and microsatellites. We will study the programs LAMARC and MSVAR in this context. The second involves the estimation of the ancestry of individuals that are sampled from admixed populations. We will study the programs STRUCTURE and BAPS in this setting. For each major topic, we will read the relevant papers from the literature and then explore the associated software using an example real data set. Guest presentations by the authors of some of the programs will be included in the couse once participants have had a chance to experiment with the programs on their own.
Interested students should enroll in one hour of EEOB 881.04, call
number 21003-3.
Note to students: I've taken all the links to papers
from this page and placed pdfs of all papers on carmen. Go to
www.carmen.osu.edu to get course materials, and e-mail me if you
can't log on. I'll continue to update the schedule at this site,
but you will need to use carmen to download course
material.
Tentative Schedule:
| Meeting | Date | Reading | Class topic | Leaders |
| 1 | Sept. 21 | Organizational meeting + guest speaker | Guest speaker: Dr. James Degnan, Dept. of Human Genetics, Univ. of Michigan, "Coalescent Consequences for Consensus Cladograms" (click here for abstract) | NOTE CHANGE IN TIME: This meeting will be held at 9:30am in ARR 104. |
| 2 | Sept. 28 | 1. Kuhner, M. K., J. Yamato, and
J. Felsenstein. 1998. Maximum likelihood estimation of
population growth rates based on the coalescent.
Genetics 149: 429-434. pdf 2. Lessa, E. P., J. A. Cook, and J. L. Patton. Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. PNAS 100(18): 10331-10334. pdf | Review of coalescent and discussion of papers | Group discussion led by Laura Kubatko |
| 3 | Oct. 5 |
Main paper: Goosens, B. et al. 2006. Genetic signature of
anthropogenic population collapse in Orang-utans. PLoS
Biology 4(2):e25.pdf
Supplemental papers: 1. Beaumont, M. Detecting population expansion and decline using microsatellites. Genetics 153: 2013-2029. pdf 2. Storz, J. F., M. A. Beaumont, and S. C. Alberts. 2002. Genetic evidence for long-term population decline in a savannah-dwelling primate: Inferences from a hierarchical Bayesian model. Mol. Biol. Evol. 19(11): 1981-1990. pdf | Discussion of papers | Group discussion led by Lisle Gibbs |
| 4 | Oct. 12 | 1. Documentation for LAMARC and
MSVAR 2. Kuhner, M. K. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22: 768-770. pdf | Intro to software | Lisle Gibbs and Laura Kubatko |
| 5 | Oct. 19 | No reading - work on data analysis | Discussion of data analysis using LAMARC | All |
| 6 | Oct. 26 | 1. Follow up data analysis as needed 2. Attend joint EEOB-Stat seminar given by Dr. Mary Kuhner, Thursday, October 25, 3:30-4:30 | Presentation given by Dr. Kuhner | All participate in discussion with Dr. Kuhner |
| 7 | Nov. 2 | 1. Pritchard J.K., Stephens M., Donnelly P. 2000.
Inference of population structure
using multilocus genotype data. Genetics, 155, 949-959.
pdf 2. NA Rosenberg, JK Pritchard, JL Weber, HM Cann, KK Kidd, LA Zhivotovsky, MW Feldman (2002) Genetic structure of human populations. Science 298: 2981-2985.pdf | Discussion of papers | Paul Fuerst |
| 8 | Nov. 9 | 1. Corander J., P. Marttinen. 2006. Bayesian identification of admixture events using
multilocus molecular markers. Molecular Ecology 15,
2833-2843.pdf 2. Corander, J., P. Marttinen, and S. Mantyniemi. 2006. A Bayesian method for identification of stock mixtures from molecular marker data. Fish. Bull. 104: 550-558. pdf | Discussion of papers/intro to software | Lisle Gibbs and Laura Kubatko |
| 9 | Nov. 16 | No reading - work on data analysis | Discussion of STRUCTURE and BAPS data analysis | All |
| 10 | Nov. 23 | No class - Thanksgiving | NA | NA |
| 11 | Nov. 30 | 1. Read paper comparing assignment/admixture
methods 2. Follow-up data analysis as needed | Guest speaker TBA | NA |