Instructor: Sharon Browning (sguy@uw.edu)
Summary: Genome-wide genetic data contain much information about past demographic events such as population split times, migration rates, bottlenecks and recent growth. A variety of approaches can be used to extract this information, including the use of patterns of linkage disequilibrium, the joint allele-frequency spectrum and rates of identity by descent. The inferred demographic models have implications for understanding human history, for developing accurate simulation models, for accurate analyses of e.g. selection, and for study design.
Jan 7: Initial meeting
Jan 14: Brenda, Taryn and Sharon Marth et al. 2004 The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations. Genetics 166:351-372 http://www.genetics.org/content/166/1/351.full
Jan 21: Caitlin, Fiona and Sharon
Schaffner et al. 2005. Calibrating a coalescent simulation
of human genome sequence variation.
Genome Research 15:1576-1583 http://genome.cshlp.org/content/15/11/1576.full
Jan 28: Jesse, Grainne,
and Sharon
Tenesa et al. 2007 Recent human
effective population size estimated from linkage disequilibrium. Genome
Research 17: 520-526 http://genome.cshlp.org/content/17/4/520.full
Feb 4: Jeremy, David and Sharon Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data. PLoS Genet 5(10): e1000695 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000695
Feb 11 (Sharon absent): Anya, Serge and Liz Coventry et al. 2010 Deep resequencing reveals excess rare recent variants consistent with explosive population growth. http://www.nature.com/ncomms/journal/v1/n8/full/ncomms1130.html
Feb 18 (Sharon absent): Brayan, Matt and Ellen Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475: 493-496 http://www.nature.com/nature/journal/v475/n7357/full/nature10231.html
Feb 25 Visiting speaker: Malgorzata Bogdan hosted by Elizabeth Title: Model selection approach for genome wide association studies in admixed populations.
Mar 4
(Sharon absent): Jan, Jun and Tim
Palamara et al. 2012 Length
Distributions of Identity by Descent Reveal Fine-Scale Demographic History. Am
J Hum Genet 91:809-822. http://www.sciencedirect.com/science/article/pii/S0002929712004727
Mar 11: CANCELLED due to special Biostatistics seminar
Gravel et al. (2013) Reconstructing Native American
Migrations from Whole-Genome and Whole-Exome Data. PLoS Genet 9(12): e1004023. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004023