Statistical Genetics Seminar, Winter 2014

Demographic Inference from large-scale genetic data in humans

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