Population genetics journal club 2005-2006

The population genetics journal club meets every other Friday 12:00-1:00pm in Palmer Commons room 2036 (on the 2nd floor of the building, right next to the elevators in the center of the building).

This is an informal gathering to discuss some of the latest topics in population genetics. In the winter term 2006, students can receive 1 unit of credit for participating. Enroll in Bioinformatics 800 "Population Genetics Journal Club."

Organizers are Noah Rosenberg and Sebastian Zöllner. To receive announcements about upcoming journal club events, send an email to Sebastian (uniqname szoellne).

Click here for directions to Palmer Commons (we meet just down the hall from the Rosenberg lab).

This website is maintained by Noah Rosenberg
+1 734 615 9556 (office phone)
+1 734 615 9551 (lab phone)

Last modified 7-12-2006

Friday, November 18, 2005, 12:00-1:00, Palmer Commons 2036 — Noah Rosenberg

Evidence of a large-scale functional organization of mammalian chromosomes. P. M. Petkov, J. H. Graber, G. A. Churchill, K. DiPetrillo, B. L. King, et al. PLoS Genetics 1, e33 (2005).

Friday, December 2, 2005, 12:00-1:00, Palmer Commons 2036 — Sebastian Zöllner

Wave-like spread of Ebola Zaire. P. D. Walsh, R. Biek, L. A. Real. PLoS Biology 3, e371 (2005).

Friday, December 16, 2005, 12:00-1:00, Palmer Commons 2036 — Trisha Wittkopp

Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. P. F. Colosimo, K. E. Hosemann, et al. Science 307, 1928-1933 (2005).

Friday, January 6, 2006, 12:00-1:00, Palmer Commons 2036 — Paul Scheet, visiting from the Department of Statistics, University of Washington

Seminar: "A fast and flexible model for population genetic data: estimation of haplotypes and unobserved genotypes"

Friday, January 20, 2006, 12:00-1:00, Palmer Commons 2036 — Michael Blum

A populationwide coalescent analysis of Icelandic matrilineal and patrilineal genealogies: evidence for a faster evolutionary rate of mtDNA lineages than Y chromosomes. A. Helgason, B. Hrafnkelsson, J. R. Gulcher, R. Ward, K. Stefansson. American Journal of Human Genetics 72, 1370-1388 (2003).

Friday, February 3, 2006, 12:00-1:00, Palmer Commons 2036 — Arindam RoyChoudhury, visiting from the Department of Statistics, University of Washington

Seminar: "Two-stage peeling algorithm and its applications to phylogeny"

We developed a peeling algorithm for likelihood estimation of a phylogenetic tree from data at independent single neucleotide polymorphism (SNP) loci. We avoided any Monte-Carlo based method, gaining on computing time and accuracy. Our method starts at the tips of tree with the data. Then it peels up the branches with the information on the distribution of number of lineages, and allelic count, conditioned on the data. The information at the root gives us the likelihood. In this talk I will first present the algorithm ignoring the effects of mutation, migration after time of divergence and ascertainment correction on likelihood. Later I will briefly outline the implementation of these factors in the algorithm.

Friday, February 17, 2006, 12:00-1:00, Palmer Commons 2036 — Davide Pisani, visiting from the Bioinformatics and Pharmacogenomics Laboratory, National University of Ireland, Maynooth

Seminar: "Phylogenomic supertrees and the recovery of the tree of life"

Friday, February 24, 2006, 12:00-1:00, Palmer Commons 2036 — Vincent Plagnol, visiting from the Department of Biological Sciences, University of Southern California

Seminar: "Evidence for ancestral structure in human populations"

Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture) using the patterns of variation in contemporary human populations. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p < 10^{-7}), with contributions to the modern gene pool of at least 7%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.

Friday, March 3, 2006, 12:00-1:00, Palmer Commons 2036 — Nicole Scott

The effects of artificial selection on the maize genome. Stephen I. Wright, Irie Vroh Bi, Steve G. Schroeder, Masanori Yamasaki, John F. Doebley, Michael D. McMullen and Brandon S. Gaut. Science 308, 1610-1614 (2005).

Friday, March 17, 2006, 12:00-1:00, Palmer Commons 2036 — Mattias Jakobsson

On the number of new world founders: a population genetic portrait of the peopling of the Americas. J. Hey. PLoS Biology 3, e193 (2005).

Friday, April 14, 2006, 12:00-1:00, Palmer Commons 2036 — Cecil Lewis

Genomics refutes an exclusively African origin of humans. V. Eswaran, H. Harpending, A. R. Rogers. Journal of Human Evolution 49, 1-18 (2005).

Friday, April 28, 2006, 12:00-1:00, Palmer Commons 2036 — Jeff Long

Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies. S. Service et al. Nature Genetics 38, 556-560 (2006).

The optimal measure of allelic association. N. E. Morton et al. Proceedings of the National Academy of Sciences USA 98, 5217-5221 (2001).