Genome Sciences 590

Evolution and Population Genetics Seminar

Winter Quarter, 2007

Topics on Phylogenies

Tuesdays
Foege Building
   (that's the new one on 15th avenue near Agua Verde)
room S-040 (not S-110 as listed in Time Schedule)
   (the small conference room in the middle of the Ground floor)
12:30pm - 1:20pm

This quarter the Evolution and Population Genetics will run on Tuesdays at 12:30 (yes, sorry, it conflicts with MathBio seminar).

I alternate between population-genetic and phylogeny topics, and this year it's phylogeny's turn. We will be taking volunteers to lead a session, which does not mean doing all the talking but does mean reading the paper assigned and making some cogent remarks, and helping stimulate discussion among all the other people, who will of course have read the paper too. Of course people registered for the course will be compelled to volunteer.

Topics

DatesTopicDiscussion leader
January 9Orientation/introductions 
January 16Trees of inversions in DrosophilaYuan Yaowu
January 23Trees from gene expression levelsChris Himes
January 30Linguistic treesChad Brock
February 6Manuscript treesMegan Carney
February 13Y chromosome treesCharla Lambert
February 20(no session: I will be away this week) 
February 27Trees of cells and organsChul Joo Kang
March 6Adaptive radiation and the scaling of evolutionary ratesLuke Harmon (UBC)
March 13TBABob Karn

References

(more will appear here soon, and suggestions will be appreciated)

Links to PDFs or links to UW library electronic copies of the paper are here -- these will work from the UW domain, or from off campus if you have a UW NetID username and password.

January 16 -- Revelations from inversion trees in Drosophila
Carson and Stalker 1983. Genetics 103 (3): 465-482
Throckmorton 1965. Systematic Zoology, Vol. 14 (3): 221-236
January 23 -- Evolutionary models for gene expression levels
Oakley, Gu, Abouheif, Patel, and Li. 2005. Molecular Biology and Evolution 22(1):40-50
January 30 -- Linguistic trees
Gray and Jordan 2000. Nature 405: 1052-1055
Atkinson and Gray 2005. Systematic Biology 54: 513-526.
February 6 -- Manuscript "traditions"
Robinson and O'Hara 1996. Research in Humanities Computing, 4: 115-137.
Spencer, Bordalejo, Robinson, and Howe 2003. Literary and Linguistic Computing 18(4):407-422
February 13 -- Trees of human populations from Y chromosomes
Underhill, P. A. and 20 others. 2000. Y chromosome sequence variation and the history of human populations. Nature Genetics 26: 358-361. (goes with a PBS show titled "The Journey of Man: A Genetic Odyssey")
Thomson, R., J. K. Pritchard, P. Shen, P. J. Oefner, and M. W. Feldman. 2000. Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data Proceedings of the National Academy of Sciences, USA 97 (13): 7360-7365.
Hurles, M. E., J. Nicholson, E. Bosch, C. Renfrew, B. C. Sykes, and M. A. Jobling. 2002. Y Chromosomal evidence for the origins of oceanic-speaking peoples. Genetics 160: 289-303.
Charla Lambert writes: For next Tuesday's seminar discussion, I plan to focus on only two of the three papers listed on the course Website:

1) The Underhill PA, et al. Nature Genetics letter http://www.nature.com/ng/journal/v26/n3/full/ng1100_358.html

2) The Genetics paper on Oceania http://www.genetics.org/cgi/content/full/160/1/289

The first reference above is credited with revealing much of the structure behind the world-wide Y-chromosome phylogeny. The PNAS paper that's listed on the Web site is a much larger and more thorough study, but ultimately the two are pretty similar.

I included the paper on Oceania to continue some of the discussion started a few weeks ago on linguistic trees. It would be great to compare and contrast the conclusions reached by the two approaches (i.e., genetic and linguistic).

See you next Tuesday

February 27 -- Trees of organs? of cells?
Serb and Oakley 2005. BioEssays 27: 1158-1166.
March 6 -- Adaptive radiation and the scaling of evolutionary rates
Abstract of Luke Harmon's talk: The evolutionary dynamics of phenotypic change provides key insights into macroevolutionary processes. One of the few results that generalizes from short-term studies of experimental evolution to long- term paleontological studies is the scaling of evolutionary rates: net rates of evolutionary change appear fastest over the shortest time scales. One explanation of this pattern invokes the effects of constraints on phenotypic evolution; the cumulative effects of constraints, such as stabilizing selection or developmental limits to adaptation, will be most apparent over long time scales. Alternatively, changing rates may reflect the dynamics of adaptive radiation, with trait evolution slowing as organisms near their selective optima and ecological space becomes filled with competitors. Here explicitly test these two models and show that, among a wide range of animal taxa, models of adaptive radiation provide the best fit to our comparative data. We hypothesize that the rate of body size evolution is highest just after a group has entered a new adaptive zone and subsequently slows as ecological space is filled. This result provides support for Simpson's suggestion that much of life's diversity originated during adaptive radiations.
March 13 -- I will be away but session will happen anyway.
(References to be supplied)

Joe Felsenstein ( joe (at) gs.washington.edu )