Journal tea: May 14th

Alisa will lead Monday’s paper about speciation in Drosophila (simulans and close relatives) using whole-genome data:
Garrigan et al. Genome sequencing reveals complex speciation in the Drosophila simulans clade

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journal tea: May 7th


Estimation of the number of individuals founding a colonized population. Anderson and Slatkin 2007

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There’s copper in dem der hills. Copperopolis or bust!

A few of us from the Coop lab (Yaniv, Joel, and I) ventured out to Copperopolis, in the sierra foothills, to visit Kevin Wright’s field site on the copper mines out there (Kathy Toll a grad student in the Willis lab was also out there with us). Kevin’s currently working on local adaptation to copper mine tailings in Mimulus guttatus and we are starting to collaborate with him and John Willis on the popgen aspects of this work. We had a great day out helping out with field work (or at least pretending to for the camera) and seeing Kevin’s great field system for ecological genomics. We also hiked out to some limestone caves on our trip. You can read more about Copperopolis here and Kevin’s work here. Stay tuned for more on our collaboration.

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Journal tea: April 30th

For Monday Peter will lead our discussion of:
Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis
by: B E Engelhardt, and M Stephens

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BAPG VI at UC Davis

The Coop Lab will be hosting the sixth Bay area population genomics (BAPG) meeting at UC Davis on May 26th. This is a great informal meeting 2-3 times a year of the Bay area evolutionary and population geneticists. The signup sheet for the sixth Bay area population genomics meeting at UC Davis is here http://tinyurl.com/72wd9xr. Details below. Please signup to give talks and posters, as this offers a great opportunity to present your work to a friendly audience of fellow evolutionary and population geneticists. Details below.

Best wishes,
Yaniv Brandvain, Alisa Sedghifar, Peter Ralph, Jeremy Berg, Graham Coop


BAPG VI: May 26, 2012

Venue
1322 Storer Hall (map: http://campusmap.ucdavis.edu/?b=145 ), UC Davis

Tentative Schedule:

9:00-10:00 – Morning reception and poster set-up, Coffee, and snacks provided
10:00-11:00 – Talks
11:00-11:30 – break
11:30-12:30 – Talks
12:30-1:30 – Lunch and Poster session
1:30-2:30 – Talks
2:30-4:00 – Hangin out

Tentative talk format: 20mins+10mins questions
Talk signup deadline May 11th
Registration (and posters) signup deadline May 18th
Signup at http://tinyurl.com/72wd9xr

AMTRAK to Davis
http://www.capitolcorridor.org/
Morning: Eastward bound Weekend schedule, the best train is #720:
7.34am Berkeley (University and 4th st)
7.42am Richmond (next to BART)
arrives in Davis at 8.52
Storer Hall is just a ~15 min walk from the train station: down 2nd and straight on through campus, by the Quad, then just across California Ave, behind Hutchinson.
Hang out with the other popgen folks in the last car. Bikes are permitted.
Return: 3.50pm train from Davis


DRIVING From Bay area

Take the I-80 East, merge onto the 113N (to Woodland) at exit 70 (one after Kidwell rd exit)
Take exit 27 to UC Davis, turn right onto Hutchison Rd. Turn left onto Kleiber Hall drive. As you approach the gate, Storer Hall will be to your right.
Parking will be free in the lot to your left.

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journal tea: April 10th

Let’s read the stickleback paper:
http://www.nature.com/nature/journal/v484/n7392/full/nature10944.html

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Intro. to Evolution (EVE100) Reading

Thought I’d quickly post our reading list from my round of teaching EVE100 intro. to evolution:

Week 1. Darwin and Wallace’s 1858 letters to the Linnean Society

Week 2. Scaduto et al. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Week 3. Grant and Grant Evolution of Character Displacement in Darwin’s Finches.

Week 5. Hoekstra et al. A Single Amino Acid Mutation Contributes to Adaptive Beach Mouse Color Pattern.

Week 6. Li et al. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude.

Week 7. Andersson. Female choice selects for extreme tail length in a widowbird.
and
Welch et al. Call Duration as an Indicator of Genetic Quality in Male Gray Tree Frogs.

Week 9. Hopkins and Rausher. Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii.

Week 10. Arnegard et al. Old gene duplication facilitates origin and diversification of an innovative communication system—twice.

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journal tea April 4th

Let’s read:
“Detecting selective sweeps from pooled next generation sequencing samples”

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journal tea: 26th March

forgot to post this but we read Simon Gravel’s paper on admixture:
http://arxiv.org/abs/1202.4811

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journal tea 20th March

For tuesday let’s read: the Hudson and Kaplan chapter from the Golding book “Non-Neutral Evolution”. A scanned copy is here. It’s good intro. to background selection.

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