2008 Workshop

Schedule

	Morning	Afternoon	Evening
Saturday		Arrivals	Setup Student Projects
Sunday	Phylogenetics Medley (Wainwright ppt) / PAUP tutorial (O'Meara) (lecture pdf)	Bayesian Phylogenetics (Rannala)	Phylogeography (Lemmon & Lemmon)
Monday	Species Concepts (de Queiroz)/ Tree-Based Species Delimitation (O'Meara) (OMearaSpeciesDelimLecture.pdf)	Species Boundaries (Shaffer) / Structurama tutorial (Thomson)	Discussion: Rank Free taxonomy (Mishler)
Tuesday	Comparative Methods I (Glor) (Lectures: Ancestral_Reconstruction.pdf), Discrete_Character_Correlation.pdf)	Comparative Methods II (Whittall)Whittall ppt.pdf	Phylogenomics (Eisen)/Web tools for Phylogenetics (Thomson)
Wednesday	Morphological Diversification (Wainwright & O'Meara) (OMearaBrownieLecture.pdf)	FIELD TRIPS	NESCent overview (O'Meara)/ R Tutorial (Glor & O'Meara)
Thursday	Divergence Times & BEAST tutorial (Moore)	Diversification Rates (Moore)	Work on Projects (also a Bay Area Biosystematists meeting)
Friday	Finish up projects & Begin Presentations	More Student Presentations	Free
Saturday	Pack up and go home

Students

Balinda	Sheila	Uganda	Makerere U	`<Sbalinda AT muienr DOT mak DOT ac DOT ug>`
Bess	Emilie	USA	Illinois	`<bess AT inhs DOT uiuc DOT edu>`
Clucas	Barbara	USA	UCD	`<baclucas AT ucdavis DOT edu>`
Drauch	Andrea	USA	UCD	`<amdrauch AT ucdavis DOT edu>`
Finger	Amanda	USA	UCD	`<ajfinger AT ucdavis DOT edu>`
Glass	Jennifer	USA	Arizona State	`<jbglass1 AT asu DOT edu>`
Greenberg	Anne	USA	Yale	`<anne DOT greenberg AT yale DOT edu>`
Grossenbacher	Dena	USA	UCD	`<dgrossenbacher AT ucdavis DOT edu>`
Grusz	Amanda	USA	Duke	`<alg3 AT duke DOT edu>`
Hornsby	Angela	USA	Idaho State	`<adhornsby AT gmail DOT com>`
Krakos	Kyra	USA	WUSTL	`<knburras AT artsci DOT wustl DOT edu>`
Kurushima	Jennifer	USA	UCD	`<jdkurushima AT ucdavis DOT edu>`
Long	Elizabeth	USA	UCD	`<eclong AT ucdavis DOT edu>`
Pennington	Jillian	USA	Yale	`<jillian DOT pennington AT yale DOT edu>`
Robertson	Kelly	USA	U Illinois	`<krober6 AT uic DOT edu>`
Robinson	Donelle	USA	Ohio U	`<dr647706 AT ohio DOT edu>`
Schirtzinger	Erin	USA	New Mexico State	`<eesem AT nmsu DOT edu>`
van Herwerden	Lynne	Australia	James Cook	`<lynne DOT vanherwerden AT jcu DOT edu DOT au>`
Anacker	Brian	USA	UCD	`<blanacker AT ucdavis DOT edu>`
Beaulieu	Jeremy	USA	Yale	`<jeremy DOT beaulieu AT yale DOT edu>`
Bloom	Devin	Canada	U Toronto	`<devin DOT bloom AT utoronto DOT ca>`
Busch	Joseph	USA	Purdue	`<jdbusch AT purdue DOT edu>`
Camargo	Arley	USA	BYU	`<arley_camargo AT byu DOT net>`
Diogo	Rui	USA	GW	`<ruidiogo AT gwu DOT edu>`
Doffitt	Chris	USA	MS State	`<chd19 AT msstate DOT edu>`
Ellingson	Ryan	USA	UCLA	`<rellingson AT ucla DOT edu>`
Hansen	Daniel	Denmark	Denmark Tech	`<daniel AT cbs DOT dtu DOT dk>`
Muir	Chris	USA	Indiana University	`<cdmuir AT indiana DOT edu>`
Pearse	Ian	USA	UCD	`<ispearse AT ucdavis DOT edu>`
Pightling	Arthur	USA	U Iowa	`<arthur-pightling AT uiowa DOT edu>`
Piwczynski	Marcin	Poland	Copernicus U	`<piwczyn AT umk DOT pl>`
Rejmanek	Daniel	USA	UCD	`<drejmanek AT ucdavis DOT edu>`
Sangula	Abraham	Uganda	Makerere U	`<aksangula AT muienr DOT mak DOT ac DOT ug>`
Sedano	Raul	USA	UCLA	`<rsedano AT ucla DOT edu>`
Sedio	Brian	USA	Michigan	`<bsedio AT umich DOT edu>`
Wolfe	Benjamin	USA	Harvard	`<bewolfe AT fas DOT harvard DOT edu>`

Student Pages

Instructors

	Institution	Topic	Email
Kevin de Queiroz	Smithsonian Institution	Species & Rank Free Taxonomy	`<dequeirozk AT si DOT edu>`
Jonathan Eisen	UC Davis	Phylogenomics	`<jaeisen AT ucdavis DOT edu>`
Rich Glor	University of Rochester	Comparative Methods	`<rglor AT mail DOT rochester DOT edu>`
Alan Lemmon	UC Davis	Phylogeographic Methods	`<arlemmon AT ucdavis DOT edu>`
Brent Mishler	UC Berkeley	Rank Free Taxonomy	`<BMishler AT calmail DOT berkeley DOT edu>`
Brian Moore	UC Berkeley	Species Diversification	`<brian DOT moore AT yale DOT edu>`
Emily Moriarty Lemmon	UC Davis	Phylogeographic Methods	`<emlemmon AT ucdavis DOT edu>`
Brian O'Meara	NESCent	Comparative Methods & Species Delimitation	`<bcomeara AT nescent DOT org>`
Tom Near	Yale	Dating Phylogenetic Trees	`<thomas DOT near AT yale DOT edu>`
Bruce Rannala	UC Davis	Bayesian Inference of Phylogenetic Trees	`<brannala AT ucdavis DOT edu>`
Brad Shaffer	UC Davis	Phylogeography & Species Delimitation	`<hbshaffer AT ucdavis DOT edu>`
Phil Spinks (coordinator)	UC Davis	Phylogenetics	`<pqspinks AT ucdavis DOT edu>`
Bob Thomson	UC Davis	Species Delimitation	`<rcthomson AT ucdavis DOT edu>`
Peter Wainwright	UC Davis	Morphological Diversification	`<pcwainwright AT ucdavis DOT edu>`
Justen Whittall	Santa Clara University	Comparative Methods	`<jwhittall AT scu DOT edu>`

2008 Workshop Participants

Students working on an exerciseLunch on the lab's patioPeter Wainwright's annual beach hike

Finished

Pre-Bodega Todo List for Students

If you get a chance it would be convenient if you can install some of the software that we'll be using ahead of time. We've compiled a list here. You can wait to do this once you get here, but doing it ahead of time will save time and won't bog down the internet connection at the lab.
Get yourself to Storer Hall
Reserve Rules (they make us distribute these, please read them)

For Sunday

Download this: PaupStuff.zip
Garli dataset: murphy32.nex
Garli manual: manual
PhyloMapper: PhyloMapper1b1.zip

For Monday

NOTE: If (and only if) you have an Intel Mac running OS 10.4 or 10.5, please grab a JIST disk at the back of the room, copy its contents to your computer, and return the disk (much faster than downloading)
Brownie (Intel Macs OS 10.4 or higher) [12.4 MB]
JistData.zip (Data for the species delimitation exercise)
marm.in (Data for the structurama exercise)
Structurama.pdf (handout for the structurama exercise)

For Tuesday

Aquilegia.nex (Mesquite Input file for Afternoon Exercises)
IndependentContrastsExercises.pdf (Tutorial for Afternoon Exercises)

For Wednesday (do this ahead of time, as it DOES require downloads)

New Get R file to edit (randomPoints.R) and the completed one (randomPointsAnswers.R). You can read more about what we're simulating in Price1997.pdf

Get BrownieHandout.pdf, Results2.xls, and Myrm.nex.
Install R (R-2.6.2-win32.exe on a PC, open R2.6.2.dmg on a Mac and run the installer)
Once R is open, install the necessary packages. We want to install ape, geiger, ouch, and ade4. You can do this by typing install.packages() and selecting the packages to install. Note that the list is alphabetical, but capital letters are first ('Z' comes before 'a'), so scroll down to get the packages we want.

BayesTraits Demonstration (Minimum Model of Pollination Syndromes in Columbines by Justen Whittall)
Bayes Multistate Treefile.txt (Treefile)
Bayes Multistate Datafile.txt (Datafile)

For Thursday

Due to a bug in the most recent version of BEAST, you'll need to get a new version of the tutorial from the thumb drive that is going around the room. Please do this before the beginning of the second morning session.