Evolutionary Biology Working Group Home Page

Announcements

No meeting on April 6, 2009.

MEETING ACTIVITIES
GROUP MEMBERS
REFERENCE LIST
DATA SITES
INSTRUCTIONS FOR DIAL-IN AND WebEx ACCESS

Meeting Activities

** Clicking on a date will take you to that date on the Meeting Summary page **

-->

DATE	TOPICS & Readings	Notes
05/04/09	Scheduled presentation by Scott and Megan of their geodesic distance results.
04/27/09	Discussion on the chapter on cophylogeny [33] Page Ch. 1, led by Julia. slides	Paper about TreeMap: [35] Page and Charleston
04/20/09	Continuation of discussion of Hein chapter on combining recombination and coalescence, led by Jason, Sonja, and Julia: [22] Hein et al. Ch. 5, pages 158-171 of Hein, improved scans of the figures [34] Wiuf and Hein
04/13/09	Continuation of discussion of Hein chapter on combining recombination and coalescence, led by Jason, Sonja, and Julia: [22] Hein et al. Ch. 5, pages 158-171 of Hein, improved scans of the figures.
04/06/09	Cancelled. Scheduled discussion has been moved to next week.
03/30/09	Presentation by Peter Huggins: Title: Parametric inference and related problems slides
03/23/09	Discussion of ancestral recombination graphs (ARGs), led by Jason Yellick. Covered sections 5.1-5.3 of [22] Hein et al. Ch. 5 (highlighted version)	Ancestral recombination graph references: [21] Simonsen and Churchill (1997) [22] Hein et al. Ch. 5 [23] Wakeley Ch. 7 [24] McVean and Cardin (2005)
03/16/09	Discussion of speciation models, led by Luis Garcia-Puente. Start with [32] Aldous (2001) (highlighted version), and then [28] Gernhard (2008).	Speciation models references: [28] Gernhard (2008) [29] Gernhard et al. (2006) [30] Aldous and Popovic (2005) [31] Aldous et al. (2008) [32] Aldous (2001) John recommends beginning with [32], which is an easy overview. Then look at sections 2.1 and 2.2 of [28], which is Gernhard's Ph.D. thesis for more on the basics of the uniform and Yule models. It would also be good to have an overview of what biological problems Gernhard is looking at. After that, turning to either chapter 4 of [28] (which is also presented in paper [29]) is a possibility. Alternately, there are other speciation models in the papers of Aldous et al. (Appendix to [30], [31], [32]) that are not so mainstream.
03/09/09	No meeting.
03/02/09	Discussion of [26] Degnan and Rosenberg (2006) and [27] Degnan and Salter (2005), led by Uwe Nagel.
02/23/09	Further discussion of phylogenetic tree spaces.
02/16/09	Continued discussion of the phylogenetic orange space, including the remainder of [19] Moulton and Steel (2004) and [20] Gill et al. (2008), led by Seth Sullivant: slides
02/09/09	Discussion of the phylogenetic orange space ([18] Kim (2000) and the first three sections of [19] Moulton and Steel (2004)), led by Megan Owen: slides 1 slides 2	Reference: [25] Steel (2009)
02/02/09	Discussion of [1] Billera et al. (2001), led by Scott Provan: slides 1
01/26/09	Presentation by Or Zuk Title: Annotating the Human Genome Using Comparative Genomics slides
01/19/09	Presentation by James Degnan Title: Gene tree distributions and coalescent histories slides
01/12/09	Organizational meeting
12/02/08	Fall summary meeting
11/18/08	Presentation by Julia Chifman: Title: Group-based models slides	References: [14] Sturmfels and Sullivant (2005) [15] Szekely, Erdos, Steel, Penny (1993) [16] Szekely, Steel, Erdos (1993) [17] Chifman and Petrovic (2008)
11/11/08	Presentation by Rudy Yoshida: Title: Open Problems in Geometry of Cophylogeny slides (math) slides (biology)	Reference: [13] Huggins and Yoshida (2008)
11/04/08	Presentation by Serkan Hosten: Title: Extended UPGMA and phylogenetic tree reconstruction slides
10/28/08	Presentation by Peter Beerli (Part 3 of the introduction to coalescent theory series): Title: Finding good trees - Simplifying Coaslescent trees slides	References suggested by Peter: bibtex file recombination (Kuhner style) [7] Kuhner et al. (2000) recombination (Wiuf style) [8] Wiuf and Hein (1999) an example of linkage disequlibirum mapping using the coalescent [9] Morris et al. (2002) slice sampling [10] Neal (2003) my own sampler (1998,1999) and extension of that more exotic approaches with the coalescent (Moehle, Limic, Schweinsberg) [10] Moehle and Sagitov (2003) [11] Limic and Sturm (2005) [12] Schweinsberg (2000)
10/21/08	Presentation by Laura Salter Kubatko (Part 2 of introduction to coalescent theory series): slides
10/14/08	Presentation by Peter Beerli (Part 1 of introduction to coalescent theory series): Title: Population genetic calculations that do not fit on the back of an envelope slides
10/07/08	Presentation by Seth Sullivant: Title: Some algebraic ideas for phylogenetic mixtures slides	[6] Sidman and Sullivant. Prolongations and Computational Algebra Seth's code
9/30/08	Presentation by John Rhodes on phylogenetic invariants slides	The chapter Phylogenetic invariants by Allman-Rhodes in the book Reconstructing Evolution: New Mathematical and Computational Advances, eds., Gascuel and Steel, Oxford University Press, 2007 [5], provides an overview. It gives exhaustive references to every paper we knew of that touched on the topic, up through about 2005.
9/23/08	Presentation by Megan Owen on the space of phylogenetic trees and the geodesic distance Title: Space of Phylogenetic Trees slides	Related references, furnished by Megan: [1] Billera et al. (2001) [2] Owen (2008) [3] Kupczok et al. (2008) [4] Amenta et al. (2008)
9/18/08	Group Introduction and organizational meeting

Group Members

(email alias for the group is alg-evol at samsi.info)

Name	Affiliation	Email Address
Elizabeth Allman	University of Alaska-Fairbanks	e.allman AT uaf DOT edu
Elisaveta Arnaudova	University of Kentucky	elicaraabe AT yahoo DOT com
Brandon Barker	Cornell University	beb82 AT cornell DOT edu
Peter Beerli	Florida State University	beerli AT csit DOT fsu DOT edu
Julia Chifman	University of Kentucky	jchifman AT ms DOT uky DOT edu
Elena Dimitrova	Clemson University	edimit AT clemson DOT edu
Andrew Francis	University of Western Sydney	a.francis AT uws DOT edu DOT au
Luis Garcia-Puente	Sam Houston State University	ldg005 AT shsu DOT edu
Serkan Hosten	San Francisco State University	serkan AT math DOT sfsu DOT edu
Thomas Kahle		kahle AT mis DOT mpg DOT de
Gary Kennedy	Ohio State	kennedy AT math DOT ohio-state DOT edu
Laura Kubatko	Ohio State University	lkubatko AT stat DOT ohio-state DOT edu
Lynn Kuo	University of Connecticut	lynn AT stat DOT uconn DOT edu
Jinze Liu	University of Kentucky	liuj AT netlab DOT uky DOT edu
Chris Manon	University of Maryland	manonc AT math DOT umd DOT edu
Catherine Matias		catherine.matias AT genopole DOT cnrs DOT fr
Uwe Nagel	University of Kentucky	uwenagel AT ms DOT uky DOT edu
Megan Owen	SAMSI	mao29 AT cornell DOT edu
Vittorio Perduca		vittorio.perduca AT gmail DOT com
Sonja Petrovic	University of Illinois at Chicago	petrovic AT math DOT uic DOT edu
Scott Provan	University of North Carolina	provan AT email DOT unc DOT edu
Christopher Randle	Sam Houston State University	cpr003 AT shsu DOT edu
John Rhodes	University of Alaska-Fairbanks	j.rhodes AT uaf DOT edu
Chris Schardl	University of Kentucky	schardl AT email DOT uky DOT edu
Jian Shen	Texas State University	js48 AT txstate DOT edu
Seth Sullivant	N.C. State University	seths AT math DOT harvard DOTedu
Amelia Taylor	Colorado College	amelia.taylor AT coloradocollege DOT edu
Caroline Uhler	Univ. of California-Berkeley	cuhler AT stat DOT berkeley DOT edu
Richard Yamada	University of Michigan	yryamada AT umich DOT edu
Saeid Yasasmin	SAMSI	syasamin AT gmail DOT com
Jason Yellick	N.C. State University	jkyellic AT ncsu DOT edu
Ruriko Yoshida	University of Kentucky	ruriko.yoshida AT uky DOT edu
Ryo Yoshida		yoshidar AT ism DOT ac DOT jp
Or Zuk	M.I.T.	orzuk AT broad DOT mit DOT edu
Piotr Zwiernik	University of Warwick	p.w.zwiernik AT warwick DOT ac DOT uk

Reference List

1. Billera, Holmes, and Vogtmann (2001), Geometry of the space of phylogenetic trees.
2. Owen (2008), Distance computation in the space of phylogenetic trees
3. Kupczok, von Haeseler, and Klaere (2008), An exact algorithm for the geodesic distance between phylogenetic trees.
4. Amenta et al. (2007), Approximating geodesic tree distance.
5. Allman and Rhodes (2007), Chapter Phylogenetic invariants in the book Reconstructing Evolution: New Mathematical and Computational Advance.
6. Sidman and Sullivant (2008), Prolongations and Computational Algebra
14. Sturmfels and Sullivant (2005) Toric Ideals of Phylogenetic Invariants
15. Szekely, Erdos, Steel, Penny (1993) A Fourier Inversion Formula for Evolutionary Trees
16. Szekely, Steel, Erdos (1993)Fourier Calculus on Evolutionary Trees
17. Chifman and Petrovic (2008) Toric ideals of phylogenetic invariants for the general group-based model on claw trees K_{1,n}
18. Kim (2000) Slicing hyperdimensional oranges: the geometry of phylogenetic estimation
19. Moulton and Steel (2004) Peeling phylogenetic 'oranges'
20. Gill, Linusson, Moulton, and Steel (2008) A regular decomposition of the edge-product space of phylogenetic trees
25. Steel (2009) A basic limitation on inferring phylogenies by pairwise sequence comparisons
26. Degnan and Rosenberg (2006) Discordance of Species Trees with Their Most Likely Gene Trees
27. Degnan and Salter (2005) Gene Tree Distributions under the Coalescent Process
28. Gernhard (2008) Stochastic Models for Speciation Events in Phylogenetic Trees
29. Gernhard, Ford, Vos, and Steel (2006) Estimating the relative order of speciation or coalescence events on a given phylogeny
30. Aldous and Popovic (2005) A Critical Branching Process Model for Biodiversity
31. Aldous, Krikun, and Popovic (2008) Stochastic Models for Phylogenetic tTrees on Higher-order Taxa
32. Aldous (2001) Stochastic Models and Descriptive Statistics for Phylogenetic Trees, from Yule to Today
33. Page (2002) Tangled Trees: Phylogeny, Cospeciation, and Coevolution, Chapter 1.
34. Wiuf and Hein (1999) Recombination as a Point Process along Sequences
35. Page and Charleston (2002) Treemap Versus BPA (Again): A Response to Dowling

Data Sites

Working Groups Dial-in & WebEx Instructions

1. Go to the email invitation that you received announcing the meeting, or go directly to WebEx: https://samsi.webex.com
2. Click on the link for the meeting you want to join
      • Enter Your Name, Your Email Address and the meeting password from the email invitation
      • The first time you use WebEx, the Meeting Manager will run and it will take about a minute to setup.
    • Now you are in the meeting and can use all the features of WebEx
3. Dial the teleconference line: 919-685-9338.
      • It is necessary to separately call into the given conference-line phone number to obtain audio interaction; we are not able to use WebEx for an audio connection. When calling in:
          o do not use a computer microphone or a speaker phone; this causes severe feedback in the system;
          o headphones and hand-held phones are fine.
      • If cost of telephone calls is an issue, consider using either Skype or JaJah to place your calls to the conference line; these are virtually free within North America, and (for example) only cost roughly 2 cents and 3 cents per minute, respectively, from Europe.
      • Please dial no earlier than 5 minutes prior to the start of the working group meeting.

Please Note: You should be seeing the screen of the presenters. If not, please send a message or call for assistance. WebEx can run slowly on Unix machines.

If you are having trouble with WebEx or the Teleconference line please contact Sue McDonald, sue@samsi.info (919)685-9359 or James Thomas, help@samsi.info (919)685-9307

You can learn more about WebEx and take tutorials at university.webex.com.