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Program on Algebraic Methods in Systems Biology and Statistics

Evolutionary Biology Working Group - Meeting Summary Page

September
October
November
December
January
February
March
April

April 2009

Local: Jason, Megan, Seth, Lynn
Remote: Sonja, Julia

Discussion on the chapter on cophylogeny [33] Page Ch. 1, led by Julia.

Local: Jason, Megan, Seth, Scott, Lynn
Remote: Elizabeth, Sonja, Julia

Continued discussion of [22] Hein et al. Ch. 5.
Meeting notes.

Local: Jason, Megan, Seth, Scott, Sonja, Julia, Lynn
Remote: Elizabeth, Rudy

Continued discussion of [22] Hein et al. Ch. 5.
Meeting notes.

March 2009

Local: Jason, Megan, Seth, Scott
Remote: Peter H., Julia, Rudy, Sonja, Uwe

Presentation "Parametric inference and related problems" by Peter Huggins.

Local: Jason, Megan, Seth, Rudy, Scott
Remote: Elizabeth, John, Amelia

Discussion of [22] Hein et al. Ch. 5.

Local: Jason, Megan, Seth, Luis, Elizabeth, John, Scott
Remote: Julia, Sonja

Discussion of [32] Aldous (2001) and [28] Gernhard (2008). Meeting notes.

Local: Jason, Megan, Seth, Luis, Saeid, Scott
Remote: Amelia, Elizabeth, John, Lynn, Rudy, Sonja, Uwe

Discussion of [27] Degnan and Salter (2005) and [26] Degnan and Rosenberg (2006). Meeting notes.

February 2009

Local: Jason, Megan, Seth, Luis
Remote: Elizabeth, John, Rudy, Sonja, Uwe

Discussion of phylogenetic tree spaces. Megan gave a counter-example (slide 1, slide 2) to the conjecture that the geodesic traverses the relative interiors of the most orthants of any path space geodesic. Seth asked if the variety of a tree containing only branches from two other trees is contained in the product of the varieties of those trees (slide ).

Local: Jason, Megan, Seth, Scott
Remote: John, Julia, Uwe

Discussion of phylogenetic orange space, led by Seth Sullivant.

Local: Jason, Megan, Seth, Scott, Luis
Remote: Elizabeth, John, Julia, Sonja

Discussion of [1] Billera et al. (2001), led by Scott Provan.

January 2009

Local: Jason, Megan, Seth, Scott, Luis
Remote: Elizabeth, John, Or, Sonja, Uwe

Presentation by Or Zuk on Annotating the Human Genome Using Comparative Genomics.

Local: Jason, Megan, Seth, Thomas, John, James, Elizabeth, Luis
Remote: Julia, Laura, Rudy, Serkan, Sonja

Presentation by James Degnan on gene tree distributions and coalescent histories.

Local: Jason, Megan, Seth, Scott, Julia, John, James, Elizabeth, Sonja
Remote:

Organizational meeting. It was decided that this semester will be a mixture of talks and reading papers. The rough schedule is on the first page of the working group website. Everyone will read the paper before the meeting, and one person will lead the discussion of the paper. The person in charge of each topic/paper should find a few relevant references and the .pdf of paper to read.

November 2008

Local: Serkan, Jason, Megan, Seth, Serkan, Uwe, Scott, Julia
Remote: John, Elizabeth, Peter Huggins, Amelia, Rudy, Chris, Sonja, Jerzy

Presentation by Serkan on his preprint "Extended UPGMA and phylogenetic tree reconstruction" (with Fahey, Kreager, and Timpe).

Local: Serkan, Jason, Megan, Seth, Serkan, Uwe, Scott
Remote: Julia, John, Elizabeth, Peter, Rudy, Laura, Sonja, ?

Presentation by Serkan on his preprint "Extended UPGMA and phylogenetic tree reconstruction" (with Fahey, Kreager, and Timpe).

October 2008

Part 3 of the Introduction to Coalescent Theory series was given by Peter Beerli. As well as the question about discrete sampling in his talk, Peter also asked about using tree space to improve the local moves made by the MCMC chain while finding the best tree.

Local: Serkan, Jason, Megan, Seth, Scott
Remote: Elissaveta (Ellie), Laura, Rudy, Jinze, Julia, Gary, Peter, Amelia, John, Sonja, Wenbin, Elizabeth, ?

Part 3 of the Introduction to Coalescent Theory series was given by Laura Salter Kubatko. Laura is interested in allowing hybridization in the species or gene trees, and the relation between Ancestral Recombination Graphs (ARGs) and haplotype data.

Local: Seth, Serkan, Jason
Remote: Peter, Catherine, Chris, Elissaveta, Elizabeth, Jerzy, Julia, Laura, Megan, Rudy, Piotr, John, Sonja, Uwe, Wenbin.

Part 1 of the Introduction to Coalescent Theory series was given by Peter Beerli.

Local participants: Jason, Seth, Megan, Saeid, Scott
Remote: Laura, John, Elizabeth, Rudy, Sonja, Julia, Piotr, Uwe

Seth gave a presentation entitled Some algebraic ideas for phylogenetic mixtures. The non-working code for the computations on slide 9 (?) is available here.

September 2008

Local participants: Catherine Matias, Megan Owen, John Rhodes, Seth Sullivant, Scott Provan, Jason Yellick
Remote participants: Elizabeth Allman, Julia Chifman, Sonja Petrovic, Piotr Zwiernik

John gave a presentation on phylogenetic models and invariants. Very rough meeting notes are here.

Local participants: Serkan Hosten, Catherine Matias, Megan Owen, John Rhodes, Seth Sullivant, Saeid Yasamin, Jason Yellick
Remote participants: Elizabeth Allman, Brandon Barker, Julia Chifman, Sonja Petrovic

Megan presented these slides on the construction of tree space by Billera et al., including the tropical geometry connection, and her algorithm to compute the geodesic distance in this space.
We then discussed ideas for a space of phylogenetic networks, computing the "average" of weighted trees in tree space, putting a Markov matrix instead of real number on the tree edges, and the "phylogenetic orange" space (links to reference papers for this space coming).

Topics of interest, and people responsible for providing introductory references and other papers of interest: (note: I have received some of these links, but they aren't posted yet.)

• Phylogenetics - Megan, Rudy (for cophylogeny problem)
• Population Biology - Andrew
• Coalescence Theory - Seth
• Evolution of Networks (ie. comparing protein-to-protein networks between species)- Or
• Open problems - everyone (if submitting an open problem, please try to include the context of the problem, possible approaches or approaches that have been tried, etc. This can be placed on the secure server.)

November 2008

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December 2008

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