Schedule for: 17w5104 - Mathematical Approaches to Evolutionary Trees and Networks

Arriving in Banff, Alberta on Sunday, February 12 and departing Friday February 17, 2017
Sunday, February 12
16:00 - 17:30 Check-in begins at 16:00 on Sunday and is open 24 hours (Front Desk - Professional Development Centre)
16:00 - 18:00 Discussions begin as people arrive at BIRS. (TCPL 201)
18:00 - 20:00 Dinner
A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
20:00 - 22:00 Informal gathering (Corbett Hall Lounge (CH 2110))
Monday, February 13
07:00 - 08:45 Breakfast
Breakfast is served daily between 7 and 9am in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
08:45 - 09:00 Introduction and Welcome by BIRS Station Manager (TCPL 201)
09:00 - 09:45 Susan Holmes: Tree Space: A Historical Perspective (TCPL 201)
09:45 - 10:15 Megan Owen: Statistics in BHV Tree Space (TCPL 201)
10:15 - 10:45 Coffee Break (TCPL Foyer)
10:45 - 11:30 Steve Evans: Big Trees (TCPL 201)
11:30 - 12:00 Likelihood challenges for big trees and networks (Claudia Solis-Lemus)
Usual statistical inference techniques for the tree of life like maximum likelihood and bayesian inference through Markov chain Monte Carlo (MCMC) have been widely used, but their performance declines as the datasets increase (in number of genes or number of species). I will present two new approaches suitable for big data: one, importance sampling technique for bayesian inference of phylogenetic trees, and two, a pseudolikelihood method for inference of phylogenetic networks. The proposed methods will allow scientists to include more species into the tree of life, and thus complete a broader picture of evolution.
(TCPL 201)
12:00 - 13:00 Lunch (Vistas Dining Room)
13:00 - 13:30 Dan Brown: Fast algorithms for phylogenetic reconstruction of aligned sequeneces (TCPL 201)
13:30 - 14:00 Elizabeth Allman: Identifiability of species tree topologies from summary statistics (TCPL 201)
14:00 - 14:30 James Degnan: Inferring rooted species trees from unrooted gene trees (TCPL 201)
14:30 - 17:00 Coffee and Collaboration Time (TCPL Foyer)
17:00 - 17:30 Tom Britton: Inference from transmission phylogenies (TCPL 201)
17:30 - 18:00 Art Poon: Likelihood-free inference on tree shapes with kernel methods (TCPL 201)
18:00 - 20:00 Dinner
A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
Tuesday, February 14
07:00 - 08:45 Breakfast (Vistas Dining Room)
09:00 - 09:30 Ziheng Yang: Bayesian inference from genomic sequence data under the multispecies coalescent (TCPL 201)
09:30 - 10:00 Amaury Lambert: A split and drift random graph (TCPL 201)
10:00 - 10:30 Chris Whidden: The shape of subtree prune and regraft tree space: current progress and open problems (TCPL 201)
10:30 - 11:00 Coffee Break (TCPL Foyer)
11:00 - 11:30 Caroline Colijn: Metrics on phylogenetic tree shapes (TCPL 201)
11:30 - 12:00 Leonid Chindelevitch: Expanding, evaluating and combining tree shape statistics (TCPL 201)
12:00 - 12:30 Giacomo Plazzotta: Cherries, trees and cherries without trees (TCPL 201)
12:30 - 13:30 Lunch (Vistas Dining Room)
13:30 - 15:00 Collaboration time (TCPL Foyer)
15:00 - 15:30 Coffee break (TCPL 201)
15:30 - 16:00 Continue collaboration (TCPL 201)
16:00 - 16:30 Olivier Gascuel: Smoothing Felsenstein’s Bootstrap (TCPL 201)
16:30 - 17:00 Cedric Chauve: Dating species trees with lateral transfers. (TCPL 201)
17:00 - 17:30 Katia Koelle: Estimating demographic parameters from viral phylogenies, with an application to flu (TCPL 201)
18:00 - 20:00 Dinner
A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
Wednesday, February 15
07:00 - 09:00 Breakfast (Vistas Dining Room)
08:45 - 09:15 Sergei Pond: Scaling up phylognetic comparative coding sequence analysis using approximations and models that adapt their complexity to the data (TCPL 201)
09:15 - 09:45 Tanja Stadler: The fossilised birth-death chronospecies model: a coherent modelling framework for the fossil record & extant species samples (TCPL 201)
09:45 - 10:15 Noah Rosenberg: Counting ancestral configurations for gene trees and species trees (TCPL 201)
10:15 - 10:45 Coffee break (TCPL 201)
11:15 - 11:45 Matthew Hall: Transmission tree reconstruction by augmentation of internal phylogeny nodes (TCPL 201)
12:30 - 13:30 Lunch (Vistas Dining Room)
13:30 - 17:30 Free Afternoon (Banff National Park)
18:00 - 20:00 Dinner
A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
Thursday, February 16
07:00 - 08:30 Breakfast (Vistas Dining Room)
08:30 - 09:00 Vincent Moulton: Assembling the network of life (TCPL 201)
09:00 - 09:30 Katharina Huber: Orthology relations: From trees to networks (TCPL 201)
09:30 - 10:00 Charles Semple: What is a typical tree-child network? (TCPL 201)
10:00 - 10:30 Coffee Break (TCPL Foyer)
10:30 - 11:00 Emmanuel Schertzer: Chromosome painting (TCPL 201)
11:00 - 11:30 Amandine Véber: How to make good resolutions (TCPL 201)
11:30 - 12:00 Dan Gusfield: The History Bound (on the number of recombinations needed) now has a static definition, but does it help? (TCPL 201)
12:00 - 13:00 Lunch (Vistas Dining Room)
13:00 - 13:30 Michael Fuchs: Two Biodiversity Parameters of Evolutionary Trees: the Fair Proportion Index and the Shapley Value (TCPL 201)
14:00 - 14:30 Nadia El-Mabrouk: A general framework for gene tree correction (TCPL 201)
14:30 - 17:30 Collaboration with coffee at 3pm (TCPL 201)
15:00 - 15:30 Coffee during afternoon collaboration session (TCPL Foyer)
18:00 - 20:00 Dinner
A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.
(Vistas Dining Room)
Friday, February 17
07:00 - 09:00 Breakfast (Vistas Dining Room)
09:00 - 09:30 Mareike Fischer: Maximum Parsimony on Phylogenetic Networks
Ever since Darwin’s first sketch of a phylogenetic tree, such trees are the model of choice for most evolutionary studies. But unfortunately, trees are unable to explain phenomena like horizontal gene transfer and hybridization. As many organisms are known to be subject to these evolutionary events, phylogenetic trees are more and more replaced by so-called phylogenetic networks. The aim is then to find the best network for a given dataset according to an optimization criterion. One such criterion often used for phylogenetic tree reconstruction is Maximum Parsimony. In my talk, I will present different ways to extend the parsimony concept from trees to networks, and I will explain some interesting properties of parsimony on networks. In particular, I will show that in networks, even the so-called “small parsimony problem” is hard, and I will also show that, in contrast, the “big” parsimony problem has some trivial solutions. The results presented in my talk are joint work with Leo van Iersel, Steven Kelk and Céline Scornavacca (small parsimony problem) as well as with Christopher Bryant, Simone Linz and Charles Semple (big parsimony problem).
(TCPL 201)
09:30 - 10:00 Teemu Roos:  Likelihood-based Inference of Phylogenetic Networks from Sequence Data by PhyloDAG
Processes such as hybridization, horizontal gene transfer, and recombination result in reticulation which can be modeled by phylogenetic networks. Earlier likelihood-based methods for inferring phylogenetic networks from sequence data have been encumbered by the computational challenges related to likelihood evaluations. Consequently, they have required that the possible network hypotheses be given explicitly or implicitly in terms of a backbone tree to which reticulation edges are added. To achieve speed required for unrestricted network search instead of only adding reticulation edges to an initial tree structure, we employ several fast approximate inference techniques. Preliminary numerical and real data experiments demonstrate that the proposed method, PhyloDAG, is able to learn accurate phylogenetic networks based on limited amounts of data using moderate amounts of computational resources.
(TCPL 201)
10:00 - 10:30 Coffee Break (TCPL Foyer)
10:00 - 10:30 Pedro Feijao: TBC (TCPL 201)
10:30 - 12:00 Collaboration and discussion; Conclusion (TCPL 201)
11:30 - 12:00 Checkout by Noon
5-day workshop participants are welcome to use BIRS facilities (BIRS Coffee Lounge, TCPL and Reading Room) until 3 pm on Friday, although participants are still required to checkout of the guest rooms by 12 noon.
(Front Desk - Professional Development Centre)
12:00 - 13:30 Lunch from 11:30 to 13:30 (Vistas Dining Room)