Phylogenetics: new data, new phylogenetic challenges

Workshop theme

Phylogenetic trees and networks are central to modern molecular evolutionary biology, with applications ranging from the origin of viruses (e.g. HIV, influenza) to modeling plant and animal radiations. As biologists attempt to reconstruct larger slices of the 'tree of life' using rapidly increasing amounts of complex data, and incorporating more accurate models of molecular evolution, mathematics (and its sister fields, statistics and computer science) is increasingly being seen as an essential tool.

This workshop will showcase some of the recent achievements, challenges and new problems that arise in using mathematical and computational approaches to understand molecular evolution.

The workshop is taking place at the Isaac Newton Institute, where the highly-successful "Phylogenetics" programme took place in Autumn 2007, and will provide an exciting opportunity to drive forward new and existing interdisciplinary interactions, as well as to develop novel ideas and directions in phylogenetics.

Topics will include

Next generation sequence data, and whole genome (non-aligned) phylogeny
Phylogenetic Trees and Networks
Genes, populations, speciation and extinction
Phylogenetic combinatorics and algebraic/geometric methods for modeling evolution
The complexities of a net of life: Networks, polyploidy, metagenomics, and horizontal gene transfer

Keynote speakers

Olivier Gascuel (France)
Dan Gusfield (USA)
Barbara Holland (Australia)
Daniel Huson (Germany)
James McInerney (Ireland)
Arne Mooers (Canada)
Luay Nakhleh (USA)
Gabriel Valiente (Spain)
Arndt von Haeseler (Austria)
Olaf Bininda-Emonds (Germany)
Tandy Warnow (USA)

The application is closed

Timetable

Monday 20th June 2011
08:30 to 09:45	Registration	No Room Required
09:45 to 10:00	Opening remarks and welcome from Dr Ben Mestel (INI Deputy Director)	No Room Required
10:00 to 11:00	Dan Gusfield University of California, Davis Recent Progress on Multi-State Perfect Phylogeny (Compatibility) Problems	Room 1
11:00 to 11:30	Morning coffee	No Room Required
11:30 to 11:50	Maria Luisa Bonet Universitat Politècnica de Catalunya The Complexity of the uSPR distance	Room 1
11:50 to 12:10	Mareike Fischer Center for Integrative Bioinformatics Vienna (CIBIV) Revisiting the question how many characters are needed to reconstruct the true tree	Room 1
12:10 to 12:30	Simone Linz Eberhard Karls Universität Tübingen On the Complexity of the Quartet Challenge	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	Free Time	No Room Required
15:00 to 15:30	Afternoon tea	No Room Required
15:30 to 15:50	Katharina Huber University of East Anglia Metrics on Multi-labeled Trees: Interrelationships and Diameter Bounds	Room 1
15:50 to 16:10	Marc Thuillard None / Other Identifying Lateral Transfers with Neighbor-Nets	Room 1
16:10 to 16:30	Katherine St John City University of New York Exploring Treespace	Room 1
16:30 to 16:50	Bjarki Eldon University of Oxford Concordance between species trees and gene trees with multiple mergers of ancestral lineages	Room 1
16:50 to 17:10	Quantifying diversity and abundance in soil microbial communities from high-throughput sequence data	Room 1
17:10 to 18:10	Welcome wine reception	No Room Required

Tuesday 21st June 2011
09:00 to 10:00	Luay Nakhleh Rice University Reconciling Gene Trees in the Presence of Incomplete Lineage Sorting and Hybridization	Room 1
10:00 to 10:20	Philippe Gambette Université de la Méditerranée (Aix-Marseille II) Quartets and unrooted phylogenetic networks	Room 1
10:20 to 10:40	On the elusivity of softwired clusters	Room 1
10:40 to 11:00	Fumei Lam University of California, Davis Ancestral Recombination Graphs for Missing and Removable Data	Room 1
11:00 to 11:30	Morning coffee	No Room Required
11:30 to 11:50	Celine Scornavacca Eberhard Karls Universität Tübingen Tanglegrams for Rooted Phylogenetic Trees and Networks	Room 1
11:50 to 12:10	Andreas Spillner Ernst-Moritz-Arndt-Universität Greifswald Visualizing reticulate evolution with planar split networks	Room 1
12:10 to 12:30	Stephen Willson Iowa State University Reconstructing the parameters of a network from its tree-average distances	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	Barbara Holland Massey University Phylogenies from DArTs: A stochastic Dollo proces with censored data	Room 1
15:00 to 15:30	Afternoon tea	No Room Required
15:30 to 15:50	Sven Herrmann University of East Anglia Phylogenetic trees and k-dissimilarity maps	Room 1
15:50 to 16:10	Ethan Jewett University of Michigan Corrections to a class of methods for inferring species trees from gene trees	Room 1
16:10 to 16:30	Anne Kupczok Institute of Science and Technology (IST Austria) Modeling the Evolutionary Dynamics of CRISPR spacers	Room 1
16:30 to 16:50	Principal components analysis in tree space	Room 1
16:50 to 17:10	Lars Jermiin CSIRO Ecosystem Sciences (CES) New methods of identifying fast-evolving sites in aligned sequence data	Room 1
17:15 to 18:00	Poster session	No Room Required

Wednesday 22nd June 2011
09:00 to 10:00	Arndt von Haeseler Evaluating the goodness of fit between a phylogenetic model and an alignment	Room 1
10:00 to 10:20	Tim Downing Wellcome Trust Sanger Institute Genome sequencing of Leishmania donovani clinical lines reveals dynamic phylogenetic variation	Room 1
10:20 to 10:40	Alexei Drummond University of Auckland Bayesian time-tree priors	Room 1
10:40 to 11:00	Denise Kühnert University of Auckland Phylodynamic inference - accounting for the interaction of evolutionary and ecological processes	Room 1
11:00 to 11:30	Morning coffee	No Room Required
11:30 to 12:30	Gabriel Valiente Technical University of Catalonia Sequence Classification using Reference Taxonomies	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	Olivier Gascuel CNRS (Centre national de la recherche scientifique) Modelling protein evolution	Room 1
15:00 to 15:20	An empirical study of the effect of sequence alignment on phylogenetic analysis	Room 1
15:20 to 15:50	Afternoon tea	No Room Required
16:00 to 17:00	James McInerney National University of Ireland, Maynooth Are there alternatives to handling site-to-site rate variation in evolutionary characters	Room 1
17:00 to 19:30	Free time	No Room Required
19:30 to 22:00	Hog Roast Garden Party at The Moller Centre	No Room Required

Thursday 23rd June 2011
09:00 to 10:00	Arne Mooers Simon Fraser University Trees as representations of evolutionary information worth keeping	Room 1
10:00 to 10:20	Wim Hordijk Université de Lausanne Speciation & Extinction Rate Estimation from Phylogenetic Trees	Room 1
10:20 to 10:40	Yufeng Wu University of Connecticut Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood	Room 1
10:40 to 11:00	Yufeng Wu University of Connecticut Tree reconciliations: beyond the LCA mapping	Room 1
11:00 to 11:30	Morning coffee	No Room Required
11:30 to 11:50	Jeremy Sumner University of Tasmania A Lie algebraic classification of continuous-time Markov models	Room 1
11:50 to 12:10	Eva Czabarka Medical University of South Carolina (MUSC) A generalization of Stirling numbers and distribution of phylogenetic trees	Room 1
12:10 to 12:30	Tanja Stadler ETH Zürich Mammalian phylogeny reveals recent diversi cation rate shifts	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	Daniel Huson Integrative analysis if environmental sequences	Room 1
15:00 to 15:30	Afternoon tea	No Room Required
15:30 to 17:30	Free afternoon	No Room Required

Friday 24th June 2011
09:00 to 10:00	Olaf Bininda-Emonds Carl von Ossietzky Universität Oldenburg Assessing the limits of phylogenomics: can too much data be a bad thing?	Room 1
10:20 to 10:40	Daniel Doerr Universität Bielefeld Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions	Room 1
10:40 to 11:00	Fabio Pardi CNRS (Centre national de la recherche scientifique) The combinatorics of distance-based tree inference	Room 1
11:00 to 11:30	Morning coffee	No Room Required
11:30 to 12:30	Tandy Warnow Japan Atomic Energy Agency & University of Texas at Austin Estimating ultra-large phylogenies and alignments	Room 1
12:30 to 12:35	Closing remarks and end	Room 1
12:35 to 13:30	Lunch at Wolfson Court	No Room Required

Phylogenetics: new data, new phylogenetic challenges

Speakers

Olaf Bininda-Emonds Carl von Ossietzky Universität Oldenburg
Maria Luisa Bonet Universitat Politècnica de Catalunya
Eva Czabarka Medical University of South Carolina (MUSC)
Daniel Doerr Universität Bielefeld
Tim Downing Wellcome Trust Sanger Institute
Alexei Drummond University of Auckland
Bjarki Eldon University of Oxford
Mareike Fischer Center for Integrative Bioinformatics Vienna (CIBIV)
Philippe Gambette Université de la Méditerranée (Aix-Marseille II)
Olivier Gascuel CNRS (Centre national de la recherche scientifique)
Dan Gusfield University of California, Davis
Sven Herrmann University of East Anglia
Barbara Holland Massey University
Wim Hordijk Université de Lausanne
Katharina Huber University of East Anglia
Daniel Huson
Lars Jermiin CSIRO Ecosystem Sciences (CES)
Ethan Jewett University of Michigan
Anne Kupczok Institute of Science and Technology (IST Austria)
Denise Kühnert University of Auckland
Fumei Lam University of California, Davis
Simone Linz Eberhard Karls Universität Tübingen
James McInerney National University of Ireland, Maynooth
Arne Mooers Simon Fraser University
Luay Nakhleh Rice University
Fabio Pardi CNRS (Centre national de la recherche scientifique)
Celine Scornavacca Eberhard Karls Universität Tübingen
Andreas Spillner Ernst-Moritz-Arndt-Universität Greifswald
Katherine St John City University of New York
Tanja Stadler ETH Zürich
Jeremy Sumner University of Tasmania
Marc Thuillard None / Other
Gabriel Valiente Technical University of Catalonia
Arndt von Haeseler
Tandy Warnow Japan Atomic Energy Agency & University of Texas at Austin
Stephen Willson Iowa State University
Yufeng Wu University of Connecticut

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