Phyloseminar

phyloseminar -- a free online seminar about phylogenetics

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1 hour 4 min ago

March 17, 2014

19:00

Genome rearrangements were discovered and used to build molecular phylogenies in the 1930s. They are implied in many cancers and their evolutionary role might be of primary importance. But the mathematical and computational tools to model rearrangements are still not as efficient as the ones developed later for local mutations as nucleotide or amino-acid substitutions. In this seminar I will report the attempts to integrate genome organisations in the usual models of genome evolution. I will explain how this can improve the inference of phylogenies, as well as ancestral genomes.

19:00

Genome rearrangements were discovered and used to build molecular phylogenies in the 1930s. They are implied in many cancers and their evolutionary role might be of primary importance. But the mathematical and computational tools to model rearrangements are still not as efficient as the ones developed later for local mutations as nucleotide or amino-acid substitutions. In this seminar I will report the attempts to integrate genome organisations in the usual models of genome evolution. I will explain how this can improve the inference of phylogenies, as well as ancestral genomes.

March 16, 2014

19:00

In this second talk of our series on genome-scale phylogeny, I build upon Gergely's introduction and present the modelling assumptions and algorithmic details behind some of the methods we and others have developed. There will be two parts to this talk. I start with the model of gene duplications and losses implemented in PHYLDOG. I present the assumptions we make and the shortcuts we take to improve the program's efficiency, and show some results on real and simulated sequence data. I notably show problems that arise when the program is confronted with data generated with a model of incomplete lineage sorting (Rasmussen and Kellis, 2012), and present avenues of research to find solutions to these problems. In the second part, I present our current efforts to use our model of gene duplication, loss, and transfer (Szöllosi et al, 2013) to infer a species tree in which speciation nodes are ordered in time. I briefly remind the forgetful viewer of what this model does and how it works, and I then explain how we devise a new MCMC algorithm to use it on data sets containing dozens of species and thousands of gene families. I finish with some perspectives of our plans uniting gene tree-species tree models and databases of gene families and phylogenetic trees.

19:00

In this second talk of our series on genome-scale phylogeny, I build upon Gergely's introduction and present the modelling assumptions and algorithmic details behind some of the methods we and others have developed. There will be two parts to this talk. I start with the model of gene duplications and losses implemented in PHYLDOG. I present the assumptions we make and the shortcuts we take to improve the program's efficiency, and show some results on real and simulated sequence data. I notably show problems that arise when the program is confronted with data generated with a model of incomplete lineage sorting (Rasmussen and Kellis, 2012), and present avenues of research to find solutions to these problems. In the second part, I present our current efforts to use our model of gene duplication, loss, and transfer (Szöllosi et al, 2013) to infer a species tree in which speciation nodes are ordered in time. I briefly remind the forgetful viewer of what this model does and how it works, and I then explain how we devise a new MCMC algorithm to use it on data sets containing dozens of species and thousands of gene families. I finish with some perspectives of our plans uniting gene tree-species tree models and databases of gene families and phylogenetic trees.

March 15, 2014

19:00

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees.

I introduce models that describe the relationship between gene trees and species trees. I begin with models that account for gene duplication and loss, and subsequently introduce models that account for the horizontal transfer of genes. I review results from simulations as well as empirical studies on genomic data that show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. I also discuss the possibility of extracting information on the timing of speciation events from ancient horizontal transfer events.

February 13, 2014

14:24

The emergence of graph databases has presented a potential alternative for ways of storing and querying phylogenetic trees. The Open Tree of Life has been exploring these options and ways that trees from multiple datasets or within a single dataset can be placed in a graph database. I will go over some of the ways that we do this and how we can query and synthesize trees as an alternative to supertrees and consensus trees. While still a work in progress, these methods show great promise for further development.

February 6, 2014

19:00

Open Tree of Life aims to synthesize published phylogenetic data into a comprehensive tree of life. The challenges associated with the collection, curation and synthesis of both phylogenetic and taxonomic input data are both technical and social. We present the first draft of the Open Tree of Life, as well as the workflow and software tools for curating, annotating and viewing phylogenetic data. In a subsequent Phyloseminar, Stephen Smith will present details of the phylogenetic synthesis methods.

14:24

The emergence of graph databases has presented a potential alternative for ways of storing and querying phylogenetic trees. The Open Tree of Life has been exploring these options and ways that trees from multiple datasets or within a single dataset can be placed in a graph database. I will go over some of the ways that we do this and how we can query and synthesize trees as an alternative to supertrees and consensus trees. While still a work in progress, these methods show great promise for further development.