There are currently 0 users and 134 guests online.
phyloseminar -- a free online seminar about phylogenetics
Last update1 hour 4 min ago
February 6, 2014
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.
January 1, 2014
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.
Karen Cranston: Technical and social challenges of synthesizing phylogenetic data across the tree of life
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.
The Barcode of Life
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution