Phylogenetics

by Cambridge University

Phylogenetics is the reconstruction and analysis of trees and networks to describe and understand the evolution of species, populations and individuals. It is widely used in molecular biology and other areas of classification (such as linguistics), and has both led to and benefited from the development of new mathematical, statistical and computational techniques. Although the foundations of phylogenetics were laid down many decades ago, it is currently experiencing an exciting renaissance due to the wealth and types of biological data that are now becoming available. This programme will bring together key researchers in phylogenetics and related areas to further develop this important area of mathematical biology.The main themes that will be worked on during this programme are new data types in phylogenetics; modelling reticulate evolution; constructing large trees; probabilistic models of evolution; and phylogenetic combinatorics. These themes provide a rich source of mathematical problems in areas such as combinatorics, graph theory, probability theory, topology, and algebraic geometry. Solutions to these problems will provide new insights to questions that are central to contemporary evolutionary biology.EVENTS:- Spitalfields Day - Yggdrasil: Reconstructing the Tree of Lifehttp://www.newton.ac.uk/programmes/PLG/PLG_Spitalfields.html- Current Challenges and Problems in Phylogeneticshttp://www.newton.ac.uk/programmes/PLG/plgw01.html- Future Directions in Phylogenetic Methods and Modelshttp://www.newton.ac.uk/programmes/PLG/plgw03.html- Phylogenetics: New data, new Phylogenetic challengeshttp://www.newton.ac.uk/programmes/PLG/plgw05.html

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Recent Episodes
  • 10 Men and 1 woman?
    Jan 14, 2008 – 40:32
  • A genealogical approach to studying asexuality
    Jan 16, 2008 – 19:02
  • A generalization of Stirling numbers and distribution of phylogenetic trees
    Jun 27, 2011 – 17:17
  • A Lie algebraic classification of continuous-time Markov models
    Jun 27, 2011 – 22:34
  • A phylogenetic definition of structure and further animations on the sequence space
    Jan 14, 2008 – 18:49
  • A signal-to-noise analysis of phylogeny estimation by neighbour-joining
    Jan 10, 2008 – 19:32
  • A simple model for a complex world
    Jan 15, 2008 – 26:29
  • Adaptive fast convergence - towards optimal reconstruction guarantees for Phylogenetic trees
    Jan 10, 2008 – 22:24
  • Advances and limitations of maximum likelihood phylogenetics
    Sep 11, 2007 – 58:23
  • Algorithm design for large-scale phylogenetic analysis
    Dec 13, 2007 – 48:34
  • An empirical study of the effect of sequence alignment on phylogenetic analysis
    Jun 27, 2011 – 20:41
  • An exact algorithm for computing the geodesic distance between phylogenetic trees
    Jan 11, 2008 – 18:49
  • Appropriate models for heterogeneous multi-gene data sites
    Sep 7, 2007 – 18:37
  • Are there alternatives to handling site-to-site rate variation in evolutionary characters
    Jun 27, 2011 – 01:06:53
  • Assessing the limits of phylogenomics: can too much data be a bad thing?
    Jun 27, 2011 – 01:04:29
  • Big trees: challenges and opportunites in the phylogenetic analysis of large data sets
    Sep 24, 2007 – 56:11
  • Branch and bound construction of balanced minimum evolution optimal trees
    Sep 13, 2007 – 19:03
  • Coalescent consequences for consensus cladograms
    Jan 15, 2008 – 23:58
  • Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood
    Jun 27, 2011 – 17:54
  • Comparing phylogenetic trees
    Sep 6, 2007 – 10:45
  • Computational and mathematical challenges involved in very large-scale phylogenetics
    Sep 11, 2007 – 01:09:25
  • Computing phylogenetic diversity for split systems
    Sep 25, 2007 – 20:14
  • Concordance between species trees and gene trees with multiple mergers of ancestral lineages
    Jun 23, 2011 – 17:57
  • Consistency of phylogenetic tree search algorithms based on the balanced minimum evolution principle
    Sep 27, 2007 – 18:37
  • Constructing level-2 phylogenetic trees from triplets
    Dec 10, 2007 – 46:37
  • Corrections to a class of methods for inferring species trees from gene trees
    Jun 24, 2011 – 15:56
  • Dendroscope - an interactive viewer for large phylogenetic trees
    Sep 7, 2007 – 17:59
  • Distribution of phylogenetic diversity under random extinction
    Jan 12, 2008 – 18:57
  • Encoding phylogenetic trees with weighted quartets
    Jan 11, 2008 – 26:01
  • Estimating ultra-large phylogenies and alignments
    Jun 28, 2011 – 56:13
  • Evaluating the goodness of fit between a phylogenetic model and an alignment
    Jun 24, 2011 – 57:49
  • Evolution of Chloroplasts
    Jan 15, 2008 – 20:07
  • Explicit bounds for the stability of maximum likelihood trees
    Sep 13, 2007 – 20:45
  • Exploring Treespace
    Jun 23, 2011 – 21:45
  • Generalising from consensus to supertree methods
    Sep 25, 2007 – 25:48
  • Genome sequencing of Leishmania donovani clinical lines reveals dynamic phylogenetic variation
    Jun 24, 2011 – 21:10
  • Glimpses from the strange world of phylogenetic mixtures
    Sep 21, 2007 – 20:22
  • Hao Bailin's whole-genome based phylogenies
    Dec 11, 2007 – 01:12:33
  • How many characters are needed to recontruct the true tree?
    Jan 10, 2008 – 16:12
  • Hybridisation in non-binary trees
    Jan 14, 2008 – 24:54
  • Identifying Lateral Transfers with Neighbor-Nets
    Jun 23, 2011 – 17:04
  • Identifying Phylogenies: extending the notion of unique
    Jan 11, 2008 – 18:57
  • Incomplete lineage sorting: consistent phylogeny estimation from multiple loci
    Jan 16, 2008 – 23:01
  • Incorporating speices phylogeny in the reconstruction of gene trees
    Sep 6, 2007 – 21:10
  • Incorporating uncertainty in distance-matrix phylogenetic reconstruction
    Jan 10, 2008 – 23:05
  • Indentifiability of the GTR=gamma substitution model of DNA evolution
    Sep 20, 2007 – 23:59
  • Inference rules for super-network construction
    Sep 11, 2007 – 18:31
  • Insertion-deletion models for dequence evolution and Bayesian sampling methods for multiple alignment
    Sep 14, 2007 – 20:26
  • Integer programming for phylogenetic computations
    Sep 12, 2007 – 24:02
  • Integrative analysis if environmental sequences
    Jun 27, 2011 – 01:00:47
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