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SUMMARY:New methods of detecting violated phylogenetic assumptions: Implic
 ations on comparative genomics - Lars Jermiin\, University of Sydney
DTSTART:20070831T100000Z
DTEND:20070831T110000Z
UID:TALK7903@talks.cam.ac.uk
CONTACT:Dr Ellen Nisbet
DESCRIPTION:Most phylogenetic methods assume that the sequences of nucleot
 ides or amino acids have evolved under stationary\, reversible and homogen
 eous conditions. When these assumptions are violated by the data\, as woul
 d be the case if there is compositional heterogeneity across the sequences
 \, the phylogenetic estimates are obtained under an incorrect model and th
 us subject to error. Methods to examine aligned sequences for violation of
  these assumptions have been available for years\, but they are rarely use
 d\, presumably because they are not widely known or because they are poorl
 y understood. Here we describe and compare matched-pairs tests for symmetr
 y of two-dimensional contingency tables from homologous sequences and show
  that the tests of symmetry\, marginal symmetry and internal symmetry can 
 be used not only to detect violation of the assumption of stationarity\, r
 eversibility and homogeneity\, but also to identify what may underpin this
  violation. Under the assumption that the sequences evolved under stationa
 ry\, reversible and homogeneous conditions\, the tests are unaffected by i
 nvariant sites and divergence between the pairs of sequences\, implying th
 at they may be used to identify suitable substitution models for estimatio
 n of evolutionary relationships under a Markovian model.
LOCATION:Semiar Room\, Department of Biochemistry\, Hopkins Building (old 
 building)
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