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Lars Jermiin
School of Biological Sciences, University of Sydney
New methods of detecting violated phylogenetic assumptions: Implications on
comparative genomics
Wednesday 30th April 14:05-14:55pm,
Eastern Avenue Lecture Theatre.
Most phylogenetic methods assume that the sequences of nucleotides or amino
acids have evolved under stationary, reversible and homogeneous conditions.
When these assumptions are violated by the data, as would be the case if
there is compositional heterogeneity across the sequences, the phylogenetic
estimates are obtained under an incorrect model and thus subject to error.
Methods to examine aligned sequences for violation of these assumptions have
been available for years, but they are rarely used, presumably because they
are not widely known or because they are poorly understood. Here we describe
and compare matched-pairs tests for symmetry 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, reversibility and homogeneity,
but also to identify what may underpin this violation. Under the assumption
that the sequences evolved under stationary, reversible and homogeneous
conditions, the tests are unaffected by invariant sites and divergence
between the pairs of sequences, implying that they may be used to identify
suitable substitution models for estimation of evolutionary relationships
under a Markovian model.
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