Holton, Therese A.
Phylogenomic supertrees: integration of maximal data and
assessment of input tree shape.
PhD thesis, National University of Ireland Maynooth.
In this thesis, three distinct studies were carried out to investigate various aspects
pertaining to the properties and applicability of phylogenomic data used in a supertree
context. While the availability of genomic scale data is rapidly diminishing as a problem
in the field of phylogenomics, there is now a greater need for an appropriate means of
analysing such data.
Supertrees have emerged as a useful approach in handling large data sets and have
been shown to work extremely well in a phylogenomic context (e.g. Creevey et al., 2004,
Fitzpatrick et al., 2006, Pisani et al., 2007). While supertree studies do generally sample
significantly more genomic data than their supermatrix counterpart, much of the genome,
which has evolved in the light of gene duplication, is not considered in this method.
Further to this, typically, in the supertree approach complete genomic data is exclusively
used, which can result in a very limited taxon sampling compared to alternative
approaches that use expressed sequence tag (EST) data. Here, in attempt to address these
shortcomings, the viability of integrating genes with a history of duplication in the
supertree approach, as well as the extent to which a combined data set of complete and
partial genomes (ESTs) can be used to increase taxon sampling in this context, is
Additionally, in this thesis, the effect of input tree shape biases is assessed. It has
been shown previously that some commonly used supertree methods are biased with
respect to the tree shape they produce (Wilkinson et al., 2005). However, since some
supertree methods (e.g. matrix representation with parsimony; MRP) have an inherent
phylogenetic component, the observed shape predispositions of these supertree methods
may be attributed to such methodological elements. As such, here the effective shape bias
of various phylogenetic methods is assessed using a phylogenomic data set.
||Phylogenomic data; Genomic scale; Supertrees; Input tree shape biases;
||Faculty of Science and Engineering > Biology
||25 Aug 2011 10:26
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