Cummins, Carla A.
A new method for identifying site-specific
evolutionary rates and its applications.
PhD thesis, National University of Ireland Maynooth.
In this thesis, I discuss each stage in the development of a new method for identifying
site specific evolutionary rates, from conception of the idea, through the
implementation to its application to data. TIGER, or tree independent generation of
evolutionary rates, is based largely around the works of LeQuesne (1989), Wilkinson
(1998) and Pisani (2004) and the premise that sites in a multi-state character matrix
could be scored based on the level of agreement it displays with the other sites. In
these earlier studies, however, agreement was measured in binary manner: sites were
either compatible with each other or they are not. TIGER allows various degrees of
agreement to occur between two sites, allowing it to pick up more subtle signals in the
After implementing the method into a software program, it could be applied to data.
Using a combination of simulated and empirical datasets, TIGER was shown to
produce desirable results. In particular, removal of sites identified by TIGER was
shown to improve phylogenetic reconstruction of deeply diverging lineages and of
taxa displaying compositional attraction. Additionally, TIGER was applied to a gene
content matrix in order to identify HGT signals and integrated into the analysis of a
current phylogenetic problem, the origin of the mitochondria.
Although it is widely accepted that eukaryotes have a chimeric genome, the specific
“parent” of the mitochondria is, as of yet, unclear. Previous studies have failed to
reach agreement regarding this issue for a number of reasons. Exploration of the
signals using TIGER and heterogeneous modelling reveal that multiple signals and
compositional heterogeneity are among the biggest problems with datasets containing
both mitochondrial and a-proteobacterial sequences.
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