The diversity of sequence alignment and tree space at high parameter density
Author(s)
Borrow, Christopher Andrew
Type
Thesis
Abstract
When attempting to characterise communities by their phylogenetic diversity,
Scarabaeinae provide an ideal model system. Historically three genes, cox1, 28S
and 16S, have been widely used in phylogenetic studies for members of the
Coleoptera and this is also the case for the Scarabaeinae. Two of these genes, 28S
and 16S, are length variable. The alignment of nucleotide sequence data containing
multiple insertion and deletion events is a notoriously difficult problem to resolve.
Accurately doing so is important, as the accuracy of the alignment is thought to play
a crucial role in determining phylogenetic tree topology. Therefore it is necessary to
find a way to accurately align the sequence data before communities can be
accurately characterised across a hypothesised phylogenetic tree. Little guidance is
available on how the users of alignment programs should go about this task. In the
following chapters an understanding of how alignment parameters act on the
alignment of 16S data from Coleoptera species is reported along with a method for
using members of the Clustal program family. The use of two scoring systems for
judging the quality of alignments is also explored. Selecting alignments based on
minimising overall alignment diversity appears to minimise synapomorphy and
homoplasy, while maximising taxonomic consistency. Therefore, using the Shannon-
Wiener or Simpsons Index of diversity to score alignment quality may prove useful to
phylogeneticists.
Scarabaeinae provide an ideal model system. Historically three genes, cox1, 28S
and 16S, have been widely used in phylogenetic studies for members of the
Coleoptera and this is also the case for the Scarabaeinae. Two of these genes, 28S
and 16S, are length variable. The alignment of nucleotide sequence data containing
multiple insertion and deletion events is a notoriously difficult problem to resolve.
Accurately doing so is important, as the accuracy of the alignment is thought to play
a crucial role in determining phylogenetic tree topology. Therefore it is necessary to
find a way to accurately align the sequence data before communities can be
accurately characterised across a hypothesised phylogenetic tree. Little guidance is
available on how the users of alignment programs should go about this task. In the
following chapters an understanding of how alignment parameters act on the
alignment of 16S data from Coleoptera species is reported along with a method for
using members of the Clustal program family. The use of two scoring systems for
judging the quality of alignments is also explored. Selecting alignments based on
minimising overall alignment diversity appears to minimise synapomorphy and
homoplasy, while maximising taxonomic consistency. Therefore, using the Shannon-
Wiener or Simpsons Index of diversity to score alignment quality may prove useful to
phylogeneticists.
Date Issued
2011-07
Date Awarded
2012-09
Advisor
Krell, F
Vogler, Alfried
Publisher Department
Biology
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)