Phylogenomics and plant evolution : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics at Massey University, Manawatu, New Zealand
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Date
2013
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Massey University
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Abstract
Phylogenomics, the study of evolutionary relationships among groups of organisms
using genome-scale data, is central to our understanding of the evolution of life. While
large amounts of data are available and methodological developments are increasing at
a fast pace, there are basic problems that are overlooked in phylogenomic analyses of
molecular sequences, which may impede the accuracy and reliability of tree
reconstruction. These problems include: How can we detect the non-phylogenetic
signals from genomic data? How can we offer a better statistical fitness between the
evolutionary model and data? How can we improve the phylogenetic inference using
sophisticated and realistic models? How can we accurately infer the species trees? How
can we quantitatively confirm the evolutionary theory? With these goals, this thesis
concentrates on phylogenomics of land plants (and their origin) and evolution in general.
• Resolving the phylogenetic position of Gnetales. We show that non-time
reversible properties of positions in the chloroplast genomes of Gnetales mislead
phylogenetic reconstruction, and highlight that the goodness of fit between
substitution model and data should be taken into account when performing
phylogenomic analyses.
• Resolving the origin of land plants: 1). The multispecies coalescent model is
applied to estimate the species tree of origin of land plants, and it is proved to be
able to estimate accurate and congruent species tree in the presence of ancient
incomplete lineage sorting from nuclear genes. 2). The chloroplast
phylogenomic analyses are conducted using sophisticated and realistic
evolutionary models that can account for site-heterogeneity and compositional
heterogeneity. These chloroplast phylogenomic results confirm the previous
nuclear data analyses.
• We develop a statistical test and demonstrate that evolutionary theory could be
tested by convergence of molecular data. It also indicates that the reality of
evolution can be tested using standard methods and tools.
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Keywords
Phylogenomics, Plant evolution