Avian phylogeny and divergence times based on mitogenomic sequences : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics, Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
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Date
2012
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Massey University
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Abstract
Despite decades of research using a variety of data sources (such as morphological,
paleontological, immunological, DNA hybridization and short DNA sequences) both the
relationships between modern bird orders and their times of origin remain uncertain.
Complete mitochondrial (mt) genomes have been extensively used to study mammalian and
fish evolution. However, at the very beginning of my study only the chicken mt sequence was
available for birds, though seven more avian mt genomes were published soon after. In order
to address these issues, I sequenced eight new bird mt genomes: four (penguin, albatross,
petrel and loon) from previously unrepresented orders and four (goose, brush-turkey, gull and
lyrebird) to provide improved taxon sampling. Adding these taxa to the avian mt genome
dataset aids in resolving deep bird phylogeny and confirms the traditional placement of the
root of the avian tree (between paleognaths and neognaths). In addition to the mt genomes, in
a collaboration between paleontologists and molecular biologists, the oldest known penguin
fossils (which date from 61- 62 million years ago) are described. These fossils are from the
Waipara Greensand, North Canterbury, New Zealand, and establish an excellent calibration
point for estimating avian divergence times. Bayesian analysis of the DNA sequence data,
using the penguin calibration point plus two others, indicates a substantial radiation of modern
bird orders in the Late Cretaceous (80 - 65 million years ago). Biotic interactions between
modern birds and declining groups such as pterosaurs and early bird groups (e.g. Hesperornis
and Ichthyornis) may thus have played an important role during this time.
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Keywords
Phylogeny, Birds, Mitochondrial DNA, Penguin, Albatross, Petrel, Loon, Goose, Brush-turkey, Gull, Lyrebird, Bird phylogeny