Postgraduate Students

Gabrielle Beans PiconPhD student

Molecular Ecology and Evolution in Adélie penguins

The Adélie penguin (Pygoscelis adeliae) is a very useful study model for population history and evolutionary biology due to its ecology and distribution. They are an indicator species of climate change in the Antarctic as they are influenced by sea-ice distribution. Approximately 2.5 million breeding pairs nest in the Antarctic on ice-free areas of the coastline, in colonies ranging in sizes from under 100 to over 100,000 breeding pairs (counted from aerial photographs of colonies showing one parent of each pair sitting on a nest, Landcare Research). The relationship between population size and genetic diversity can be tested in this species, and also the usefulness of genetic markers for estimating effective population size. The first year of my PhD has been dedicated to studying this using mitochondrial DNA HVR1 sequences as well as demographic data. Adélie penguins are also an ideal source for ancient DNA, as penguin remains accumulate stratigraphically in the Antarctic soil and are well preserved by the freezing temperatures and dry conditions. Bones have been be radiocarbon dated. Previous work has been carried out to estimate the evolutionary rate of the mitochondrial control region using an ancient DNA approach. I plan to take advantage of the high quality of Adélie penguin aDNA to target nuclear genes and introns using multiplex PCR techniques and modern genomics approaches, and compare these to modern sequences. This study will give us insight into the evolution of nuclear sequences over thousands of years.

Supervisor: Distinguished Professor David Lambert

Susan Biering PhD student

The solid state of group 12 oxides and relativistic effects

My thesis deals with relativistic effects in the solid state, more precisely, with the influence these effects may have on the solid state symmetry and other properties. The first part of my research makes relativistic and non relativistic ab-initio calculations to investigate the symmetry changing in group 12 chalcogenides.

Supervisor: Professor Peter Schwerdtfeger

Barbara Binney

The Kiwi (Apteryx spp) is an important part of New Zealand ecology and culture. The major histocompatibility complex (MHC) gene codes for an important part of the immune system in gnathostoma (vertebrates with jaws). The aim of this project is to examine the range of diversity (polymorphism) in the MHC gene in the kiwi, first by developing a process to be based on PCR to multiply and sequence the class 2 B area of the MHC, then apply the process to compare kiwi populations. A good range of MHC polymorphism in the protein binding regions (PBR) is considered a healthy sign in a population, indicating a population has a good range of ability to detect to a range of pathogens.

Supervisor: Distinguished Professor David Lambert

Haydn Cooper

My project concerns the study of spaces of discrete groups and in particular computational methods to investigate two-generator discrete groups and their parameter spaces.

Supervisor: Distinguished Professor Gaven Martin

Andy Farr

Following a bachelors of Biomedical science specialising in genetics, he as commenced a honours year in the Rainey lab under the guidance of Dr. Refardt, studying the evolutionary consequences of host density on the model organism bacteriophage Lambda. This study hopes to elucidate through experimental evolution, how much the population structure of the host can select for levels of transmission and/or virulence.

Supervisor: Professor Paul Rainey

Jenna Gallie

The evolutionary success of many microbial populations is contingent upon their ability to adapt to rapidly changing environments. Bistable switches provide a unique mechanism to enhance the phenotypic diversity – and thereby overall fitness in fluctuating environments – of clonal microbial populations.

Through repetitive, cyclic manipulation of environmental conditions we have evolved a heritable, bistable switch in Pseudomonas fluorescens SBW25, the operation of which results in phenotypic dichotomy at the cellular level. My research focuses on unraveling the sequence of evolutionary events that gave rise to the bistable behaviour, and characterizing the genetic causes and mechanistic bases of the switch.

Supervisor: Professor Paul Rainey

Katie Hartnup

Kakahu or Maori cloaks are taonga. They are as unique to New Zealand as the materials and dyes used to create them. They represent iconic representations of Maori culture. Unfortunately much of the original information relating to the origins of the cloaks has been lost. Using a combination of traditional knowledge and ancient DNA technology, we are now able to unravel some of the mysteries surrounding cloak construction and the traditions surrounding the collection of materials used. We are in the process of recovering information about the species, sex and geographic provenance of the feathers used to make cloaks. With this information we will be able to test the suggestion that feathers were traded among iwi for cloak making, along with valuable items such as greenstone. Similarly, we also plan to perform molecular studies of the kuri (dog) that was used to make the earliest cloaks, kahu kuri and of the harakeke (flax) used to make the Korowai Kaupapa or the body of the cloak. By comparison with reference samples, these data will enable us to document the geographic provenance of cloaks and kete, thus allowing the stories of these taonga to be told again.

Supervisor: Distinguished Professor David Lambert

Maarten Jordens

My project investigates new phenomena in the calculus of variations and non-linear elasticity generalising earlier work in study the deformations of elastic bodies which minimise certain energy functionals related to the mean pointwise distortion. The project looks at this problem in other integrability classes. We expect to see various critical phenomena related to the Nitsche conjecture of 1962.

Supervisor: Distinguished Professor Gaven Martin

Michael McDonald

Investigating the genetic changes that underlie evolution and the factors determining the path that evolution takes.

We have demonstrated that although natural selection the drives evolution, in our system the underlying genetic architecture also effects the probability with which genes sustain adaptive mutations. We are determining what aspects of the genetic architecture affect which genetic changes are presented to natural selection for sorting We also have an interest in the effect of conflict mediation on co-operating bacteria.

Supervisor: Professor Paul Rainey

Peter Meintjes

My primary research interest is on the evolution of individuality from cooperating groups which I study using the Pseudomonas fluorescens experimental system developed in the Rainey Lab.

I have completed a Masters in phylogenetic methodology, in particular the statistical tests of phylogenetic hypotheses, and maintain this as a secondary interest.

Supervisor: Professor Paul Rainey

Elmira Mohandesan PhD student

Estimating the evolutionary rate in the mitochondrial genome of tuatara (Sphenedon punctatus)

I’ve started my PhD with Professor David Lambert in Alan Wilson Centre since October 2006. The aim of my research is to estimate the evolutionary rate of whole mitochondrial genome of Tuatara based on both ancient and pedigree approaches and also looking for the pattern of mutation on this molecule.

The name Tuatara derives from the Maori language meaning “Spiny back” and is regarded as the messenger of Whiro, the God of Death and Disaster.

Tuatara is a living fossil of the order Sphenodontida, which was well represented by many species during the age of dinosaurs and did not show considerable morphological changes since the Cretaceous period.

In addition to their stable morphology, Tuatara have a low body temperature, long generation time, slow rates of reproduction and metabolism which suggest the slow rate of neutral molecular evolution. Contrary to this expectation, the rate of molecular evolution for mitochondrial control region has been estimated as one of the highest rates ever reported for vertebrates. Tuatara is therefore of huge international interest for evolutionary biologists.

Supervisor: Distinguished Professor David Lambert

Christian Thierfelder PhD student

Parity violation in chiral molecules

The weak neutral current (Z-boson exchange) between electrons and nucleons (quarks) introduces a small energy difference between enantiomers of a chiral molecule owing to parity violation. This parity violation has not been detected by experiment. I perform relativistic Dirac-Hartree-Fock calculations on molecules like CHFClBr to calculate the parity violation contributions to vibrational transitions which can be directly measured.

Supervisor: Professor Peter Schwerdtfeger

John Waugh PhD student

CO1 barcoding of the New Zealand avifauna

A comprehensive inventory of the life forms on earth is at the heart of any scientific study of evolution and biodiversity. My research is part of an international Barcoding of Life project, which is an attempt to characterise the earth's biodiversity using short signature DNA sequences. The hypothesis underlying the DNA barcoding project (namely that single gene sequences can identify species' status) requires comprehensive testing. The world's avian fauna has been identified as a good candidate to test the principle of DNA barcoding because birds have been well studied using a range of techniques such as morphology, ecology and behaviour, and consequently the number of avian species has been well established.

To date, the majority of DNA barcoding studies have been conducted on Northern Hemisphere species. However, it has been questioned whether DNA barcoding will work as well using species from other geographic regions. We propose to construct a DNA database of the mitochondrial gene cytochrome c oxidase subunit 1 (COI) for the avian fauna of New Zealand. This gene has been shown to be a powerful indicator of species status in a large sample of North American birds. It is hoped that once this data set is complete it will be possible to identify every avian species in New Zealand by these DNA signatures.

In order to produce a concise and accurate picture of the genetic makeup of New Zealand's bird population, ten samples per species, from different geographical locations throughout New Zealand, need to be collected and processed. Museums, bird recovery centres, zoos, bird sanctuaries and DoC have been approached for samples and have agreed to help with the collection of the feather and tissue samples needed to complete this study. To date, a search of the literature regarding DNA barcoding has been carried out, a draft of a review paper on DNA barcoding written, contact has been established with the various organisations identified above and collection and analysis of specimens has commenced. Laboratory work is ongoing and entails the development and refining of extraction and sequencing techniques to suit New Zealand taxa.

Beyond establishing DNA barcodes for New Zealand species, the thesis will address issues such as how species concepts relate to DNA barcoding, can DNA barcoding assist in lineage sorting and can it inform a phylogeny of New Zealand birds.

Supervisor: Distinguished Professor David Lambert

Shuqiao Yu

Chromosomal interactions surround the yeast Galactose structural genes.

For a long time, DNA had been considered as a stabilized, rigid, and “linear” structure, which acts as a platform for the molecular helpers to function. However, genome structure in living cells is far more complex than the linear representation of the primary DNA sequence implies. The galactose (GAL) gene family of Saccharomyces cerevisiae enables yeast cells to utilize galactose as a carbon source and their expression is strictly regulated by the availability of nutrients. Structural genes GAL1, 10, and 7 exist in a cluster on yeast chromosome II. My Masters thesis has been established based on the hypotheses that chromosomal interactions help to regulate their activation.

In order to study the relative position of the GAL genes within the nucleus, novel molecular techniques Chromatin Conformation Capture (3C) and Circular Chromatin Conformation Capture (4C) are applied to map the positions of genes in the context of the overall genome structure. The current results demonstrate that on chromosome II, GAL1, 10 and 7 genes are divided into two ‘interaction zones’ in a carbon source independent manner. Furthermore, DNA loops formed around these interaction zones; switching on the GAL genes seems to help this formation. I have also found that inter-chromosomal interactions occur between chromosomes II and XVI (GAL7-SVL3 and GAL10-HOS1). Although these interactions occur under all induction conditions (Galactose, Glucose and Glycerol), I have found that variations in induction time affect the level of interaction in a carbon source dependent manner.

The results indicate a novel and exciting connection between chromosome positioning and gene expression, which provide a significant advance in our understanding of the link between genome structure and the regulation of gene activity. Such a process has important implications in disease development.

Supervisor: Distinguished Professor David Lambert

Qing Zhang

My project aims to describe spaces of discrete groups - particularly two generator discrete groups - with an aim to give applications in the theory of hyperbolic 3-manifolds and their associated universal constants. We initially plan to find sharp bounds describing the isolation of the elementary Kleinian groups (such as the spherical and Euclidean triangle groups) from the non-elementary groups.

Supervisor: Distinguished Professor Gaven Martin