INSIDE THIS ISSUEAn Environmental Legacy 1

NEWSBug Hunting 2

Researcher Profile: PhD Student Robin Atherton

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RESEARCHRutherford Discovery Fellowships

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New Zealand’s Next Top Model ... Ecosystem

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Scaling Up DNA Sequencing 6

IN REVIEWThe Transit of Venus Project 8

2010 Annual Meeting 8

MAY 2011 | ISSUE 1

Canadian scientist and educator Dr David Suzuki visited Wellington in November to present his ‘Legacy’ lecture, in association with the Allan Wilson Centre. The event, held at the Embassy Theatre, sold out.

Originally a geneticist, Dr Suzuki is now known for his work in climate change, sustainability and clean energy. He delivered a message about humanity’s role in environmental issues and what changes we can make. “Human beings have exhausted the limits of Planet Earth and there is an urgent need to rethink our relationship with the natural world,” he said.

Dr Suzuki described humans as a super-species, and said our numbers, technology, consumptive habits and economy have dramatic effects. He believes we are altering the chemical, physical and biological features of

the planet on a huge scale. “We forget that earth, air, fire and water are our most fundamental needs that we should value, treasure and protect above everything else”, he said.

Dr Suzuki stressed the importance of understanding ecology, noting that ecology not economics determines the limits we have to live within. He sees science and humanity’s capacity for innovation as having the potential to turn around environmental degradation. This could be done through development of zero waste industries that mimic nature, and clean energy technologies like solar panels incorporated into roads and buildings. His talk ended on a positive note as he urged the audience to imagine how we can live in a more sustainable way.

Before his lecture, Dr Suzuki spoke at Zealandia to 50 conservation workers, graduate students and researchers, including around 25 Allan Wilson Centre members. Researchers met him in person and asked questions about his philosophies and his hopes for the future of the Earth. He also had dinner with six Allan Wilson Centre members after his talk.

Dr Suzuki’s visit to New Zealand was part of a five-week speaking tour of Japan, Australia and New Zealand. While here, he spoke to the Green Party conference and participated in several events sponsored jointly by the Royal Society of New Zealand, the Auckland Writers and Readers Festival, Allen & Unwin and the Allan Wilson Centre.

ALLAN WILSON CENTREFOR MOLECULAR ECOLOGY AND EVOLUTION

David Suzuki, Wellington, Nov 2010

AN ENviRONmENTAL LEGACy

“We forget that earth, air, fire and water are our most fundamental needs that we should value, treasure and protect above everything else”

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NEWS

A common source of infection is undercooked food. identifying the cook solves only one part of the puzzle, however. The next mystery is: where did the pathogen in the food originate from? This question is at the heart of the Allan Wilson Centre’s new strategic initiative in disease ecology and pathogen evolution. Led by Professor Nigel French from massey University, this project uses advanced molecular technology and evolutionary modelling to track the source of human Campylobacter infections. Professor French and colleagues identified that up to 76% of cases came from contaminated chicken. Policy changes in the poultry industry were implemented, halving the infection rate in one year.

Research by Professor French and others has also shown that we have unique strains of disease-causing microorganisms. New Zealand was last to be colonised by humans, has only recently introduced ruminants and European birds and has been subject to a rapidly growing poultry industry. These conditions have likely played a major part in the development of the unusual strains, which in turn have led to a unique molecular epidemiology. For example, one third of all human cases of infection from Campylobacter in New Zealand can be attributed to the strain Campylobacter jejuni ST-474, which is seldom found anywhere else in the world. Similarly, we have Salmonella strains that cause large outbreaks here that do not cause outbreaks elsewhere.

Bug HUNTiNG

One third of all human cases of infection from Campylobacter in New Zealand can be attributed to the strain Campylobacter jejuni ST-474, which is seldom found anywhere else in the world.

Food and water-bourne illnesses such as Campylobacter are accepted as a fact of life by many New Zealanders, but the significant impact of these diseases on the economy of the country and the long-term health of the population is less often considered. Some estimates indicate that infection from Campylobacter alone costs the economy more than $40 million per year in lost workforce productivity. Serious health effects include severe neurological pathologies, arthritis and, rarely, death.

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in a new project, Professor French and colleagues will track the source of water-borne pathogens, sequencing microbial DNA directly from samples obtained from water supplies, avoiding the need to culture any microorganisms. Not all microbes grow well in culture, so entire species can be missed even though they were present in the original sample.

Directly sequencing of DNA gives a better representation of the species and concentrations present in the sample.

Overall, the new Allan Wilson Centre strategic initiative will enable scientists to gain insight into the mechanisms of disease transmission between animals and humans, and the forces that have shaped the evolution of populations of microbes that are so important to human and animal health. This will lead to better methods of reducing human exposure to infections arising from animals, a better understanding of the how pathogens are disseminated between wildlife species and new insights into emerging diseases.

Not all microbes grow well in culture, so entire species can be missed even though they were present in the original sample.

ReseaRcheR PRofile: PHD STUDENT ROBiN ATHERTON

The karaka is one of New Zealand’s most distinctive and culturally significant trees. Its bright orange fruit are an important food for Māori and Moriori of Rekohu/Chatham Islands. PhD student Robin Atherton is taking a new approach to tracing the history of karaka, by combining genetic data with information gleaned from oral histories.

Karaka trees were most likely restricted to the far north of New Zealand in pre-human times. Their occurrence in the rest of the mainland and the Chatham and Kermadec islands is strongly associated with māori and moriori archaeological sites, indicating that human habitation spread karaka more widely. By tracking this movement, Robin aims to identify the origin of cultivated karaka trees, and to infer how māori themselves travelled and settled in pre-European times.

A particular focus of Robin’s project is the history of karaka on the Chatham islands.

Karaka are especially significant there as they are the bearers of the famous moriori tree carvings, known as rakau momori.

Robin is using both genetic data and oral histories in her research. Oral histories are a valuable source of information for complementing and refining the genetic data. in some cases, they provide information that cannot be determined from genetic data, such as migration direction. The genetic data will make it possible to pin-point exactly where various trees came from, and when combined with traditional knowledge will provide a more complete picture of the history of karaka. The genetic component of Robin’s project

has so far focussed on developing molecular tools that will enable the origin of translocated populations to be traced, and changes in genetic diversity as karaka were cultivated to be measured. Preliminary data suggest that karaka were domesticated a number of times, and that the Chatham island trees originated from the east coast of the North island.

Robin received her undergraduate degree from the University of Reading in the UK and arrived in New Zealand in 2008 to begin her PhD at massey University in Palmerston North. She plans to submit her thesis in 2012.

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Hauturu (Little Barrier island) is a special place, even by New Zealand standards. Located on the outer edge of the Hauraki Gulf, about 80km

from Auckland, and comprising just over 2,900 hectares of relatively untouched native forests, Hauturu rises to 722m.The elevation provides a range of native forest habitats, including broadleaf forests with pohutukawa and beech around the rocky shores, tawa and rata in the inland forests, kauri dominating the ridges, and moss and lichen-encased trees crouching under the clouds that often surround the summit. This varied array of native forests means that Hauturu is home to many species of endangered wildlife and functions as one of the most important island sanctuaries in New Zealand.

New ZealaNd’s NExT TOP mODEL ... ECOSySTEm

Congratulations to Associate Professor Alexei Drummond from the University of Auckland and Dr Murray Cox from Massey University, who have received Rutherford Discovery Fellowships. These awards are offered to first class early to mid career researchers, and provide up to $200,000 per year for five years.

Associate Professor Drummond emphasised how proud he is of being a New Zealander. The support from his Rutherford Discovery Fellowship will allow him and the other recipients to practice world-class science whilst located here. He explained that many famous New Zealand scientists, including Ernest Rutherford and Allan Wilson, often did their best work overseas, because support did not exist for them at home. This type of funding, he believes, will mean that New Zealand will not lose some of its best early to mid-career researchers. Further, as Dr murray Cox explained, it allows Fellowship recipients to build on their existing research capability by bringing international research talent into New Zealand.

Rutherford discovery fellowships

Left: Two old kauri found on HauturuRight: The big climb

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There is little wonder that Associate Professor Alexei Drummond and colleagues from the Allan Wilson Centre and partner institutes identified this island for use as a model New Zealand ecosystem, despite the arduous fieldwork required. The development of model ecosystems, where the biological and physical components of a particular location are comprehensively identified and catalogued, this is a significant advance concept in community ecology and evolutionary biology. Using modern DNA sequencing, bioinformatics, niche modelling and traditional field ecology, the aim is to characterise every species within the Hauturu ecosystem phylogenetically as well as environmentally, and then use this information to improve conservation management across New Zealand. So far, the research has involved plotting out ten 20 x 20 m sampling blocks on Hauturu, arranged along a large altitudinal gradient designed to intersect each of the five main forest habitat types present on the island.

The researchers collected soil and leaf litter from each plot, and deployed a variety of traps, nets, and recorders in an effort to collect samples from all species of birds, reptiles, plants, invertebrates, and microorganisms.

The team is now sequencing DNA from every species collected in their samples, from the largest trees to microscopic bacteria. This is an ambitious target and when achieved will be the first model ecosystem project in New Zealand to tap into as many species in an ecosystem as possible, including what Associate Professor Drummond refers to as the ‘ecological dark matter’ – soil microorganisms, invertebrates, lichen, mosses and liverworts, that other studies of terrestrial forest habitats often overlook.

Ultimately, the researchers aim to develop two or three model ecosystems of comparable size and altitudinal gradient, but differing in their connectivity to the New Zealand mainland and their history of human modification. Although the initial focus has been on Hauturu, the researchers

now aim to conduct research on a mainland site with geographical and ecological similarities with Hauturu. Comparing these two locations will provide insight into the impact of humans and the environment surrounding the model system.

The project is ambitious, designed to stretch both the science and the scientists and make use of the broad variety and depth of skills present in the Allan Wilson Centre’s repertoire, while developing connections to like-minded researchers outside the centre. A major outcome will be the ability to define ecological niches and interactions between key species. This will provide valuable data for Department of Conservation managers aiming to conserve entire ecosystems rather individual species, and will form the basis for studies aimed at improving our understanding of how species are connected, how ecological communities assemble, and the impact of human modification and climate change. increasingly, financial pressures are forcing hard decisions to be made about conservation activities. The results of this research project will enable the dollars to be stretched further, to achieve more with our country’s conservation budget.

It a step beyond any previous research, as rather than attempting to understand in detail the habitat and behaviour of a single species, the focus is on the full ecosystem, and all of the plant and animal interactions within it.

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why sequence dNa?By sequencing DNA (determining

the order of the bases A, G, C and Ts in a strand of DNA), researchers can learn about the makeup of an organism’s genome. They can discover the functions of particular genes and identify changes that alter the way the genes works. For example, through DNA sequencing researchers have discovered that people with red hair have a particular form of the melanocortin-1 receptor gene. This gene controls the type of skin and hair pigments that are produced, and by sequencing the gene in people with a range of hair colours, researchers pinpointed changes in the DNA sequence that result in the production of red pigment.

DNA sequencing also allows identification of genetic markers – parts of the genome that vary in a predictable manner among populations or species. Researchers use genetic markers to trace how individuals or populations are related to each other, as closely related individuals are likely to have the same (or very similar) DNA sequence at a particular marker, while more distantly related individuals show fewer similarities. Genetic markers are also used to study how populations are formed and trace how species have evolved.

developments in dNa sequencing technology

DNA sequencing was developed in the 1970s, but early methods were painstakingly slow, with only a few dozen base pairs of a single DNA strand revealed at a time. A method called Sanger sequencing was quickly developed which made it possible to sequence several hundred base pairs of DNA at once. With the invention of automated machines, DNA sequencing became routine.

However, it was still only possible to produce up to 96 sequences from one region of DNA at a time.

in about 2005, a major change occurred with the invention of ‘high-throughput’ DNA sequencers, which can read millions of strands of DNA at once. instead of producing one long sequence from a single gene, a high-throughput sequencer produces millions of shorter sequences, potentially from thousands of different genes or pieces of the genome. High-throughput sequencers have revolutionised the

way researchers obtain and use DNA sequences. They have streamlined existing applications and developed new ones, such as investigating how genes are switched on and off.

high-throughput sequencing at the allan wilson centre

Allan Wilson Centre researcher Dr Kristina Ramstad is using high-throughput sequencing to develop genetic markers for studying inbreeding depression in rowi, our most endangered kiwi species. Dr Ramstad sequenced some of the rowi genome, then searched for areas in the DNA sequence known as microsatellites, where there are repeats of two to four base pairs of DNA. The number of repeats varies between individuals, but closely related individuals are more likely to have the same number of repeats. This makes microsatellites useful for determining how individuals and populations are related. Dr Ramstad will use these markers to assess how closely related birds are to their mates, and how inbred their offspring are. Finding microsatellites would previously have required many hours of labour-

DNA sequencing has undergone a revolution recently, with the invention of ‘high-throughput’ sequencing machines that cheaply produce large amounts of data. Here, we look at some of the uses of DNA sequencing, and discover how the new technology is changing the way Allan Wilson Centre researchers use DNA to study New Zealand’s native flora and fauna.

scaliNg uP DNA SEqUENCiNG

In about 2005, a major change occurred with the invention of ‘high-throughput’ DNA sequencers, which can read millions of strands of DNA at once.

A Tuatara hatchling

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intensive work in the laboratory, screening thousands of pieces of DNA to find the repetitive sequences. However, with high-throughput sequencing and computerised analysis, Dr Ramstad was able to screen millions of base pairs in a few hours, and has found more than 300 potential microsatellite markers for rowi.

Allan Wilson Centre researchers are also using high-throughput sequencing to help decipher parts of the tuatara genome. Postdoctoral fellow Dr Hilary miller has examined genes expressed in a developing tuatara embryo with the aim of finding genes involved in sex determination. So far she has investigated around 10,000 genes, many of which had not previously been identified in tuatara. High-throughput sequencers are particularly suited to this type of work, as they can sequence directly from mRNA, the molecule that translates the DNA’s genetic code into protein when a gene is expressed. The ability to look at millions of mRNA molecules at once provides a snapshot of all the genes that are expressed at any given time in a particular tissue.

from biology to bioinformatics

The advent of high-throughput sequencing has transformed the study of evolution by providing biologists with an avalanche of DNA information, but the sheer volume of data can be a problem in itself. Even a small sequencing run produces millions of base pairs and over a terabyte of data, more than would fit on the entire hard drive of many desktop computers. Files are generally too large to even be opened on a standard computer. Sophisticated software is also needed to assemble the millions of individual short DNA sequences into identifiable genes. This ‘bioinformatics’ software is still being developed.

Today, molecular biologists, evolutionary biologists and geneticists have to be proficient in bioinformatics to make full use of the new DNA sequencing technology, and researchers with both computer programming skills and a biology background are much in demand.

Dr Hilary Miller has examined genes expressed in a developing tuatara embryo with the aim of finding genes involved in sex determination. So far she has investigated around 10,000 genes, many of which had not previously been identified in tuatara.

The Genome Analyzer IIx offers powerful applications for unlimited discovery. Gain unexpected insights. Find unprecedented answers. Publish results faster than ever.

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IN REVIEW

of London has already supplied a list of the specimens from Tolaga Bay in their collections to help with the restoration.

Allan Wilson Centre Director Professor Charles Daugherty, manager ms Wendy Newport-Smith, Professors Lisa matisoo-Smith and Hamish Spencer, and Dr Nicola Nelson made a first visit in February to meet the people, see the land, and begin developing plans with the local community.

2010 annual Meeting

led to much discussion about the direction they might take.

Days two and three included sessions on new outreach activities and on research ethics. Communications advisor Glenda Lewis and representatives from Tolaga Bay outlined plans to celebrate the Transit of venus on the east coast in 2012 and discussed how the Allan Wilson Centre could contribute to this event. Ethical aspects of scientific research were covered by Professor John O’Neill from massey University, who talked about the importance of collective research integrity within organisations like the Allan Wilson Centre, and Linda Faulkner from the Environmental Risk management Authority, who discussed how to improve maori engagement in research.

The meeting also provided an opportunity for researchers to meet the Governance Board and hear more about their role, and for students, postdoctoral fellows and investigators to present the highlights of their research over the past year.

Allan Wilson Centre researchers from across the country gathered at Massey University last October for their 2010 Annual Meeting. Over three days, the latest research from the Centre was shared and plans were discussed for some exciting new directions.

After introductions from Allan Wilson Centre Director Professor Charles Daugherty, massey vice-Chancellor Steve maharey and Allan Wilson Centre Governance Board Deputy Chair Professor Carolyn Burns, the first day was dedicated to discussing the Centre’s new research initiatives. Professors Nigel French and Paul Rainey outlined plans for their disease ecology program and Associate Professor Alexei Drummond gave an update on the Little Barrier island model ecosystems research.

These are large-scale, innovative projects designed to bring together researchers from across the Centre and foster links with organisations such as the Department of Conservation, and the presentations

Soon after completing their mission to observe the 1769 Transit of Venus from Tahiti, James Cook and his crew sailed westward, to find the fabled Great Southern Continent. Instead, they found New Zealand. After a tragic and violent first encounter with Māori at the place they named Poverty Bay, they sailed along the coast. Eventually, a rangatira of local iwi Te Aitanga-a-Hauiti guided them to a cove by Tolaga Bay, where they Signalled their peaceful intentions. Banks and naturalist Daniel Solander were delighted by this new paradise, and immediately started gathering specimens of plants they had never seen before.

A project partnership between Te Aitanga-a-Hauiti and the Tolaga Bay community, the Royal Society of New Zealand, a team of academics at victoria University of Wellington headed by Sir

Paul Callaghan, and the Allan Wilson Centre will mark the next Transit of venus on 6 June 2012.

This rare astronomical event will be an occasion to celebrate our dual heritage and express our long term aspirations and possibilities. The Allan Wilson Centre has offered the community practical help with an ecological restoration plan for the local area as part of a bold new vision for a sustainable economy. The Natural History museum

THE TRaNsiT of VeNus PRojecT

From left to right: Reverend Stephen Donald, Professors Hamish Spencer, Lisa Matisoo-Smith and Charles Daugherty, and Dr Nicky Nelson.

CONTACT USMs Wendy Newport-Smith Centre Manager

Phone: +64 6 350 5448Fax: +64 6 350 5626w.newport-smith@massey.ac.nz

Postal Address:Allan Wilson Centre for Molecular Ecology and Evolution (AWC)Massey University,Private Bag 11 222, Palmerston North

Courier Address:Allan Wilson Centre,Level 2, Science Tower B, Massey University, Private Bag 11 222Palmerston North

The University of Otago,P.O. Box 56, Dunedin

Massey University,Private Bag 11 222, Palmerston North

The University of Auckland,Private Bag 92019, Auckland

Victoria University of Wellington,P.O. Box 600, Wellington

Canterbury University,Private Bag 4800, Christchurch

Plant and Food Research,120 Mt Albert Road, Sandringham, Auckland 1025

Visit the Allan Wilson Centre athttp://www.allanwilsoncentre.ac.nz/

© Allan Wilson Centre 2011. Pheno is available on request. Please email Joy Wood, j.r.wood@massey.ac.nz

Any information in this newsletter may be reused provided the Allan Wilson Centre is acknowledged as the source of the information.

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