APRIL 2015 ISSUE 15 ISSN 2324-5670

World leading molecular biologist and conservationist, Dr Stephen O’Brien, is the next speaker in the Allan Wilson Centre’s international public lecture series, touring the country 21–30 April.

Tackling Salmonella at home and in Africa

The Bioblitz experience – 24 hours in Uawa

Postdoctoral fellowships awarded for 2015

Alexei Drummond one of the world’s “most influential scientific minds’

Teaching excellence prizes for centre advisers

Pg 3 Pg 4 Pg 6 Pg 6 Pg 8

He is Chief Scientific Officer at St Petersburg State University, co-founder of the Genome 10K Project, and author of science adventure stories, “Tears of the Cheetah and other Tales from the Genetic Frontier”. One of the founders of conservation genetics, Stephen will explain how powerful new genetic technologies have revolutionised our ability to understand

the natural history of threatened mammals and recognise hidden perils that afflict them, informing conservation efforts to protect them.

The dwindling wildlife species of our planet has become a burning issue for conservation groups, governments and concerned citizens throughout the world. Conservation genetics, a

field that began just 30 years ago, is now an important factor in every management decision about saving wildlife.

“I feel proud of that because we were in at the beginning and showed that genetics is helpful for conservation,” says Stephen. “Scientists, ecologists and conservationists discover as much information as possible so management decisions can be made on data rather than assumptions and guesswork.”

The lecture will connect recent applications of conservation

genetics and natural history to uncover adaptive adventures that left footprints in the genomes of tigers, cheetahs and the Florida panther.

In the case of the Florida panther this led to “bold genetic action”. In the 1990s there were fewer than 30 animals left of this subspecies. The demographic and genetic computer models were quite clear – if nothing was done there was a 95% chance that the species would become extinct within 25 years.

“That was the headline that finally turned the heads of even the most vociferous objectors to invasive action,” says Stephen. “We supplemented the population with a handful of ‘first cousins’ from across the Mississippi, called Texas cougars – but not until after a long political exchange where objectors and self-proclaimed experts were arguing that we should just leave them alone.

“This story has a lot of interesting angles that illustrate that conservation has political, cooperative and educational as well as scientific components. The people who are the most effective conservationists are those who appreciate just how broad that field is and accept help from anyone, in any area from economics to science to ecology to genetics.”

Genetics is particularly useful for identifying the numerous “hidden perils” that threaten endangered mammals. These include historic events that indicate the natural and evolutionary history of a species – such as inbreeding or near extinction. Another is infectious disease, for example Ebola affects chimpanzees, canine distemper decimated the wild dog in East Africa, and the coronavirus affects dolphins and seals.

“This story has a lot of interesting angles

that illustrate that conservation has

political, cooperative and educational

as well as scientific components.”

Stephen O’BrienWILDLIFE GENETICS – UNCOMMON GLIMPSES

WELLINGTONTuesday 21 April, 6.00pm, Te Marae, Te Papa Tongarewa, Museum of New Zealand

NELSONWednesday 22 April, 6.00pm, Old St Johns, 320 Hardy Street

CHRISTCHURCHThursday 23 April, 6.30pm, Central Lecture Theatre 1, University of Canterbury

DUNEDINFriday 24 April, 6.30pm, St David Lecture Theatre, University of Otago

PALMERSTON NORTHTuesday 28 April, 6.30pm, Globe Theatre

TAURANGA Wednesday 29 April, 6.30pm, Tauranga Yacht & Power Boat Club

AUCKLANDThursday 30 April, 6.15pm, Auckland Museum Auditorium

GOLD COIN DONATION ENTRY is by gold coin donation.

SEAT RESERVATIONS RESERVE a seat for these popular lectures at www.allanwilsoncentre.ac.nz Click ‘Register Online’ under ‘Events’.

PUBLIC TALKS BY DR STEPHEN O’BRIENThese are hidden agents that can easily be seen by blood sampling and analysis.

Stephen believes that New Zealand is a world leader in conservation. “I think we’ve all learned from the public experiments that New Zealand has tried. We know that marsupials and flightless birds are at a disadvantage if you release mammals – when the Panama land bridge appeared three million years ago, North American mammals outcompeted the South American marsupials until only the opossum was left. New Zealand is doing a good job of controlling invasive species, and shows that conservation can make a difference.”

“Allan Wilson was a friend of mine and I learned so much from him. He changed the world – the whole

field of molecular evolution stands on his shoulders.”

Stephen O’Brien is a world leading molecular

biologist, genome bioinformatician and conservationist. He uses the tools of molecular biology

to help protect endangered species

and understand devastating diseases such

as cancer and AIDS.

Stephen has discovered new species

of elephant, clouded leopard and orang-utan; and is credited with the discovery of CCR5-∆32,

the first of 40 human AIDS restriction genes

that impart natural immunity to HIV.

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Their work helped to more than halve the rate of New Zealand’s Campylobacter infections, which were the worst in the western world, costing more than $60 million a year. The group works with Crown Research Institutes, regional public health units, and other academics to understand the epidemiology, evolution and control of infectious disease caused by pathogens such as Campylobacter, Salmonella, E. coli, Leptospira, Cryptosporidium, and Giardia. Their work informs policy and public health decision making, and Nigel sits on the Food Safety Assurance and Advisory Council and the MoH/MPI Technical Advisory Group on working together for food safety and protecting human health.

Nigel is nationally and internationally recognised for his expertise in molecular epidemiology and pathogen evolution. In November 2014, he was an invited contributor to a workshop in Malawi discussing invasive Salmonella in Africa. The workshop was organised by the Wellcome Trust, the second-largest funder of biomedical research in the world, and attended by representatives from the Gates Foundation and National Institutes of Health (USA).

“Invasive Salmonella is much more severe than the usual disease,” says Nigel. “As well as diarrhoea and vomiting, patients can develop septicaemia. There’s a high fatality rate, particularly in children.”

“This type of Salmonella (non-typhoidal) is usually associated with animal infection, but this strain seems to have adapted human-to-human transmission. This is a concern as it may mean there isn’t an animal reservoir to target control measures at.”

An important topic discussed at the workshop was the use of genome sequencing to investigate the disease. Nigel’s AWC research was particularly relevant as his group is analysing the genomes of more than 100 Salmonella strains obtained from humans, birds and cattle to investigate how the bacteria’s population in New Zealand changed following a major human epidemic of Salmonella DT160 in 2000–2001.

This human epidemic was shortly preceded by a similar outbreak in wild birds, which caused significant mortality in sparrow and silvereye populations. The strain was also recovered from domestic fowl and ruminants.

PhD student Samuel Bloomfield is investigating how the Salmonella DT160 population changed in the following decade, using epidemiological analysis to see if the wild bird die-off and increase of human disease were linked, and exploring the role of other hosts, such as cattle, in the chain of infection. The aim is to trace the epidemic back to a point source and map how it spread. Preliminary results have already been reported at national and international meetings.

APRIL // Dr Stephen O’BrienSt Petersburg State University; Genome 10K Project. A moving landscape of wildlife genetics: uncommon glimpses (see cover story) Dr O’Brien will visit Auckland, Christchurch, Dunedin, Nelson, Palmerston North, Tauranga, and Wellington.

AUGUST // Professor Scott EdwardsHarvard UniversityBird evolution: from dinosaurs to DNAProfessor Edwards will visit Auckland, Christchurch, Dunedin, Napier, Nelson, Palmerston North, Tauranga, and Wellington.

SEPTEMBER // Professor Tom HighamUniversity of OxfordWhen Neanderthals and modern humans (and Denisovans) met: Human evolution from 60,000–30,000 years agoProfessor Higham will visit Auckland, Christchurch, Dunedin, Hamilton, Napier, Nelson, Palmerston North, and Wellington.

OCTOBER // Professor Hopi HoekstraHarvard University[topic tbc]Professor Hoekstra will visit Christchurch, Dunedin, Napier, New Plymouth (tbc), Nelson, Palmerston North, Tauranga, and Wellington.

Tackling Salmonella at home and in AfricaPrincipal Investigator Nigel French leads a large research team at Massey University. The mission of the French lab is to “improve the health of New Zealanders by developing and applying new techniques to inform decision making and guide the prevention and control of infectious disease”.

2015 SPEAKERSThe AWC public lecture series features four world-renowned international scientists, who will all tour New Zealand over the coming months. Make sure you don’t miss out – email awc-lectures@massey.ac.nz with your city of residence in the subject line to receive advance information about the talks and how to book.

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24 HOURS IN UAWATHE BIOBLITZ EXPERIENCE

In mid-February, the AWC took a team of its scientists, local Department of Conservation staff, a Gisborne District Council freshwater fisheries specialist, botanists from Te Papa, and other interested locals, to Tolaga Bay Area School to conduct a 24-hour census of life in Uawa. Four teams, along with enthusiastic Tolaga Bay Area School students, identified as many insects, shells, plants, observations of birds and other animals, from six different sites, bringing back any unidentified specimens to Bioblitz headquarters for identification. Scientists showed the students, aged 5-18, the wondrous world of life under the microscope, and between field trips, gave them short talks on various topics, including life in the Antarctic.

A full report of the results will be published in a special edition of PHENO and distributed to the students, and people in the community. This Bioblitz forms a part of the wider Uawanui Project. The AWC thanks fellow scientists and conservationists, Sandy Bull, Rebecca Lander, Don McLean, Trudy Ngawhare, Bridget Parker, Leon Perrie, Jaimie Quirke, Lara Shepherd, and Bill Wheeler, for giving their time and expertise to the children – and Wendy Newport-Smith, Lorraine Bergen, and Peter Handford (Groundtruth) for organising this complex and inspiring expedition.

How to tell the difference

between kanuka and manuka

That hedgehogs hibernate in winter

WHAT ARE SOME OF THE THINGS WE LEARNED? That some limpets

are golden on the Uawa Coast (they can be found from

the East Coast to Kaikoura and

occur on soft sandstone)

Why a weed is a weed, and how to recognise some of the most common

ones in Uawa – like Japanese

honeysuckle which is smothering the

native bush

That eels swim to Tonga to spawn

and then die. The baby eels have to

get all the way back to New Zealand by themselves.

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WHAT AMAZING DISCOVERIES DID WE MAKE?526 Species of plants and animals living in the Uawa/Tolaga Bay area were discovered during the BioBlitz.

More than one pair of the NZ Dotterel, a shorebird – rarer even than kiwi or tigers – were sighted by Jaimie Quirke (DOC) in the Kaitawa Estuary. The work Hauiti Incorporation has done to keep stock out of the Estuary, and future work on waterways flowing into the Estuary, plus ongoing pest trapping efforts by the teachers and students, will protect and help grow this small population.

Long tail bats were detected at the Mangatokerau River. A handy device, made by DOC, converts the inaudible bat cries (around 45kHz) to a frequency in our hearing range (up to around 20kHz).

Jaimie Quirke, DOC, reported: I placed two bat detectors on the Mangatokerau stream on Monday afternoon. These switch on at 8 30pm and switch off at 6 30am. The detectors listen for a signal at 45khz. Over the four nights that the detectors were out they recorded nine Bat Passes. We have not recorded bats in the Mangatokerau previously and have no visual or historic records of bats being in Mangatokerau.

SOME QUESTIONS FROM THE STUDENTSDo we have penguins in NZ?Do penguins have teeth?Were any penguins killed in the Erebus disaster?Why were female moa so much larger than the males?Why does New Zealand have only two native land mammals – the long and short-tailed bats?

SO WHAT DID EVERYONE THINK OF THE EXPERIENCE?Mr Rauru Kirikiri, Member of the AWC Governance Board

… it was one of the most inspiring things that I’ve been involved in for some time. The kids at Tolaga Bay Area School were a joy to behold. They were the most polite and culturally attuned (in a Maori sense) kids I’ve come across for a long time, and they were totally engaged in the Bioblitz. Their enthusiasm and vigour for what the Bioblitz was about was fantastic.

But what was equally inspiring for me was the way in which staff of the AWC interacted with the local community. I could go on ad finitum on this but suffice it to say that the AWC was superbly represented on this occasion. I was literally blown away by the way in which they all went about their “business”.

Mrs Nori Parata, Principal, Tolaga Bay Area School

It was an absolute pleasure having you all here in Uawa. We were honoured to host everyone and the kids absolutely loved it. I was so pleased with the level of their engagement in the whole process. We are still identifying species and have decided to make increasing the number of Tuturiwhatu (New Zealand dotterel) one of our immediate projects within Uawanui. I was heartened to hear from AWC scientists that their chances are already being increased just by the fencing of the Kaitawa estuary and our attempts at pest control.

Timothy Logan, winner of the 2014 Prime Minister’s Future Scientist Prize ($50,000). Tim, a student at Darfield High, Canterbury, was invited to join the expedition

I’m incredibly grateful to the Allan Wilson Centre for inviting me to attend the Bioblitz in Tolaga Bay. This has been an amazing experience for me to meet dozens of experts in their respective fields, learn about the biodiversity of a different part of New Zealand, and to be immersed in a social environment dominated by Māori culture. As a student learning Te Reo Māori, this experience has been especially worthwhile.

I found it especially interesting seeing a completely different range of plant species to what I have seen before in Canterbury, including species like karaka and puriri. Tasting the karaka kernel was a particularly interesting experience for me, albeit a worrying one.

That lots of creatures come

out at night

That a stoat can defer the birth of their young

until conditions are favourable

That scientists are just people

That spiders play a

valuable part in nature’s systems

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Catherine CollinsCatherine is working towards the sequencing of nuclear DNA (nDNA) from some of the koiwi tangata (skeletal remains) from archaeological sites across the Pacific, including some of the first people to arrive in New Zealand. Her initial focus is on bone and tooth samples from Wairau Bar, near Blenheim, one of the earliest and most important sites in New Zealand and the only early burial site in the country. This project is in collaboration with Rangitane o Wairau.

She is working under the supervision of founding member and AWC Principal Investigator Professor Lisa Matisoo-Smith, whose team has already examined the mitochondrial DNA (mtDNA) of these ancient people.

Analysing ancient DNA is a challenge compared with fresh DNA because when an organism dies its DNA begins to degrade so only tiny amounts (often damaged) can be recovered. Contamination of the sample is also a problem. Because ancient DNA research is by nature destructive, Catherine will have to balance removing enough of the bone or tooth sample to get sufficient nDNA with destroying as little as possible of these important human remains.

POSTDOCTORAL FELLOWSHIPS AWARDED FOR 2015

Karen AdairKaren is investigating how native New Zealand tussock grasslands are responding to global change – particularly increased temperature due to climate change and increased nitrogen deposition in the soil from human activity like agriculture; and whether their combination amplifies their individual effects.

Until recently, most ancient DNA research has focused on mtDNA not nDNA, because every cell contains much more mtDNA. However, new extraction and sequencing techniques mean that we can now obtain nDNA (see Pheno, June 2014, p4).

“It’s amazing that we are able to find out yet more information from the same ancient samples,” says Catherine. “These bones have been examined by bioarchaeologists to provide information about the first settlers and how they lived, then genetic techniques meant that mtDNA provided more information about these populations and their origins. Now we can investigate ancient nDNA, which can tell us about the health and physical characteristics of the Pacific ancestors and the genetic diversity of the founding populations, allowing us to reconstruct the population history.”

This is Catherine’s first postdoctoral position. Her PhD, also funded by AWC, investigated ancient sea lion DNA and determined that the New Zealand mainland sea lion population became extinct within a few hundred years of Polynesian arrival. It was repopulated by sea lions from the sub-Antarctic.

Postdoctoral fellowships foster early-career scientists who have demonstrated excellence in their doctoral studies. Catherine Collins is investigating ancient DNA to help better understand the initial settlement of New Zealand and the Pacific, while Karen Adair’s work will provide insights into how our native grasslands are responding to global change.

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In a fully factorial experiment at the Cass Mountain Research Area, Karen will analyse soil and plant communities which have been adapting to different temperature and nitrogen conditions since 2009. The temperature levels were based on estimates of the levels modelled for New Zealand by the end of

this century – so this work is relevant to New Zealand’s likely future climate conditions.

Using metagenomics, Karen is examining whether there are changes in composition (which taxa are present); diversity (how many taxa are present and their distribution); and functional capacity (protein-coding genes) of the soil microbial community. She is also quantifying change in the plant community, both from a taxonomic perspective and in terms of their ecological roles. Key questions are: how do soil microbe and plant communities respond to these global change drivers; do they respond in the same way; and are there interactive effects when both drivers occur simultaneously?

“Investigating the soil and plant communities at the same time is what makes this experiment so exciting. Most people focus on one or the other but they are intrinsically linked,” says Karen. “We’ve got fantastically detailed data sets looking at which plant and soil microbes are present and their relative abundance, as well as their traits.”

‘Traits’ are well-defined, measureable properties that can be linked to an organism’s ecological strategy or its contribution to ecosystem functions. This approach is usually used for studying plant communities, but Karen will also be applying it to the soil microbial community.

AWC Associate Investigators Professor Jason Tylianakis and Associate Professor Anthony Poole are supervising this project. Karen’s previous postdoctoral position was at the Bio-Protection Research Centre based at Lincoln University, investigating the influence of biofuel crop production on soil health and biodiversity. Her PhD in soil microbial ecology was at Northern Arizona University in USA.

ALEXEI DRUMMOND - ONE OF THE WORLD’S “MOST INFLUENTIAL SCIENTIFIC MINDS’

AWC Principal Investigator, Professor of Computational Biology, Alexei Drummond, has been named by Thomson Reuters as one of the “world’s most influential scientific minds” on the basis of a decade-long assessment of published papers. He was one of seven New Zealand scientists in their top 1%, but is out in front with over 22,000 citations.

In the introduction to the 2014 Thomson Reuters’ report, it states “…the identification of these individuals is rooted in the collective, objective opinions of the scientific community. Fellow scientists, through their citations, give credit to these people and their work. Everyone acknowledged in this book is a person of influence in the sciences and social sciences. They are the people who are on the cutting edge of their fields. They are performing and publishing work that their peers recognize as vital to the advancement of their science. These researchers are, undoubtedly, among the most influential scientific minds of our time.”

Alexei works on one of the Allan Wilson Centre’s strategic initiatives: Hidden Treasures. This research project on Hauturu/Little Barrier Island is a survey of all life – including bacteria and fungi – found on 20 square metre plots at different altitudes. The computer analysis of the DNA to identify species and their abundance is an example of Alexei’s applied skills. His methods reduce the tedium and volume of taxonomical work and speed up analysis. Speed and efficiency will be of the essence if the information is to be used to hold on to our biodiversity – some of which we don’t even know about.

Azra, who has taught all levels from pre-school to postgraduate trainee teachers, was also recognised as an outstanding teacher, being awarded one of a handful of Victoria University Teaching Excellence awards. In 1996, Azra received a national award for excellence in teaching. Azra has a very influential role at the College of Education, and for beginning science teachers, models a classroom style of clarity, organisation, firmness and good humour. She has “a

presence that commands respect and attention as soon as she enters the room,” according to one former student teacher.

Azra reflects on her long career, “I am a learner and have learnt that caring about my students and their learning underpins what I do in the classroom. It has been a privilege to have the opportunity to spend a lifetime in New Zealand classrooms. We often do not give our teachers the credit they deserve. Most New Zealand teachers are there because they want to make a difference to those they teach. As a teacher educator, I would be happy for any of the many student teachers I have had in my classes to teach my own children.”

For these outstanding professionals, it is love of teaching, young people, and the science itself that drives them to

Allan Wilson CentreScience Tower B, Level 2, Massey University, Private Bag 11 222, Palmerston North 4442, New ZealandPhone | 06 951 6357awc-lectures@massey.ac.nzwww.allanwilsoncentre.ac.nz

Professor Hamish Spencer Director Phone | 03 479 7981 Fax | 03 479 7584hamish.spencer@otago.ac.nz

Ms Wendy Newport-Smith Centre ManagerPhone | 021 423 757w.newport-smith@massey.ac.nz

Robin WilkinsonPheno Researcher and Writerwilkinson.robin@gmail.com

Partner InstitutionsMassey University, Private Bag 11 222, Palmerston North

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

Landcare Research NZ Ltd, PO Box 69040, Lincoln

The University of Auckland, Private Bag 92019, Auckland

University of Canterbury, Private Bag 4800, Christchurch

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

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

© Allan Wilson Centre 2014. Pheno is available on request. Please email, awc-lectures@massey.ac.nz. Any information in this newsletter may be reused provided the Allan Wilson Centre is acknowledged as the source of the information.

Terry’s dedication to the profession and excellent teaching were recognised by the 2014 Prime Minister’s Science Teacher Award in December. The Prize comes with $100,000 for her School, and $50,000 for Terry to spend as she chooses.

Terry says, ‘Teaching and learning science can be quite a lonely process if it is stuck within the walls of a school...but when scientists are ready to reach out and connect with teachers and with students, sharing their ideas and their research findings, then science becomes real and exciting for both teachers and students. Science comes alive!”

As well as her role as adviser to the Centre, Terry has been seconded to a number of expert panels and national science groups, including the National Animal Ethics Advisory Group. She was also a lead writer for the senior science teaching and learning guidelines to support the implementation of a revised science curriculum.

TEACHING EXCELLENCE PRIZES FOR CENTRE ADVISORSIn 2011, the Allan Wilson Centre asked three very experienced science teachers to advise the Centre on how best to support general science and biology teaching in schools – Ms Terry Burrell, Dr Azra Moeed and Ms Barbara Mavor.

Ms Terry Burrell, Learning Area Leader for Science at Onslow College, Wellington

Ms Barbara Mavor, formerly Vice-Principal and Teacher

at Queen Margaret College, Wellington, and

currently an evaluator at the Education Review Office

Dr Azra Moeed teaches trainee science teachers at the

VUW College of Education in Karori, Wellington, following

decades in the classroom

Same and Different – an introduction to the basic rules of heredityAWC education adviser, Barbara Mavor, has produced a powerpoint presentation, with notes and class exercises, that teachers can use from Year 6 upwards. Students are bound to like it, because it’s about ‘them’, and explains simple rules of heredity, using classmates, muggles and wizards for comparison.

devote many extra hours to their jobs, and support of their colleagues through teacher associations such as BEANZ (Biology Educators Association), NZASE (NZ Association of Science Educators), and Capital City Science Educators.

The Centre congratulates and thanks Terry, Azra and Barbara, for their ongoing advice and, in particular, practical help to produce teacher resources on evolution and related topics. These resources can be found at http://www.allanwilsoncentre.ac.nz/massey/

learning/departments/centres-research/allan-wilson-centre/our-research/resources/educational-resources.cfm