JUNE 2015 ISSUE 16 ISSN 2324-5670

Scott EdwardsBird Evolution - From Dinosaurs to DNA

A Small Sample of a Big Journey

Ancient DNA - Secrets from the Past

Uawa / Tolaga Bay Bioblitz Energy and Excitement Continue

An Uncommon Glimpse of Stephen O’Brien

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Some of you will be aware of the news that the AWC’s application for continued funding in the latest Centre of Research Excellence (CoRE) round was unsuccessful. This result means that the AWC will close at the end of this year, and the support for our science projects and outreach programmes will cease.

I have to say I am extremely disappointed by this outcome, but I am not alone. Massey Vice Chancellor, Professor Steve Maharey wrote, “The Government’s decision to

end funding for the CoRE is not easy to understand given the outstanding record established by the AWC.” The quality of our research and personnel was never in doubt. Our scientists are at the cutting edge of world-class research and are among New Zealand’s finest: we count 8 Fellows of the Royal Society of New Zealand among our 21 Investigators,

a proportion greater than any other CoRE.

It is widely acknowledged that

the Allan Wilson Centre's outreach is outstanding. The review panel

that evaluated our proposal described

our interactions with Māori as “exemplary”. And the scientists who

come to New Zealand as part of our International

Speaker Series reach about 10% of the population through a combination of public

lectures, radio interviews and magazine articles.

Professor Maharey believes that an intention to fund new CoREs meant the AWC missed out. This conclusion, if right, is very worrying. CoREs should be about excellence, not about giving everyone a turn; by their nature, CoREs should be carrying out the very best science.

It seems to me, however, that there is a more likely explanation and one that is ultimately of even greater concern. There is now no CoRE whose primary focus is on New Zealand’s biodiversity and that is part of a trend of reducing scientific research funding in that area. Readers will be familiar with the decisions to reduce Department of Conservation research capabilities. Even more recently the Biodiversity Science Challenge was subsumed (in a cabinet-level decision) into the Biological Heritage Challenge, which now appears to be dominated by agricultural and bioprotection research. Scarily, all this is happening at a time when our biodiversity is under unprecedented pressure, with widespread scientific concern for our country’s future.

I do not want to finish on a down note, so let me say that our next two speakers in the International Speaker Series are among our very best. Harvard University’s Scott Edwards, recently elected to the elite American National Academy of Sciences, and New Zealander Tom Higham, now at Oxford, are both accomplished scientists and riveting speakers. I urge you to come to their talks: they will be opportunities not to be missed!

THE END OF THE JOURNEY FOR ALLAN WILSON CENTRE

Professor Hamish Spencer speaking to expatriate New Zealanders in London, 17 June

Using evolutionary history, population genetics, and comparative genomics, Scott has spent his career investigating how birds’ distinctive traits evolved, how they are diversifying, and how they cope with environmental challenges.

Scott is Alexander Agassiz Professor of Organismic and Evolutionary Biology at Harvard and curator of the ornithology collection in Harvard’s Museum of Comparative Zoology. Birds are a lifelong passion for Scott, whose interest in these “hybrid animals” was sparked after a neighbour in New York took him birdwatching when he was 10 or 11.

“They’re fascinating to study because they have an affinity with mammals such as being warm blooded, but they’re also very different – they lay eggs, have feathers and have scales on their legs.”

The theory that birds are the living descendents of dinosaurs, put forward not long after Darwin’s On the Origin of Species was published, has become increasingly accepted over the years – but until recently, it was based almost entirely on the fossil record. Scott’s work investigating bird genome sizes and how feathers arose showed that they go back a very long way.

“It was exciting to discover that although feathers are a unique trait of birds, the genes that make a feather are old. Humans, fish, turtles – all have the genes but seem to be missing regulatory machinery, the switches needed to turn genes on and off and make them interact in appropriate ways.”

Many dinosaurs are now known to have had feathers, although simpler ones than modern birds.

Scott is also investigating why birds have such (comparatively) small genomes, and how this reflects their streamlined and high energy lifestyles. Bird genomes are just 1–1.5bn base pairs; humans have about 3bn base pairs.

“This is a big difference between two groups that, in the grand scheme of things, are actually fairly closely related.”

Birds have less repetitive DNA than mammals. A major part of the loss is non-coding DNA. As some non-coding DNA is functional it may be that birds have simpler regulatory networks with less redundancy than mammals.

One theory to explain birds’ small genomes is that high metabolic rate activities (such as flight and developing rapidly from egg to chick) are facilitated by having small cells, because large surface area/volume ratio enables efficient gas exchange.

Another hypothesis is ‘developmental time’ – other vertebrate species that develop rapidly, like salamanders, also tend to have smaller genomes. If an evolutionary driver is to have rapid cell division then jettisoning DNA may be an advantage.

Interestingly, flightless birds tend to have bigger genomes than birds that fly. Scott is using genome sequencing to determine which genes and/or regulatory regions distinguish flightless from flighted species.

Scott is also known for his work in avian disease genetics. He found that immune genes are extremely polymorphic (variable between individuals), which at the time was an “eye-opener”. He is currently investigating a parasite interaction between Mycoplasma (a bacterial pathogen) and the North American house finch. These two species first came into contact about 20 years ago.

“Some of our studies have brought us back to these highly polymorphic immune genes. We haven’t yet figured out all the details of how the disease has affected the house finch, but we’re homing in on the kinds of genes that may have been important for survival of the species in the face of this disease.”

This work is providing exciting insights into how birds respond at the genetic level to environmental challenges and novel threats such as pathogens.

FROM DINOSAURS TO DNAThe Allan Wilson Centre welcomes Professor Scott Edwards, renowned ornithologist and evolutionary biologist, as the next speaker in our public lecture series. He is touring New Zealand 11-20 August.

“It was exciting to discover that although feathers are a unique trait of birds, the genes that make a feather are old. Humans, fish, turtles – all have the genes...”

BIRD EVOLUTIONScott Edwards

WELLINGTON Tuesday 11 August, 6.00pm Te Marae, Te Papa Tongarewa, Museum of New Zealand

NAPIER Wednesday 12 August, 6.00pm Napier Aquarium Exhibition Hall, Marine Parade

CHRISTCHURCH Thursday 13 August, 6.00pm The Chateau on the Park, 189 Deans Avenue, Riccarton

NELSON Friday 14 August, 6.00pm Maitai Room, Rutherford Hotel, Nelson

PUBLIC TALKS BY PROFESSOR SCOTT EDWARDS

REGISTER ONLINE: Reserve a seat for these popular lectures at www.allanwilsoncentre.ac.nz Click ‘Register Online’ under ‘Events’.ENTRY BY GOLD COIN DONATION

DUNEDIN Monday 17 August, 6.30pm St David Lecture Theatre, University of Otago

PALMERSTON NORTH Tuesday 18 August, 6.30pm The Globe Theatre, Main Street

TAURANGA Wednesday 19 August, 6.30pm Tauranga Yacht and Power Boat Club, 90 Keith Allan Drive, Sulphur Point

AUCKLAND Thursday 20 August, 6.15pm Auckland Museum Auditorium

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CharingCross

The National Gallery

St. Paul’sCathedral

Sampling in progress

Ngati Ranana Allan Wilson Centre Researchers Lisa Matisoo-Smith, Hamish Spencer and Russell Gray

A SMALL SAMPLEOF A BIG JOURNEY

Over 200 expatriate New Zealanders gathered at New Zealand House, London in June to contribute their DNA to Lisa Matisoo-Smith's deep ancestry study (The Longest Journey: Africa to Aotearoa). The mitochondrial DNA result each person receives will place their maternal ancestor on their particular branch of the human family tree, going back many thousands of years.

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Russell Gray's parallel story of the evolution of language, and the strong similarities between languages in the Pacific region, was just as powerful. This, and the story of Allan Wilson and his discovery that all humans alive today on Earth have a common maternal ancestor who lived in Africa c150,000 years ago, were revelations to most of the guests. We all came out of Africa.

The events of 16 and 17 June were attended by a range of expatriates from very young New Zealanders on the classic OE, to Sir Robin Clark,an eminent chemist from Cambridge, famous chef, Peter Gordon, and Dame Judith Mayhew (lawyer and academic). Sir Anand Satyanand (former Governor General), Sir David Skegg (President of the Royal Society of NZ), Mr Rau Kirikiri (Allan Wilson Centre Governance Board Member), and Professor Hamish Spencer (Director of the Allan Wilson Centre) co-led this extraordinary scientific and cultural expedition. It was a celebration of science, of discovery, and new understandings of who we are, where we come from and what our future might be.

We still don't know what motivated the migration from the Pacific Islands to Aotearoa 750 years ago, but the research by Lisa and others is continuing to fine-tune our knowledge. Her analysis of ancient DNA recovered from koiwi tangata (human remains) from the archaeological site of Wairau Bar, near Blenheim, has

radically changed assumptions about the first human settlement of Aotearoa. The diversity of the DNA strongly suggests a much larger founding population than previously thought, and a planned mass migration.

We do know that in more recent times, many other brave people also left everything they knew, and family they loved, to make a new life in New Zealand. They included refugees from World War II, survivors of Pol Pot's genocide, and further back, agricultural labourers impoverished by a depression in the UK in the late 19th century. Many never returned home, and some perished on the long and dangerous journey.

While we know more and more about our origins and diverse genetic make up, to actually feel what it means to be a New Zealander, and what binds us, gather together with your fellow New Zealanders in a place far from home - London, in this case - and sing waiata such as Pokarekare ana and Whakaaria mai.

LondonEye

Big Ben &Westminster Palace

St. James’sPark

BuckinghamPalace

Memorial to the former inhabitants of Shipton Under Wychwood, Oxfordshire, who died on the

voyage to New Zealand

Allan Wilson Centre Researchers Lisa Matisoo-Smith, Hamish Spencer and Russell Gray

The Royal Society of New ZealandMassey UniversityUniversity of OtagoMax Planck Institute for the Science of Human HistoryKiwi Expats Assn (KEA)

Radio NZ NationalNZ House staff Ngati RananaRoyal Society of LondonLisa’s husband and daughter, Brent and Tessa Smith

The amazing 360 degree view from NZ House, Haymarket, London. Photo Credit: Matthew Breen

Taking part in the sampling, NZ High Commissioner,

Sir Lockwood Smith

NZ House staff Ceilidh Dunphy, Elizabeth Walker,

and Tracey Curtin, in front of the carving by Inia te Wiata

WestminsterAbbey

The Allan Wilson Centre is grateful for the partnership and assistance of:

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Some interesting facts: an estimated four million mummified Ibis birds were found in one Egyptian catacomb alone… and being attacked by a penguin “is like being grabbed by needle-nose pliers and thwacked by a pair of jandals at the same time”. Craig would know. He’s been working in the Antarctic for over a decade collecting blood from the living and bones from sub-fossil penguin, the comparative analysis

of which can be used to work out the rate of evolution.Deciphering DNA from the swags of moa fossils has been

another important area of work for Craig. They have resolved the mixed sub-fossils into 11 species or so, including the 250kg North Island giant female moa. A bird that large is ill-designed for incubating eggs. It is suggested that they curled around them instead. Interestingly for us humans, the job was allocated to males, which were much smaller than the females. Craig gave his audiences a basic introductory course in sexing

birds using DNA. Sex specific DNA can be obtained from both the inside and outside of egg shell fragments.

Craig paid homage to the heroes of DNA sequencing technology, such as Kary Mullis and Michael Smith, who developed the polymerase chain reaction (PCR) which amplifies small amounts of DNA into readable quantities. The rapid advances in the art are truly impressive and have outrun our capacity to make sense of it. Biologists now need help from mathematicians and computer scientists to answer the questions hidden in the massive amounts of data now being collected. The next quantum leap after the polymerase chain reaction is already here: massively parallel DNA sequencing. Its name says it all.

ANCIENT DNA: SECRETS FROM THE PASTAssociate Professor Craig Millar intrigued and entertained audiences in Nelson and Queenstown with his talk on ancient DNA methods and discoveries.

Craig Millar, Wendy Newport-Smith, holding Moa fossil bone

Well known photographer, Distinguished Professor Anne Noble, and Masters photography student, Tom Hoyle, accompanied the Allan Wilson Centre mission to London in June. They invited expatriate New Zealanders attending the events at NZ House to have their silhouette portrait taken, as an extension of Lisa’s ancient ancestry study, using DNA analysis. These portraits may be used in a book Lisa is planning, and possibly an exhibition.

Says Anne, “There are numerous traditions of photographic portraiture that presuppose that an image of an individual can be read for information about race, character and rank within a society. We make many assumptions through visual cues, and the histories of human portrait typologies are fascinating because of how they have contributed to communicating mistaken meanings of racial variation, physical attributes and cultural belonging within a population.”

Visualising Evolutionary Genetics is a collaboration between the Massey University School of Fine Arts and the Allan Wilson Centre to develop innovative approaches to communicating the outcomes of this study. Its purpose is to re-imagine and explore forms of portraiture in the light of new scientific and cultural understandings of personal identity and human descent.

VISUALISING EVOLUTIONARY GENETICS

Sir Anand Satyanand6A

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UAWA / TOLAGA BAY BIOBLITZENERGY AND EXCITEMENT CONTINUE

Rather than interest waning with time, the drive to understand and nurture the important biodiversity of Uawa/Tolaga Bay has gained momentum since the February 2015 Bioblitz. Final collation of results has been completed and an attractive summary of the species found has been published. You can find it at www.allanwilsoncentre.ac.nz or request a hard copy from Allan Wilson Centre Administrator, Lorraine Bergen, l.bergen@massey.ac.nz

The Bioblitz was a key event in continuing to raise awareness of the local environment as part of the Uawanui Project that has been developed jointly by Te Aitanga a Hauiti, the Uawa/Tolaga Bay community and the Allan Wilson Centre. Some key findings from the Bioblitz are helping to drive work on the

ground with an expansion of predator trapping around Kaitawa Estuary to protect NZ Dotterel and other birds present. Tolaga Bay Area School is

also starting a novel project with Groundtruth (who have been involved with the Uawanui Project from the beginning) to use a range of

technologies to transmit image, video and audio data to learn about, and monitor, the rare NZ Dotterel and also Bats, which are our only

native mammal. The community was very excited when the presence of bats was detected in February and Allan Wilson Centre Director, Professor Hamish Spencer, sighted the Dotterel in the Kaitawa Estuary.

The information from the Bioblitz is both an important benchmark of the species that are present at Uawa/Tolaga Bay today, and a turning point for Te Aitanga A Hauiti and the community in building greater understanding and management of their valuable biodiversity.

Report by Pete Handford, Manager of Groundtruth, a company contracted by the Allan Wilson Centre to help the Uawa/Tolaga Bay community formulate a vision and practical plan for restoring their area, and developing a sustainable economy based on local resources.

WHEN NEANDERTHALS MET (MODERN) HUMANS

It seems possible, given the recent history of modern humans and the ultimate extinction of Neanderthals, that most encounters were hostile rather than amorous. Nevertheless, the evidence of sexual liaison is undeniably present in the genomes of all non-African humans, a recent discovery that turned all those Neanderthal jokes on us. Tom and colleagues are trying to determine when modern humans came out of Africa and what happened when they met Neanderthals, using novel scientific dating and genetic methods. The universality of Neanderthal DNA in non-African genomes suggests that the sexual encounter/s took place soon after our departure from Africa 60,000 years ago, as it is present even in Aborigines who reached Australia up to 50,000 years ago.

Even more surprising, non-Africans also carry remnants of another extinct human species named Denisovans after the Siberian cave in which a tiny, but well preserved, finger bone was discovered. It was so well preserved that it yielded a complete genome. Tom and his team are involved in research at Denisova and have new results to share with audiences in New Zealand. If you want to make sure of a place at this fascinating talk, register interest at awc-lectures@massey.ac.nzThe final AWC international guest speaker is

expatriate New Zealander, Tom Higham, Professor of Archaeological Science at the University of Oxford. He’ll be touring from 15 to 24 September (see schedule below). It is an enthralling idea – the first meeting between our long lost cousins, the Neanderthals - and a best selling one as imagined by author Jean Auel in Clan of the Cave Bear and its sequels.

SEPTEMBER // Professor Tom HighamUniversity of OxfordWhen Neanderthals and modern humans (and Denisovans) met: Human evolution from 60,000–30,000 years agoProfessor Higham will speak in Wellington (15 Sep), Palmerston North (16 Sep), Napier (17 Sep), Hamilton (18 Sep), Nelson (21 Sep), Christchurch (22 Sep), Auckland (23 Sep), Dunedin (24 Sep)

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Steve O’Brien is a charismatic and compelling story-teller. And what greater story to tell than the touch-and-go recovery of the big cats from near extinction. Cheetahs are so reduced in genetic diversity that they can accept skin grafts from each other – a novel experiment directed by Steve to demonstrate

that they were virtual clones. There is only an average of one difference in 300,000 DNA base pairs between them, compared to c100,000 base pairs in humans. The “DNA clock” dates the genetic bottleneck back 10,000 years to the late Pleistocene, when some catastrophic event in America wiped out 40 species of large mammals, including mammoth and giant sloth. Fortunately, some cheetah had migrated to the East over an Ice Age land bridge and ensured the survival of this magnificent triumph of bio-engineering just long enough for conservationists like Steve to bring science to their aid.

Steve played a direct role in saving the Florida panther (aka cougar, puma). In 1980, the population of the Florida panther was just 50 and confined to swampy ground east of

Florida. They were degenerate, with over 85% malformed sperm, a high incidence of cryptorchidism (where one or both testicles do not descend), and a much higher susceptibility to disease. It took some time for Steve to convince all the parties involved to import eight female Texas cougars from the other side of the Mississippi. The population is now over 500, and has recovered its vigour in that short space of time.

The reluctance to import the cougars stemmed from common, pre-genetic era confusions about species purity. Geographical separation doesn’t always mean a genetic difference. Sorting out tiger sub-species, using genetics, may be just the breakthrough needed to save them from extinction. The total tiger population has reduced from 100,000 to 3,000 in a century, and nothing seems to be working despite the backing of people like Vladimir Putin and Brad Pitt. Genetic analysis showed that the small population of Amir tigers hanging on in far north east Asia was in fact the same as the thought-to-be extinct Caspian tiger, and therefore could theoretically be reintroduced to the enormous territory around the Caspian Sea, where humans are sparse. Whether the politics allow this to happen is another matter. But there is no more persuasive advocate than Steve O’Brien, who can articulate the scientific arguments so powerfully.

Allan Wilson CentreScience Tower B, Level 2, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand

Phone | 06 951 6357awc-lectures@massey.ac.nz

www.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

Glenda LewisEditor and writer,glendajanelewis@gmail.com

Partner Institutions

Massey 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.

AN UNCOMMON GLIMPSE OF STEPHEN O’BRIEN

Conservation geneticist STEVE O’BRIEN toured New Zealand in April as the AWC’s first international series speaker for 2015

Steve O’Brien meets the cheetah brothers at Wellington Zoo