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Issue 6 (March 2008) ISSN 1178-6892

Falling for Science: asking the big questions

I recently saw a documentary where a

gentleman stared solemnly at the

camera and pronounced 'there is no

external reality. The only reality is inside

our heads.' Yet I wonder where the

limits of this heroic conviction lie. Were I

to take him to the top of a tall building

and invite him to step off (because

realities like gravity, kinetic energy and

collision forces are after all, only inside

his head), shouldn't I expect him to

decline my offer? Sure, the picture of

the world we carry inside our head is

just an interpretation of reality, but only

in the banal sense that the meal we eat

in a restaurant is the chef's

interpretation of the raw ingredients.

That doesn't make the food, nor indeed

the external world, any less real. A chef

can't turn a carrot into an apricot, and

even a person in a deep hallucinatory

state would have their experience

altered by a high force collision with the

tarmac. So to simply say 'science is

story telling' and leave it at that seems

to miss something important. For

science, unlike other story forms,

makes uncannily accurate predictions;

here we're talking about the sort of

precision required to land a vehicle on

Mars, zap a malignant tumour or

bounce a cellphone signal off a satellite.

Things we haven't always been able to

do, indeed once couldn't have even

dreamed of doing. And that remarkable

power needs explaining.

But, and here's where it really gets

fascinating to me, the 'it's all just

science you know' approach is just as

problematic. The suggestion that we

use story to fill in the gaps that science

has not yet shone its light on is a

natural extrapolation. Many things we

once used non-predictive stories to

explain (eclipses, plagues, floods) now

have scientific explanations. Hence

some choose to view science as a

slowly encroaching tide, washing the

shore clean of myth and superstition.

But while it might in principal be

possible to reduce something as

complex as a funny joke down to

physics, I wonder if that might not rather

ruin the moment. And as it is with

laughter, so it is with love, justice, fear

and longing. To simply say it all comes

down to science is to deny the rather

vital point that as a struggling Homo

sapian I desperately crave knowledge

of things which are too complex, too

subjectively slippery, too infected by

humanity, to be captured by a

mathematical formula.

Inside this issue

Falling for Science: asking the big questions .............................1 Book Review ...............................2 Science Wānanga Wows Māori Community..................................4 Gene Geniuses ...........................6 DNA Barcoding Life: Part II how the past can help the future .....................................8 Population Genetic Theory: how can selection help maintain variation? .................................11 Traditional Kiwi-Feather Cloaks: throwing new light on a tradition .....................................14 Charles Darwin, evolution simple and testable...............................18 Recent Publications ................25 Contact Us ................................28

TThhee AAllllaann WWiillssoonn CCeennttrree NNeewwsslleetttteerr

Bernard BeckettWriter An excerpt from the introduction to Falling for Science

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In his first work of non-fiction – the

result of a year-long teacher’s

fellowship in the Allan Wilson Centre –

Bernard Beckett asks what science is

and where its limits are.

Charles Darwin was a Christian. This

quiet little fact sits off to one side of

modern evolutionary discourse, not so

much forgotten as deemed irrelevant.

And, in fact, it is irrelevant. The theory

of evolution is a robust scientific model,

not a stick for atheism to beat religion

with.

As Bernard Beckett puts it in his new

book Falling for Science, “For every

person who says, ‘See, God didn’t

make the world after all’, there will be

another who responds, ‘Ah, that’s how

God did it.’”

Beckett is a secondary school teacher

and a writer of teen fiction (Jolt, Home

Boys, Malcolm and Juliet among

others). Falling for Science is a

departure for him, a major work of non-

fiction that asks what science is (the

book’s subtitle is Asking the Big

Questions) and where its limits are.

“Can science,” it asks, “get inside this

business of making meaning in our

lives, or are there places where its light

simply won’t shine? Can we define what

those places might be, what their nature

is? Because those are the places where

we’re dependent on story to make

sense of things. The modern danger is

to let science and story merge, and

then claim that our stories are backed

up by science.”

The evolution/creation debate is a

classic example, argues Beckett, of two

competing stories appealing to the

authority of science in order to be taken

more seriously. He spends some time

in the book explaining why the pseudo-

scientific creationist arguments, of

which intelligent design and irreducible

complexity are the most recent,

collapse under their own weight.

But he also explains why it would be

helpful if the likes of Richard Dawkins

could bring themselves to stop sniping

at creationists. “Really, I think this

debate could have a lot of the heat BOOK REVIEW

of Falling for Science asking the big questions

published in the NZ Listener

by David Larsen

taken out of it – although I say that from

the slightly privileged position of not

living in the US.”

“Why should I care whether people

believe in evolution or not? In the end, I

care because I want each generation to

provide me with a resource of people

who understand things like genetics, so

they can contribute to things like cures

for cancer. I’d hate to think that kids

were being brought up to believe DNA

didn’t exist, mutations don’t exist, cells

don’t develop in this way. Forget about

bird flu, kiddies, we all know viruses

don’t really evolve! That would be

bizarre and terrifying. But weirdly,

creationists accept all that stuff. They

just want to tell another story on top. At

that point, I say let them be.”

Beckett points out that the word

“scientist” was actually coined by

Thomas Huxley, Darwin’s bulldog, as a

weapon in his campaign against the

19th-century religious establishment.

Huxley was socially progressive, the

Church was not; Huxley was also well

aware that evolution challenged the

Church’s position on biblical literalism,

and that if enough clergymen could be

ABOUT THE AUTHOR - Bernard Beckett grew up in the lower part of the North Island. He has a degree in

Economics, and has taught in the Wellington region for several years. Bernard writes plays for teenagers and

has published eight novels, including the popular Jolt (2001), which was a finalist in the 2002 New Zealand

Post Children's Book Awards. Bernard was a RSNZ Teaching Fellow at the Allan Wilson Centre during 2006.

For more information about this Author, visit: http://www.longacre.co.nz/authors/beckett.html

baited into condemning Darwin’s ideas,

they would in the long run lose prestige.

So he deliberately framed the argument

as one between rationality and

superstition: the Church was wrong

about evolution, and therefore it was

wrong about everything else.

In other words, Huxley front-loaded the

creation/evolution debate with moral

and metaphysical baggage that it’s

never since managed to shake off. And

yet, Beckett stresses, evolution, being a

scientific model, “is purely predictive. It

can tell us how physical relationships in

the world are built. What it cannot do is

provide us with a compulsory mode of

interpretation.”

Beckett first read about Huxley – “this

mathematician I was talking with just

gave me Adrian Desmond’s biography

of Huxley out of the blue; really, the way

knowledge gets around is so fortuitous”

– while he was on a Royal Society

Fellowship for Teachers, at Massey

University’s Allan Wilson Centre for

Molecular Ecology and Evolution.

“That fellowship – it’s a wonderful thing,

actually. There are about 50 or so given

out a year, it’s the one major sabbatical

scheme available in New Zealand

teaching. “The thinking behind it is for

the teachers to propose something

they’d like to look at. It’s not allowed to

be about provision of resources or

anything specific to the classroom, it’s

meant to be about the teacher just

going out and broadening their own

mind, getting back into some sort of

passion for the subject.”

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In 2004, the Allan Wilson Centre sent a

letter around secondary school maths

departments offering to host any

teachers interested in taking up a

fellowship. “I’d been reading quite a bit

of popular science at that time,” recalls

Beckett, “so my head was already

there, and spending some time around

people working in molecular evolution, it

just looked like a lot of fun. And, being a

writer, I naturally assumed there’d be a

book in it somewhere.”

He was supposed to work with a group

studying DNA mutations in taro, with

the aim of unravelling the history of the

plant’s migrations around the Pacific.

But taro DNA turned out to be very

difficult to sequence, and while the

biologists were struggling to produce

the raw data for the historical study,

Beckett kept busy figuring out what the

centre’s other researchers were

working on.

“Initially, I was just puzzling out how this

whole organisation worked, and trying

to get my understanding of the

background science up to speed. That

drifted over into philosophy of science

quite quickly.” Hume, Kant, Popper,

Kuhn. “The Allan Wilson Centre very

much has the culture that everybody

should be feeding back in. It’s a very

intellectually fertile sort of place.

Philosophy of science became the thing

I could feed back to them, and people

were interested in it, and that’s

incredibly encouraging in itself.”

Meanwhile, he was writing a futuristic

novel, Genesis, which subsequently

won the 2006 New Zealand Post Book

Award for Young Adult Fiction, and will

shortly become the first of his books to

be released in Australia. And he began

writing essays about science.

“It was a way of clarifying my own

thoughts, primarily. It kept looking as

though it might be a book, but I wasn’t

confident it was something worth

throwing into the world. I’m still not in

any way confident that in five years I’ll

look back on this book and agree with

it, you know?

“There’s one big question left hanging

over everything I say in the book, and

that’s whether science is really

describing the final reality of the world,

or just giving us a model we can use to

make good predictions.

“I think the argument I made to other

people was if I had all these

uncertainties, the thing wasn’t worth

putting into print. To which at least one

person replied, ‘Well, that’s true of

everything that everybody writes. Think

of it as a contribution to a discussion.’

“And that was probably the liberating

understanding for me. You’re not meant

to be saying, ‘Here’s how it is.’ You’re

trying to say, ‘Here’s where I’m at.’”

Falling for Science, by Bernard Beckett.

(Longacre $39.99)

This book review was from the Listener Archive: Dec. 22-28 2007 Vol 3528(211) http://www.listener.co.nz/issue/211/artsbooks/10181/a_passionate_mind.html

Science Wānanga Wows Māori Community Te Wānanga Pūtaiao Pukemokimoki Marae, 13th - 16th January 2008

Can a science wānanga (school) help

to increase the number of Māori

scientists, architects and engineers?

Comments from the inaugural Te

Wānanga Pūtaiao at Pukemokimoki

Marae in Napier suggest that taking

science from the laboratory to the

marae can inspire new generations of

Māori scientists.

“I thought science was boring, but this

wānanga has made me think it’s fun”.

- High-School aged participant.

Pukemokimoki Marae and Victoria

University’s Science Faculty joined

together to host Te Wānanga Pūtaiao.

This successful event is an extension of

the Science Faculty’s Āwhina outreach

programme, which is a mentoring

scheme for Māori and Pacific students

that has been running for 9 years

(http://www.victoria.ac.nz/science/Awhina/).

The central focus of Āwhina is Māori

and Pacific development, which was

also the central theme of Te Wānanga

Pūtaiao.

The aim of this particular wānanga was

to encourage participation and

achievement among Māori rangatahi

(youth) and tamariki (children) in

science. Excitement for science was

generated by concentrating on themes

that were relevant to Māori

communities including sessions on

DNA and Whakapapa and the Marine

Environment. Drs Hilary Miller (AWC),

Kristina Ramstad (AWC), and Adele

Whyte (Centre for Marine

Environmental & Economic Research,

Victoria University) designed and

taught the genetics portion of the

wānanga. Āwhina mentors also formed

a vital part of the team, contributing to

the DNA extractions and the smooth-

running of the whole programme. The

genetics portion of the wānanga also

included discussion of AWC research

into the whakapapa of kiore (Dr Lisa

Matisoo-Smith and Judith Robins),

kumara (Andrew Clarke), hue (Andrew

Clarke), and chickens (Alice Storey)

from throughout the Pacific.

Tamariki doing a DNA extraction under the watchful eyes of Dr. Kristina Ramstad.

Support from whānau is vital to

encourage more Māori youth to seek

careers in science and technology.

For this reason, the wānanga was

pitched for students of all ages, with

participants ranging in age from under

4

5 to over 75 years of age. More than

seventy people participated in the

wānanga, and everyone really enjoyed

the hands-on activities, which included

physics demonstrations and what could

be the world’s first DNA extraction on a

marae!

5

The project was also an education for

the scientists as Kaumatua and Kuia

(elders) also contributed their

knowledge to this wānanga. In many

instances, the observations of their

tūpuna (ancestors) highlighted obvious

parallels between Māori oral tradition

and science. This reinforces the idea

that Māori have been scientists for

many years! If tamariki can continue

on this rich tradition of seeking

knowledge, incorporating the

knowledge of their ancestors with

technical advances, then the scientific

future of Aotearoa is in good hands.

This project was led by Dr. Adele Whyte with financial support from Te Puni Kōkiri.

Co-authored by:

Adele Whyte

Māori Fellow, Āwhina Alumni, Ngāti Kahungunu

Victoria University of Wellington

adele.whyte@vuw.ac.nz

Kristina Ramstad

Postdoctoral Fellow

AWC-Victoria University of Wellington

kristina.ramstad@vuw.ac.nz

Hilary Miller

Postdoctoral Fellow

AWC-Victoria University of Wellington

hilary.miller@vuw.ac.nz

Te Whānau o Pukemokimoki Marae, Jan 2008

Gene Geniuses Gene Geniuses

A large grey metal box sits on a bench

in a lab at Massey University’s Allan

Wilson Centre for Molecular Ecology

and Evolution. But this isn’t just any old

piece of lab equipment. This

nondescript box is the new Solexa

Genome Analyser system, and it

represents the future of genetic

analysis.

A large grey metal box sits on a bench

in a lab at Massey University’s Allan

Wilson Centre for Molecular Ecology

and Evolution. But this isn’t just any old

piece of lab equipment. This

nondescript box is the new Solexa

Genome Analyser system, and it

represents the future of genetic

analysis.

6

The Solexa, located at The Allan Wilson Centre, Massey University, Palmerston North. Photo credit: Nathalie Loussert

Gene analysis is widely used by

universities, government departments,

pharmaceutical and biotechnology

companies worldwide. When in 2003

the Human Genome Project finished

decoding the human genome,

researchers were able to pinpoint

genes responsible for several different

diseases and develop drugs to target

them. This year, the Wellcome Trust

identified genes involved in seven

Gene analysis is widely used by

universities, government departments,

pharmaceutical and biotechnology

companies worldwide. When in 2003

the Human Genome Project finished

decoding the human genome,

researchers were able to pinpoint

genes responsible for several different

diseases and develop drugs to target

them. This year, the Wellcome Trust

identified genes involved in seven

diseases: bipolar disorder, Crohn’s

disease, coronary artery disease,

hypertension, rheumatoid arthritis, and

types 1 and 2 diabetes. The UK’s

Home Office also has the world’s

largest DNA database containing

samples from four million people, a fifth

of the population, for crime

investigations.

diseases: bipolar disorder, Crohn’s

disease, coronary artery disease,

hypertension, rheumatoid arthritis, and

types 1 and 2 diabetes. The UK’s

Home Office also has the world’s

largest DNA database containing

samples from four million people, a fifth

of the population, for crime

investigations.

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The Solexa uses high-speed genome

sequencing to analyse DNA a hundred

times faster and much more cheaply

than before. The scientific possibilities

seem almost endless.

The Solexa uses high-speed genome

sequencing to analyse DNA a hundred

times faster and much more cheaply

than before. The scientific possibilities

seem almost endless.

Private companies are also getting in

on the act. In the USA and Europe,

businesses are offering services

including ancestor tracing, and diets

tailored to genotype. Google has

bought a stake in Californian

biotechnology start-up 23andme, which

uses Solexa to read and store

customers’ DNA, ready for the slew of

personalised information, medicines

and foods predicted to be coming. But

as well as looking into our futures, DNA

analysis can be used to interpret our

past.

Private companies are also getting in

on the act. In the USA and Europe,

businesses are offering services

including ancestor tracing, and diets

tailored to genotype. Google has

bought a stake in Californian

biotechnology start-up 23andme, which

uses Solexa to read and store

customers’ DNA, ready for the slew of

personalised information, medicines

and foods predicted to be coming. But

as well as looking into our futures, DNA

analysis can be used to interpret our

past.

This month [October 2007], Minister for

Research, Science and Technology,

Steve Maharey, launched the $700,000

Solexa, the only one in the Southern

Hemisphere, at the Allan Wilson

Centre for Molecular Ecology and

Evolution on Massey’s Palmerston

North campus.

This month [October 2007], Minister for

Research, Science and Technology,

Steve Maharey, launched the $700,000

Solexa, the only one in the Southern

Hemisphere, at the Allan Wilson

Centre for Molecular Ecology and

Evolution on Massey’s Palmerston

North campus.

The Allan Wilson Centre is a

Government-funded Centre of

Research Excellence. It is at the

cutting edge of research into molecular

ecology and evolution, and runs a

genome sequencing service for

customers here and overseas.

The Allan Wilson Centre is a

Government-funded Centre of

Research Excellence. It is at the

cutting edge of research into molecular

ecology and evolution, and runs a

genome sequencing service for

customers here and overseas.

Kiwi scientist Allan Wilson, after whom

the centre is named, was a pioneer in

Kiwi scientist Allan Wilson, after whom

the centre is named, was a pioneer in

studying evolution using molecular

biology. His innovative theories turned

the study of human evolution on its

head and made Wilson a controversial

figure with scientists and religious

groups.

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In 1967 he proposed that the origins of

the human species could be calculated

through an ‘evolutionary clock’ which

counts the regular genetic mutations

that have occurred since humans and

other primates diverged from a

common ancestor. The larger the

mutations, the longer the time since

divergence. Wilson found that genetic

material from humans and

chimpanzees differed only by about

one percent, and deduced that the

human species is only five million years

old, compared to the 15-30 million

years old previously calculated by

palaeontologists using fossils.

In 1987, Wilson discovered that

mitochondrial DNA, which is passed

down the maternal line, mutates quickly

and could be used to estimate not just

when, but where, the first modern

human evolved. After comparing a

range of ethnicities and regions, Wilson

argued that all modern humans had a

common African female ancestor about

200,000 years ago – the ‘mitochondrial

Eve’. This ‘Out of Africa’ theory, as it

was quickly dubbed by the media, is

now widely accepted by scientists.

Mr Maharey said the Solexa would

enable the centre to lead the world in

genetic research. “The new Solexa will

advance our knowledge of the causes

of diseases,” he said. “It will also help

us find tests for diseases. It can also be

used to study the genetic diversity of our

native plants and animals or to identify the

microbes that cause diseases on

grapevines, which could be a huge benefit

to the New Zealand wine industry.”

Professor Mike Hendy, centre co-director,

says the Solexa will contribute to all

genomic research in New Zealand. “By

sharing the facility we are able to reduce

costs and increase efficiency for all

researchers. The Allan Wilson Centre, as

a cooperative interdisciplinary research

organisation is well placed to take a major

role in the world-wide effort to interpret

and process this new information.”

The Centre’s Executive Officer Susan

Adams talks a lot about cooperation too,

and the benefits of the Solexa to New

Zealand as a whole, and to science in

general. “The service here isn’t run for a

profit – we pass on the savings to the

scientists,” she says. “Year on year we’ve

reduced our prices, and the more people

who use it, the more the prices drop.” But

they still run as a business. “We’re

competing in an international market,

and our service is about quality and

speed, not just cost. We have a 48-

hour turnaround for our ABI sequencing

service, whereas some places take a

week.”

The Solexa and the existing ABI 3730

sequencer are complementary, and the

combination means that almost all

projects that need next-generation

sequencing can be carried out in New

Zealand.

Websites to visit

http://www.wtccc.org.uk/info/070606.shtml

(Online press release: The Wellcome Trust

Case Control Consortium, has undertaken the

largest ever study of the genetics behind

common diseases and has identified genes

involved in seven diseases.)

http://www.homeoffice.gov.uk/science-

research/using-science/dna-database/

(Learn more about the UK Home Office

National DNA database and how it is used in

solving crimes.)

https://www.23andme.com/

(23andMe, a web-based service that helps you

read and understand your DNA. Also includes

educational material, just click on Genetics 101

and learn about you and your genes.)

http://www.ornl.gov/sci/techresources/Human_

Genome/project/about.shtml

(Learn about the Human Genome Project, its

history, goals, progress and applications.)

http://www.genome.gov/12011238

(The National Human Genome Research

Institute website provides an overview of the

Human Genome Project.)

Miriam Sharland, Bio Commerce Centre Communications Manager

DNA Barcoding Life: Part II How the past can help the future

What are the limits of science?

Sometimes, the most productive

scientific research pushes the

boundaries of conventional thinking by

relying on a combination of curiosity

and creativity. Recently, one of

science’s more unusual projects has

emerged from New Zealand, where

molecular biologists have used extinct

animals to help understand the future of

living ones. To achieve this, the project

combined old and new analytical

techniques, and, in the meantime, also

helped to solve a century-long debate

regarding the taxonomy of New

Zealand’s extinct moa.

This research was all part of a major,

international project to catalogue every

living species on Earth, using a

common genetic signature, or barcode.

Professor David Lambert of the Allan

Wilson Centre for Molecular Ecology

and Evolution plans to extend it to the

sub-fossil remains of other extinct

animals, in addition to moa. Although

these ancient, enigmatic birds might

seem an unusual inclusion in a global

inventory of living species, they are, in

fact, an ideal test of the molecular

barcode’s reliability in identifying

ancient species. This is primarily

because moa were a group of related

species that are now preserved as sub-

fossil bones, containing a wealth of

genetic information.

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Molecular barcodes are similar to those

on supermarket products; however,

they use species-specific DNA

sequences instead of black-and-white

bars. Their potential to identify species

was first recognised by Canadian

evolutionary biologist Paul Herbert, who

used a portion of the cytochrome c

oxidase (CO1) gene. Herbert and

colleagues tested this DNA sequence

on North American birds, and found

that it varied by more then two per cent

between bird species, but by less than

one per cent between members of the

same species, making it an ideal

molecular barcode–for living North

American birds, at least.

But would it work on other animal

species? This question is central to the

DNA-barcoding project, because if the

amount of CO1 variation is common to

most organisms, it has the potential to

be used as a high-throughput,

standardised method of identifying

species with accuracy and efficiency.

Taxonomists, biologists, and

conservationists argue that such a tool

is needed to keep pace with

accelerating global extinction rates,

which are reaching a critical level.

Estimating these rates–using both past

and present levels of biodiversity–might

be the first step in preventing them from

increasing further. According to

Professor Lambert, the effects of

humans on the Earth’s other organisms

can only be interpreted through an

understanding of what was here in the

past.

Enter the moa. This extinct group of

flightless birds consisted of separate

species, although the exact number

has been the subject of debate since

they were ‘discovered’ in the mid-

nineteenth century. The number of

described species has fluctuated

between 30 and 64, based on the

morphological characteristics of bones

and teeth, as well as variation in body

size. Skeletal reconstructions show that

moa ranged from the size of a chicken

to more than three metres tall. More

recent studies using genetic analyses

revealed just 11 species. This

significant decrease was largely due to

a phenomenon called reverse sexual

dimorphism: female moa were, without

exception, larger than males. Despite

this, the exact number of species

remains contentious and difficult to

Modified from: http://www.uoguelph.ca/~phebert/coi/target.htm

9

solve using the existing database of

genetic and morphological methods.

However, moa, as an extinct group of

closely related species restricted to a

defined geographical area, were an

ideal feasibility test for DNA-barcoding

ancient organisms. At the same time,

the number of moa species could be

resolved. To make the study easier,

numerous sub-fossil moa bones

provided an exceptional source of well-

preserved DNA, allowing the CO1 gene

to be extracted and copied easily.

Using 27 sub-fossil bones from

museum collections around New

Zealand, Professor Lambert’s group

extracted and amplified the 596-base

pair CO1 sequence. Their results were

encouraging–both for moa classification

and for the prospects of the DNA-

barcoding project.

The molecular barcode results

correlated with the species identified

using the older, more comprehensive

dataset, with one exception. It

appeared that the barcode reduced the

number of described species from 11 to

ten; however, Professor Lambert warns

that this number may change again as

more bone samples are tested.

Nevertheless, these results

have helped to bring the debate

that has dominated 165 years

of moa research closer to

resolution, and will be useful for

re-classifying unknown or

misidentified moa remains in

museums. This, in turn, will

enhance the value of these

collections and increase

existing knowledge of moa

distribution and morphology.

The project also showed that

molecular barcodes were both

useful and accurate for identifying

moa species. CO1 sequence

variation within moa species

matched Herbert’s calibrations for

North American birds–taxa that are

geographically and genetically

distant from moa. This, in particular,

suggested that it may be possible to

extend molecular barcoding to other

ancient organisms, to complement a

large-scale inventory of Earth’s

living biota.

So far, the international DNA-

barcoding project has mainly

focused on extant organisms in an

effort to estimate the total number of

species alive. How this differs from

past biodiversity remains unknown.

Estimates of the total number of

living species fluctuate between

three million and more than 100

million; however, after 250 years of

taxonomic study, only 1.7 million

species have been formally

described. Clearly, an efficient,

high-throughput method of identifying

and cataloguing living organisms before

they become extinct is needed–

particularly if it can be extended to

extinct species to measure how quickly

our biodiversity is disappearing.

Perhaps the current crisis of

endangered species may be better

managed through an understanding of

past extinctions, such as the moa.

Biologists now realise that a

microgenomic approach using a portion

of the genome, such as the CO1

sequence, may be the solution.

Moa skull: Pachyornis elephantopus Source: www.azdrybones.com/birds.htm

source: http://barcoding.si.edu/

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The moa barcoding project has built on

and refined a century’s knowledge of

moa taxonomy, and shown that

barcoding ancient life is possible. DNA

can be successfully retrieved from old

tissues, and levels of CO1 sequence

variation appears to be universal, even

among genetically unrelated species.

Moa are a New Zealand emblem with

global implications for conservation

biology. These extinct birds are now

helping to extend the already

ambitious, international DNA-barcoding

project to its limits. It seems fitting that

this extraordinary science begins with

such a remarkable bird.

The moa barcoding project has built on

and refined a century’s knowledge of

moa taxonomy, and shown that

barcoding ancient life is possible. DNA

can be successfully retrieved from old

tissues, and levels of CO1 sequence

variation appears to be universal, even

among genetically unrelated species.

Moa are a New Zealand emblem with

global implications for conservation

biology. These extinct birds are now

helping to extend the already

ambitious, international DNA-barcoding

project to its limits. It seems fitting that

this extraordinary science begins with

such a remarkable bird.

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, 10 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.

Source: http://imbs.massey.ac.nz/Albany/current_projects.htm

John Waugh The Allan Wilson Centre Current Postgraduate Projects Massey University - Albany Campus

Meg Heaslop Science Journalist Massey University, Albany, Auckland

DNA Barcoding Websites to visit

http://www.uoguelph.ca/~phebert/coi/index.htm

(A link from Paul Herbert’s website, an introduction to

DNA Barcoding.)

http://barcoding.si.edu/

(The Consortium for the Barcode of Life (CBOL) is

an international initiative devoted to developing DNA

barcoding as a global standard for the identification

of biological species.)

http://www.barcodinglife.com/

(The Barcode of Life Data Systems (BOLD) is an

online workbench that aids collection, management,

analysis, and use of DNA barcodes.)

Population Genetic Theory: How can selection help maintain variation?

Natural selection and variation

The presence of large amounts of

variation in natural populations of plants

and animals is perhaps the most

important central observation in

biology. Variation may exist on many

different levels of organization;

countless different species exist in our

biosphere and these species exhibit

further differences in behaviour,

morphology and genes, not only

between populations, but also among

individuals. It is this variation among

individuals that is of utmost importance

for the most influential theory in biology,

that of natural selection, first published

by Charles Darwin and Alfred Wallace

(figure 1). Variation between

individuals is partially caused by

differences in the genes that each

individual carries. Slightly different

variants of a particular gene (alleles)

and changes in the frequencies of

these variants over subsequent

generations of a species are the basis

of evolutionary change, responsible for

processes such as adaptation and

speciation. Therefore, understanding

how genetic variation is introduced to

natural populations and how much is

present at a given time has been one of

the long-term goals of population

genetics.

The paradox of variation

Surprisingly large amounts of genetic

variation exist in natural populations,

revealed in 1960’s by enzyme

electrophoresis. These large amounts

of variation are paradoxical,

considering the theory of natural

selection; if a particular type of

individual has a higher chance of

survival, it is likely that over many

generations those individuals will leave

more offspring compared to individuals

with lower chances of survival.

Similarly, if a certain allele provides a

benefit compared to other alleles (i.e.

has a selective advantage) in the

population, it is likely that the frequency

of this allele will increase. Over time,

such an allele may increase in

frequency until no other alleles are left,

resulting in a population without genetic

variation.

Balancing selection

11

If selection is so effective in eliminating

this variation, then why is there still so

much genetic variation found in natural

populations? Some forms of selection

can actively maintain rather than just

eliminate variation. Forms of selection

that maintain genetic variation are

called balancing selection as opposed

to directional selection which favors

only a single variant. One example of

such a form of selection is balancing

selection due to heterozygote

advantage (see box). Another example

of balancing selection can occur when

selection takes place in different

populations. Species do not typically

exist in one large population but are

often present in multiple smaller sub-

populations, connected by varying

levels of migration. If each sub-

population experiences slightly different

environmental conditions (e.g.

differences in temperatures, rainfall,

predators, parasites, etc.) then some

alleles may be favoured in one

situation, but not in another situation. In

such cases, more variation may be

Figure 1. Charles Darwin (left) and Alfred Russel Wallace (right).

12

maintained than in a single population

alone. Balancing selection due to

selection in multiple sub-populations is

often invoked as a general solution to

the high levels of genetic variation

found in natural populations.

Nevertheless, no one really

understands how effective this process

is for higher levels of genetic variation.

Computer simulations

We have investigated this problem is by

using computer simulations. In effect

we create a computer program that

simulates the course of evolution in a

model with either one single population

or two sub-

populations

(figure 2) and

compare the

results. The

model simulates

mutation (the

emergence of a

new allele in an

individual),

selection (to see

if the mutated

allele increases

or decreases in

frequency) and

migration

towards the other sub-population (if

there are two sub-populations in the

model). Whenever a new allele

emerges, we assigned a

random fitness value (one for

each sub-population) to this

allele. Therefore, over the

generations, alleles emerge

with different fitness qualities.

Figure 2. The computer model uses mathematical calculations to simulate the

introduction of new alleles (mutation) and selection within two populations (P1

and P2). After selection, individuals either stay in their ‘home’ population

(black arrow) or migrate to the other population (dashed arrow). These basic

steps are repeated for each generation. The model is stopped after a period of

Fate of new alleles

The eventual fate of a new

allele depends on its fitness

quality relative to the average

fitness of the other alleles in the

total population. A detrimental

allele will not be able to

increase in the population and

goes extinct, whereas a

beneficial allele can increase in

frequency and stay in the

population. If such beneficial

allele increases in frequency, it

also increases the average

fitness of the whole population and the

population becomes fitter. The most

beneficial alleles will have high fitness

values in both sub-populations.

Figure 3. The number of alleles (black line) and average

fitness (grey line) for three separate simulations over

10,000 generations. Simulations were run in two sub-

populations, with low (m = 0.05) and high (m = 1.0) levels

of migration and in a single population.

Because we start the model with a

relatively low average fitness, many

new alleles are initially more fit and

quickly invade in the first few

generations (figure 3). Due to the

increase of these alleles, average

fitness ( ) rapidly increases and once

fitness has increased, newer alleles

that posses an even higher fitness

become rare. Moreover, some of the

alleles that previously invaded may now

be detrimental due to the increase in

average fitness, and decrease in

frequency until they go extinct. This

process of invasion and extinction

settles down after a number of

generations and the number of alleles

and average fitness more or less

stabilize.

13

Influence of migration

Box: Further reading

Star, B., R. J. Stoffels and H. G.

Spencer, 2007a Single-locus

polymorphism in a heterogeneous

two-deme model. Genetics 176:

1625-1633.

Star, B., R. J. Stoffels and H. G.

Spencer, 2007b Evolution of

fitnesses and allele frequencies in a

population with spatially

heterogeneous selection pressures.

Genetics 177: 1743-1751.

The level of migration between the sub-

populations is important since this level

determines the amount of isolation that

each population experiences. For very

low levels of migration, the two sub-

populations will develop more or less

independently, whereas for high levels

of migration the sub-populations

behave more similarly to a single larger

population. The amount of variation that

can be maintained due to selection in

these two sub-populations is known to

be highest for low levels of migration.

This is also apparent in our results:

Most alleles are maintained when the

sub-populations have little or no

migration between them (figure 4).

More interestingly, for higher levels of

migration, less variation is maintained

compared to a single population model.

These results show that the intuitive

idea of selection in multiple sub-

populations resulting in higher levels of

variation is not always true. Moreover,

because these results come from

selection models that have only been

simulated in two sub-populations, it is

maybe possible to maintain an even

larger number of alleles by adding more

sub-populations with low levels of

migration.

Bastiaan Star PhD Studentc University of Otago, staba228@student.otago.ac.nz

Box: Heterozygote Advantage

Most sexually reproducing organisms (such as humans) receive two copies

of their genetic material (DNA) from their parents: one copy from each

parent. This means that, for a particular gene, an individual organism can

either have two different or two identical copies of DNA.

If the two copies are different, an organism is called a heterozygote and if

the two copies are identical it is called a homozygote. If having two different

copies of a particular gene give an advantage (i.e. helps the organism to

survive relative to individuals with identical copies) this is called

heterozygote advantage; the heterozygote organism will ‘perform better’

than the homozygote organism and therefore has a selective advantage.

Because both different DNA copies are needed to create this selective

advantage, both the two different copies are selectively favoured and

conserved. Therefore, heterozygote advantage can result in selection

maintaining genetic variation for long periods of time.

Balancing selection due to heterozygote advantage can maintain a moderate

number of genetic variants, but it is not sufficient to explain some of the very

high levels of genetic variation that are found in some natural populations.

Figure 4. Total number of alleles after 10,000

generations for different levels of migration. The red

symbol indicates the results for a single population

model.

Traditional Kiwi-Feather Cloaks Throwing new light on a tradition

In the Hawke’s Bay Museum, Napier, a

collection of kiwi-feather cloaks–

traditional Maori garments and cultural

treasures–was being examined and re-

housed to preserve them for future

generations. Unfortunately, no one

knew their history. The cloaks’ exact

origins, weavers, and place of

collection were unknown. Maori textiles

conservator Rangi Te Kanawa, who

was in charge of assessing their

preservation, was interested in solving

this problem. To do so, she needed the

help of molecular biology. Specifically,

she needed the help of Professor

Lambert, an expert in ancient DNA

analysis of New Zealand native

species. The project that eventuated–

using kiwi-feather DNA to provenance

the cloaks–demonstrated how science

and cultural heritage could collaborate

to throw new light on a tradition and

treasure, and, at the same time, help to

conserve an endangered national icon:

the kiwi.

Traditional Maori cloaks are considered

to be one of the most important ‘taonga’

(treasures), and continue to have an

important role today. Cloaks

symbolised the wearers’ prestige,

power, and wealth. When worn or

presented as a gift, they transferred

these qualities to the recipient. Cloak

designs and materials have evolved

over time to reflect New Zealand’s

changing natural and social

environments; however, their cultural

significance remains unaltered.

Little was known about cloaks before

the arrival of Europeans. The earliest

written records date from Captain

Cook’s first visit to New Zealand in

1769-1770. At this time, the most

common type was a utilitarian rain cape

made from New Zealand flax

(harakeke), a plant with fibrous, sword-

shaped leaves. Fibre was stripped from

the leaves, rolled into cords, and

softened by soaking and beating. The

cords were teased into finer threads

and woven using techniques passed

down through generations from mother

to daughter. This flax weave formed the

backing of all cloaks.

Rain cloaks, woven with a simple and

coarse pattern, were the earliest style

of cloak. They were often worn in two

parts, with one for the shoulders and

another around the waist. In remote

areas, these cloaks were still

sometimes made and worn into the

twentieth century. Elsewhere, cloaks

became less functional and more

ornamental. Decorations ranged from

tags of rolled or dyed flax to the

prestigious dog-skin ‘kahu kuri’,

adorned with narrow strips of dog-hair

in alternating colours. Decorations were

woven into cloaks as they were made,

rather than being added after

completion. Thus, the design of each

cloak was planned before the weaving

process began.

One of the most important cloaks of all,

however, was the ‘kahu kiwi’, or kiwi-

feather cloak. Although Maori and other

Polynesian myths often featured

feathered garments, they were not

commonly used at the time of Cook’s

visit. Gradually, some cloaks with

sparse feather decorations began to

emerge; however, it was not until the

mid-nineteenth century that feather-

covered cloaks appeared. Maori use of

Cloaks, Dog skin cloak (left), raincoat (middle), and kiwi feather cloak (right). Pictures from: http://whakaahua.maori.org.nz/kakahu.htm

14

Source: http://www.nzetc.org

kiwi was highly symbolic and governed

by ritual. All body parts were used, and

often only chiefs were allowed to eat

kiwi meat and wear feather cloaks.

Accordingly, kahu kiwi were of great

significance and were highly valued.

The feathers of Brown Kiwi were most

frequently used for kahu kiwi, and, like

other decorations, they were woven

into the cloak as it was made. Feathers

were bundled in threes and stitched

into the cloak’s flax underlay with the

underside of each feather (originally

against the bird’s body) facing

outwards. Cloaks were woven upside-

down, and the quill of each feather was

stitched and then bent backwards and

stitched a second time to prevent it

from falling out. When finished, the

cloak was turned upright so the

feathers pointed downwards. Kiwi

cloaks were matched for feather colour,

although occasionally, white feathers

from rare albino kiwi were included as

decoration. Often, cloaks were trimmed

with intricately woven flax borders

(‘taniko’).

The evolution of cloak styles reflected

external influences, and later designs

incorporated feathers of other bird

species, both native and introduced.

With the availability of European

materials such as dyed wool, cloak

patterns became more elaborate and

colourful. Unfortunately, the European

clothing trade of the 1870s meant that

kiwi feathers were in great demand as

hat trimmings. In addition, extensive

hunting and habitat destruction

devastated bird populations. Within a

century, kiwi numbers had declined so

drastically that kiwi-feather cloaks could

no longer be made. Kiwi cloaks are

now regarded as heirlooms and are still

used for important ceremonies. During

the twentieth century, much of the

knowledge about weaving techniques

was lost; however, today there is a

revival of these skills, and traditional

cloaks act as educational resources

and represent a spiritually significant

link with the past.

In 2002, the Hawke’s Bay Cultural Trust

initiated a conservation program to

assess the condition of each cloak and

develop appropriate preservation and

storage procedures for the collection.

The cloaks were examined by textile

conservator Rangi Te Kanawa, who

identified rare examples of weaving

styles. They were also photographed to

create a database of images for

research and teaching purposes, and to

minimise future handling.

However, there was a problem. Many

of the kiwi-feather cloaks were of

unknown age and origin. Some had

been gifted to the museum in 1935 by

Lady Maclean, a member of one of

Hawke’s Bay’s early settler families.

Information about the weavers of the

cloaks and their accompanying stories

was not recorded at the time of

collection. This made it difficult to trace

the evolution of cloak styles and

patterns, as well as their origins.

Fortunately, there was a solution to this

problem. Using DNA from feather

fragments, the cloak materials’

geographical origins could be

determined, thus providing information

about the weaving styles of different

regions.

The study was also significant from an

ecological perspective as well as a

cultural one. Once common across

New Zealand, Brown Kiwi–the main

component of kiwi cloaks–are now only

found in discrete areas, and their

genetic variation has decreased by

one-third over the last generation. Kiwi

have been described as an indicator

species: their survival and well-being

reflects that of their environment and

the relationship between other animals

and plants within it. Unfortunately, for

kiwi, this survival seems tenuous, and

the numbers of all five described kiwi

species continue to fall.

15

Before the arrival of people, New

Zealand had only two native species of

terrestrial mammals–both small bats.

Consequently, it was an avian paradise

and birds, such as the kiwi, evolved to

fill the niche that would otherwise have

been occupied by land mammals. They

did this so successfully that William

Calder, a twentieth century biologist,

described kiwi as ‘honorary mammals’,

because of their enlarged olfactory

system, leathery skin, and low body

Temperature – characteristics that

were most unbird-like.

When new mammal species were

introduced to New Zealand, this avian

oddity began to disappear. In as little as

200 years, new predators and habitat

destruction reduced kiwi numbers from

in the millions to fewer than 70 000.

Extensive conservation management

and breeding programs are currently

helping to stem the decline; however,

smaller population numbers–and,

therefore, decreased genetic variation–

has resulted in a species with

increased interbreeding and a reduced

ability to adapt to changing

environments. Because the decrease in

kiwi numbers has been so rapid,

information about the amount of genetic

variation in kiwi populations as little as

a century ago could be useful for

measuring the rate and extent of kiwi

loss. Feathers from kiwi cloaks are a

potential database for such information,

and because of their experience with

ancient DNA from other New Zealand

animal species, Allan Wilson Centre

researchers were selected for the

project.

16

At the request of Roger Mulvay, CEO of

the Hawke’s Bay Museum, Professor

Lambert sampled 15 kiwi-feather cloaks

to determine their genetic origins, and,

in addition, help the survival of living

kiwi. The most important consideration

was to prevent damage to the cloaks,

many of which were already in a fragile

state. Sensitive DNA analysis

techniques meant that only a fragment

of tissue was needed for the reactions–

perfect for rare, valuable, or culturally-

important artefacts, such as the kiwi

cloaks. Professor Lambert removed a

two-millimetre fragment from the base

of the feather quills. This section of the

feather was chosen because it

contained nucleated cells and it could

be removed easily without causing

visible damage to the cloak. Several

feather samples were taken from each

of the 15 cloaks.

North Island Brown Kiwi.

Although most of the cloaks sampled

were made from Brown Kiwi, one was

unusual because it consisted entirely of

black feathers–something uncommon

in kiwi cloaks. Feather samples from

this cloak were taken and carefully

posted back to Massey University’s

Allan Wilson Centre in Auckland. Back

in the laboratory, the quills were

prepared for genetic analysis. To avoid

contamination with modern kiwi DNA,

sample preparation was done in a

laboratory designated for ancient DNA

research. Separation of modern and

ancient samples is crucial to the

success of ancient DNA analysis. The

molecular characteristics of ancient

DNA are conferred by its typically poor

preservation and relatively few

numbers of surviving molecules. In

contrast, modern DNA is intact, in great

abundance, and can contaminate

reactions at any time from the original

sampling process to the final analysis.

Consequently, strict anti-contamination

procedures and highly sensitive

extraction and amplification techniques

are needed to detect ancient DNA.

From such minute feather fragments,

Professor Lambert was able to extract

a huge amount of genetic information.

His target was a short stretch of extra-

nuclear DNA contained within

mitochondria–tiny cellular organelles

that use nutrients to generate energy.

Within the mitochondrial genome is the

control region, a non-coding DNA

sequence. This sequence is one of the

most rapidly evolving portions of the

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genome, and, because of its high

mutation rate, it is commonly used for

studying populations and species

relationships.

After sampling, the genetic analyses of

the kiwi cloaks began with the

polymerase chain reaction (PCR). This

reaction makes use of some of the

normal cell physiology that occurs

during cell division. Using polymerase

(a heat-stable protein enzyme), one

molecule of DNA can theoretically be

copied an unlimited number of times.

This is particularly useful for old or

degraded materials, which may contain

relatively few surviving DNA molecules.

Although half of the feather samples

were too degraded to yield a DNA

product, the results from the black kiwi

17

cloak were surprising. Three different

haplotypes (DNA sequences that vary

between individuals) were present,

indicating that the cloak was made from

the feathers of at least three kiwi. Two

of these haplotypes matched DNA

sequences of Brown Kiwi in the Bay of

Plenty, but the third sequence differed

from all modern kiwi populations.

Perhaps the new haplotype discovered

in the Hawke’s Bay cloak represented a

now-extinct kiwi population from

Hawke’s Bay or the surrounding region.

According to Professor Lambert, a

large percentage of kiwi haplotypes

from ancient bird populations has been

lost, and studies such as the kiwi-

feather cloak project highlight the need

to preserve the genetic diversity that

remains.

cloak were surprising. Three different

haplotypes (DNA sequences that vary

between individuals) were present,

indicating that the cloak was made from

the feathers of at least three kiwi. Two

of these haplotypes matched DNA

sequences of Brown Kiwi in the Bay of

Plenty, but the third sequence differed

from all modern kiwi populations.

Perhaps the new haplotype discovered

in the Hawke’s Bay cloak represented a

now-extinct kiwi population from

Hawke’s Bay or the surrounding region.

According to Professor Lambert, a

large percentage of kiwi haplotypes

from ancient bird populations has been

lost, and studies such as the kiwi-

feather cloak project highlight the need

to preserve the genetic diversity that

remains.

Katie Hartnup The Allan Wilson Centre Current Postgraduate Projects Massey University - Albany Campus

Kakahu: Revealing the Hidden Histories of Maori cloaks using DNA

Kakahu or Maori cloaks are taonga

(treasured things) and are a unique part of New

Zealand culture, as are the materials used to

create them. My research comprises of using

DNA analysis to unravel some of the histories

surrounding these treasured items.

Concentrating initially on feather cloaks, I aim

to discover the sex, species and geographical

origin of the feathers used to make cloaks

through mtDNA sequence analyses. From this, along with historical records and expert

advice, inferences can be made into Maori culture such as hunting trips or trade between iwi.

Furthermore, the data will allow me to look at feather use on temporal and spatial levels. I

also intend to extend the study by looking at the genealogy of kuri (dog skin) cloaks using

mtDNA markers and microsatellites, in addition to analysing the geographical origin of

harakeke and flax capes using cpDNA markers.

This project benefits greatly from the collaboration of Rangi Te Kanawa, a textile conservator

from a family of famous weavers. Her knowledge of traditional weaving practises and ability

to liaise with museums is paramount to the success of this project.

Source: http://imbs.massey.ac.nz/Albany/current_projects.htm

Just as important as the project’s

ecological implications was its cultural

significance. The Hawke’s Bay

Museum collection is important as a

resource for maintaining and reviving

weaving traditions. A more complete

understanding of the collection’s

geographic provenances through the

genetic origins of cloak feathers will

increase its value for this purpose and

strengthen links with the past.

Just as important as the project’s

ecological implications was its cultural

significance. The Hawke’s Bay

Museum collection is important as a

resource for maintaining and reviving

weaving traditions. A more complete

understanding of the collection’s

geographic provenances through the

genetic origins of cloak feathers will

increase its value for this purpose and

strengthen links with the past.

Of the samples taken, approximately

half have yielded DNA so far. Work is

continuing through the cultural trust’s

conservation program, and results will

be combined with traditional knowledge

to augment the value of the cloak

collection, both as an example of

weaving styles and materials, and as a

library of past kiwi genetic diversity.

Future research will focus on the

cloaks’ flax backing, using similar

techniques to elucidate its origins so

that a more comprehensive

assessment of each cloak can be

made.

Of the samples taken, approximately

half have yielded DNA so far. Work is

continuing through the cultural trust’s

conservation program, and results will

be combined with traditional knowledge

to augment the value of the cloak

collection, both as an example of

weaving styles and materials, and as a

library of past kiwi genetic diversity.

Future research will focus on the

cloaks’ flax backing, using similar

techniques to elucidate its origins so

that a more comprehensive

assessment of each cloak can be

made.

The project’s potential also reaches

beyond New Zealand to overseas

The project’s potential also reaches

beyond New Zealand to overseas

museum collections, where many

unprovenanced feather cloaks dating

museum collections, where many

unprovenanced feather cloaks dating

from the eighteenth century are

housed. Resolving the origins of these

from the eighteenth century are

housed. Resolving the origins of these

taonga may assist their repatriation to

appropriate custodial groups, thereby

returning cultural heritage to its origins

and ensuring that an important tradition

is revived.

taonga may assist their repatriation to

appropriate custodial groups, thereby

returning cultural heritage to its origins

and ensuring that an important tradition

is revived.

Meg HeaslopScience Journalist Massey University, Albany, Auckland

Kakahu or Māori cloak from the Hawkes Bay region

18

Charles Darwin, evolution simple and testable

Evolution is testable like all good normal science as Prof. David Penny, Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, explains:

A striking feature of evolution is that it is

made up of a number of very simple

parts – each of which is fully testable.

Nevertheless, taken together, the ideas

put forward by Charles Darwin − and

developed mathematically over the last

half century − can appear complex. The

aim here is to identify the main

components of the theory; show how

they relate to developments in physics

and geology; to demonstrate that each

part is both simple and testable; and

thus show that evolution is just good

normal science.

Charles Darwin’s family and science background

We will look quickly at Charles Darwin’s

family background, and then the state

of biology at that time. His paternal

grandfather, Erasmus Darwin, was by

the late 1700s a leading doctor, poet,

inventor and scientist (a member of the

Londonbased Royal Society made up of

leading scientists). Erasmus also

proposed evolutionary ideas, but unlike

his grandson two generations later,

Erasmus’ ideas lacked a testable

mechanism. Charles’s maternal

grandfather was Josiah Wedgwood,

inventor, scientist, and founder of

Wedgwood potteries. Both families

were leaders in the early Industrial

Revolution that introduced the start of

modern scientific and technological

society as we know it today. Both

families were progressive liberal, and

very anti-slavery. Erasmus Darwin also

founded a private school for girls

(Ashbourne) because at that time there

were so few opportunities for their

education.

Charles’s father, Robert, was also a

doctor and had published some early

scientific work. Charles, himself, tried

studying medicine at Edinburgh but

dropped out after two years –

apparently he did not like the sight of

blood! He then attended Cambridge

University, and was expected to

eventually earn a respectable living as

a village vicar. (At that time there

weren’t many professional career

opportunities for sons of the well-to-do!)

However, as an undergraduate he

became more and more interested in

geology and biology, and this led to his

next step of being invited to be the

naturalist on the voyage of the H.M.S.

H.M.S Beagle, starting at the end of

1831.

First we need a quick look at the

scientific understanding of ‘species’ at

that time. Until about 1700, almost

everyone in Europe accepted continued

spontaneous generation – life continued

to arise from non-living matter. There is

clearly no problem about the origin of

different forms of life − in this theory life

continued to arise from Earth through

the power of a creator, as described in

Genesis. This continued spontaneous

generation stage is just European

Indigenous Knowledge, and these

beliefs in Europe certainly trace back to

at least the earliest part of the Old

Testament, written in the Near East.

From around 1700 the hypothesis that

‘species’ had a permanence over

thousands of years became popular in

scientific circles. There were many

good experiments that showed that, at

least for multicellular organisms, ‘all life

came from eggs’ (or seeds). So the

next idea was that ‘the work of the

creator’ was finished – species had all

been formed by special creation, but

only in the past! Strictly speaking, this is

consistent with species created and

then evolving, but the idea of species

being unchangeable fitted in with the

philosophy of an ancient Greek (Plato,

from the 5th Century BC) who

postulated unchangeable ‘essences’.

This idea of an unchangeable essence

from Plato has been very influential in

Western philosophy. Thus the theory of

unchangeable species being created

only in the past was a mixture of two

components – a creator, and the ideas

of Plato, the pre-Christian philosopher.

There was no evidence for Plato’s

unchangeability of species, and surely

an allpowerful creator could make a

system that evolved! This switch from

continued spontaneous generation to

special creation occurred between the

time of Abel Tasman’s (1642) and

Captain Cook’s visits to New Zealand

(1769). In North American history the

change would have occurred between

the arrival of the Pilgrim Fathers (1620)

and the War of Independence. Thus, by

the time the young Charles Darwin was

studying it in the 1820s, biology was

(apart from a few doubters who lacked

any testable mechanism) firmly in the

natural theology phase we now call

classic creationism. We will return later

to follow these changing concepts

through time, some of which are shown

in Figure 5.

The present is the key to the past

The major event that led Charles

Darwin towards evolution was his

(almost) five-year voyage around the

world on the British navy survey vessel,

H.M.S Beagle. His first major scientific

step was convincing himself of the

validity of the ‘new geology’ advocated

in the early 1830s by the Scottish

geologist Charles Lyell. Lyell (following

an even earlier Scottish geologist,

James Hutton, whose main works were

in the 1780s and ‘90s) aimed to explain

ancient geological events by

mechanisms that can be studied in the

present - ‘the present was the key to

the past’. During the voyage, Darwin

saw for example, how earthquakes in

Chile raised the coastline several

metres—and then found evidence for a

series of raised beaches and/or

remains of fossil seashells higher and

higher up the adjacent hillsides, and

later to the tops of the passes over the

Andes. The simplest explanation was a

series of similar earthquakes in the past

– the present processes (earthquakes

in this case) were explaining past

events. At the same time, geology was

gathering evidence for the Earth being

at least hundreds of millions of years

old, rather than the 6000 years

favoured since the late 1600s. The new

geological timescale allowed plenty of

time for similar events to have

continued back into the past.

Thus the ideas underpinning the

scientific advances in geology were an

important key. And geology itself was

fitting with the new models from physics

and mathematics. Ever since Sir Isaac

Newton, physicists explained the

movements of planets by the combining

the measurements of mass, gravity

and acceleration that they could make

here on Earth. They postulated a

continuous series of intermediate steps

to the position of planets, thus bringing

in calculus with its integration and

differentiation – similarly assuming

continuity of intermediate states. So

physics, calculus and now geology

were adopting models based on a

continuous series of intermediate states

with small incremental changes; would

the same approach work with the more

complex systems in biology? But again,

coming from physics and geology, there

had to be a mechanism, or force, that

could be studied independently.

Darwin’s next major step was to

transfer to biology these principles he

had learned from geology, using current

mechanisms to explain past events. For

example, as the H.M.S Beagle sailed

up and down South America he

observed that a given species could

vary − and finches on the Galapagos

Islands appeared more similar to South

American species than to any other.

The simplest explanation was that

South American finches had got to the

Galapagos Islands (after the islands

had formed from volcanoes) and then

these South American finch species

had adapted to local conditions. Other

hypotheses were possible – a Great

Gardener could have taken species

from anywhere on Earth – in which

case there was no reason

for Galapagos’ species to

be closest to South

American species.

However, because of these

regional similarities of

species it was a simpler

hypothesis that natural

mechanisms were

responsible for finches

getting from South America

to the Galapagos. By the

19

Figure 1. Subspecies of Brassica oleracea - artificial selection can modify species well beyond the limits of the species seen in nature. (a) The wild form is subspecies ssp. oleracea and is found on rocky cliffs. (b) Kale and collards are members of the ssp.viridis; curly kale (not shown) is ssp. sabellica. Jersey kale (not shown) can grow to be 2 m (7 ft) in height and belongs to ssp. palmifolia.(c) Brussel sprouts are classified as ssp. gemmifera (d) Kohlrabi as ssp. gongylodes. (e) ssp. capitata includes red and green cabbage. The English word cabbage comes from the French word caboche which means head. (f) Savoy cabbage belongs to ssp.sabauda. From http://serc.carleton.edu/files/genomics/units/cauli_lab_handout.doc.

end of the voyage of the H.M.S Beagle,

the question of the origin of species

was uppermost in Darwin’s mind. He

still needed a mechanism, a

mechanism, a mechanism, a mech…!

Although Darwin’s main publications

from the voyage were in geology, he

increasingly transferred the mechanistic

approach into biology.

The importance of plant and animal breeding On his return to England, he searched

for mechanisms that would help explain

how populations could change with

time. He quickly recognized that plant

and animal breeding was an excellent

model, in the sense that new ‘varieties’

of plants and animals had been

generated by breeders, and that these

were now very different from their

parent species. Consider a giant Great

Dane and a small Chihuahua; they are

so different in size and appearance that

if they were the only dogs known then

they would be classified as separate

species, and almost certainly in

different genera. Similarly, for plants,

one original species (Brassica oleracea,

if you really want to know) has led to

20

cabbages, cauliflowers, kale, Brussel

sprouts, kohlrabi, and broccoli – see

Figure 1. So in this sense it was ‘known’

for both animals and plants that there

were no absolute boundaries to

variation within a species – a very

fundamental point that contradicted the

application of Plato’s ideas to species.

Thus, artificial selection by humans

could change existing species well

beyond the limits of what was found in

nature.

Plant and animal breeders already

knew that there was variation within

species and varieties, and that some of

the variation was inherited. Yes, Mendel

and his laws of genetics came later, but

people already knew both about

inheritance (‘breeding true’) and also

about environmental variation. For

example, botanists had transplanted

plants from their natural environments

into gardens, and had observed that

some differences persisted, others

disappeared. Thus some differences

were inherited and persisted, others

were dependent on environmental

conditions (genotypic and phenotypic in

modern terminology). Again, it was

known that some of the inherited

differences were ‘useful’ to plant and

animal breeders – organisms having

certain inherited features were selected.

All that was required for

Darwin to make the

intellectual leap to his

‘mechanism’ was that

some of this inheritable

variation increased (or

decreased) the chance of

an individual surviving in

nature and leaving

offspring. Note that this

statement is quite weak –

‘some’ of the variability

affected the probability of

survival and reproduction,

we come back to this later.

The inherited variability is

important; if all individuals

in a species were

genetically identical, there

would not be any genetic

change between

generations.

However, inheritable variation

(genetics) was not sufficient by itself,

and so we turn to the population parts

of the theory; the first is the potential for

a geometric increase in population

numbers. It is well known that Charles

Darwin was impressed by the

mathematical rigor of Robert Malthus’

calculations on the potential for

increase in population numbers. For

example, a unicellular individual

dividing into two offspring per cell

division has the potential to increase to

2, 4, 8, 16, and so on, in succeeding

generations. As an aside, Malthus (a

pastor) used his calculations to come to

very conservative conclusions about not

helping the poorer groups in society for

fear that they would increase in

numbers exponentially. As such, was

‘politically incorrect’ in the circles of

Figure 2. Bold simplicity; evolution is the simplest possible hypothesis! The basic postulate is that there is a continuous series of generations back through time to ancestral species. If we allow an average of 25 years per human generation, then after 10 generations we are back 250 years, back 1000 years after 40 generations, 10,000 years after 400 generations, and so on. Nothing could be simpler. To suggest that everything appeared at one point in time, thousands of galaxies, our solar system, the Earth and its organised geological strata, and 5-10 million species (each with extremely long DNA sequences that look as if they have shared common ancestors, see Figure 3) is just unbelievably complex.

Darwin’s extended family. Even

decades later, Darwin (in his

autobiography) had almost to apologise

to his family for reading Malthus – his

excuse was that he was reading it ‘for

amusement’. Without knowledge of

birth control, alternative conclusions

from Malthus’ calculations were not

obvious at that time. Nowadays we

know better (or should know better) that

the mathematics is neutral; it is our use

of it that causes problems.

Returning to the potential for the

increase in population numbers, it was

also known that, on average, and

although numbers varied between

years, such an exponential increase

didn’t occur. Yes, the potential was

there, but there were obviously other

limitations. Darwin’s next logical step

was his awareness of the limited nature

of resources. For example, for plants

the amount of sunlight for

photosynthesis is limited by the surface

of the globe – there is a maximum

amount of light energy per square

metre. Consequentially, for herbivores

there are limitations on food from the

biomass of plants. Further

downstream, some bacteria and

protists in the rumen are limited by

the amount of grass a sheep or cow

eats, and so on. Obviously, many

other factors can be limiting under

some circumstances. The simple

consequence, given the potential for

increase in numbers and limited

resources from ecology, was that there

must be competition for resources –

both within populations and between

them.

At this point, there are two important

generalizations about Darwin’s theory.

Clearly it was very mechanistic in that it

was aiming to explain past events

(changes in species over time) by

mechanisms that can be studied today

in the laboratory and in the field. The

other novel aspect for science was that

his theory used probabilistic thinking – a

specific outcome depended on chance

events. This was well before physicists

adopted probabilistic thinking for

quantum effects, so physicists were

initially sceptical of Darwin’s

mechanism – they were thinking far

more deterministically in the mid-19th

Century. But Darwin reasoned that if

you had large numbers of individuals,

and long periods of time, then you could

make strong statements about the

‘average’ (or expected) outcome.

Today, we are quite used to statistical

reasoning, but it was a radical step for

science then. Thus the use of known

mechanisms, and probabilistic

reasoning, were major features of his

theory, and major intellectual leaps for

his time.

21

Microevolution, then, is the combination

of these populational, ecological and

genetic processes, and results in a

mechanism for ‘natural selection’.

However, we should be careful here −

calling it ‘natural selection’ makes it

almost like something that ‘exists’ as a

separate entity. Rather, referring to

natural selection as the inevitable

outcome of microevolutionary

processes is a more accurate picture

(but more tedious in everyday

conversation). Nevertheless, it is an

error to consider ‘natural selection’ as

an entity − it is just the automatic

consequence of the above processes. It

is very important to note that all those

components of Darwin’s proposed

mechanism, as is summarized in Table 1, can be tested independently. If we

combine the population, genetic,

ecological and resource limitations,

together with the hypothesis of a

continued series of generations in the

past, then we expect some limited

changes between generations (though

the amount of change per generation

can obviously vary). A representation of

this continuity between generations is

shown in Figure 2, and is the simplest

possible hypothesis for the origin of

biological diversity − I have labelled it

as ‘bold simplicity’. This continuity of

states (generations in this case) links

evolutionary biology into the

explanations used in physics,

chemistry and geology – it is standard

science. The continuity between

generations means that mathematics

also fits well with evolution −

evolutionary biology is one of the most

mathematically developed parts of

biology.

This continuity, further and further back

in time leads these microevolutionary

processes to Darwin’s ‘theory of

descent with modification’. This is

usually expressed as an evolutionary

tree − even though it was known from

100 years earlier (the time of Linnaeus)

that hybrids occurred. Thus, the tree is

always a simplification. Changes

certainly need not be equal between

generations − Darwin expected rates to

be variable depending on any number

of factors. Nowadays, some biologists

seem just to accept the evolutionary

tree, but as scientists we expect the

tree to be able to make predictions −

the tree is a testable hypothesis.

Predictions and testing from new data A mark of any scientific theory is that it

makes predictions that can be tested

when new data becomes available. For

evolution, the availability of DNA

sequences is now the most powerful

form of evidence used for

reconstructing evolutionary trees (and

New Zealanders are among the leaders

in this area). Consider humans and the

great apes as an example. Based on

morphological (and probably

behavioural) evidence, Charles Darwin

suggested chimpanzees and gorillas

were our closest relatives. In the late

1980s, long lengths of DNA sequences

(over 10,000 nucleotides) became

available for several primates. A very

small proportion of the data for (what is

now) an inactive form of hemoglobin is

shown in Figure 3; being an inactive

copy means that most of the changes

we see are chance events. The human

sequence is given at the top: chimps;

gorillas; orang-utan; and rhesus

monkeys are identical to humans

unless an alternative nucleotide is

shown. The figure strongly supports

Darwin’s prediction that humans are

most closely related to chimpanzees

and gorillas. DNA sequences go further

in grouping chimpanzees and humans,

with gorillas just slightly older. Theory

predicts that occasionally there will be

support for either human and gorillas, or

gorillas and chimpanzees. These

exceptions are very important because

they allow estimates of the population

size of the common ancestors – but that

is well beyond our scope here. The

fundamental point is that hypotheses

about relationships can be tested as

more data becomes available.

Now we have whole genomes from

humans, chimpanzees and gorillas, and

so the testing gets even stronger. For

example, are there any new genes

inserted into the human genome by a

kindly creator or a group of itinerant

space travellers that might lead to

higher wisdom and intelligence?

Unfortunately, not. We have had to

make do with millions of small changes

to existing genes, but the idea of

special new genes was worth testing!

As scientists, we must always be open

to new ideas, but must subject them to

testing. Alternatives to mainstream

evolutionary thought are no exception,

and Figure 4 shows one example of

comparing predictions from the theory

of descent and from Intelligent Design.

The latter assumes some greater force

has general oversight of the running of

the Universe, whilst not getting actively

involved in its day-to-day running. It is a

bit like a mixture of personal

trainer/coach/ referee that helps

individuals, improves overall strategies,

but also ensures the rules of the game

[laws of nature] are obeyed. A simple

prediction from Intelligent Design might

be that it would be sensible to use

similar enzymes that do the same

function in similar environments.

22

For example, photosynthetic enzymes

in plants that live in very hot and dry

climates might be expected to be

designed similarly. The example

compares a cactus and a grass living

under the same desert conditions

(under-water stress) with a grass that

lives in moist temperate conditions, that

is, without either temperature or

moisture stress. I am deliberately

leaving it as a prediction (and not telling

you the result) so that you can

concentrate on the logic behind the test.

You could make a similar test with the

proteins that make up hairs in a

mammal. A polar bear and a snow

rabbit living in the Arctic might be

expected to have proteins well-

designed to maximize insulation – at

least compared to a sun bear or to a

rabbit from more tropical conditions.

Where are we up to now with evolution?

I have emphasized the testability of all

aspects of Darwin’s evolutionary theory,

but obviously there are still many

conflicting views. My approach is to

show a spectrum of views (Figure 5),

and look for the predictions that can be

tested. We have already considered the

traditional view of continued

spontaneous

generation, and then the

mixture of Plato and

special creation in the

past, that arose around

1700. From this point

everyone will have their

own variants of the

alternatives − I find the

version in the figure

helpful. There are those

who are happy just to

describe nature and not

to consider origins – this

was almost the norm in

early science where

origins (such as the

origin of the solar

system, or the origin of

species) were outside

the realm of science.

Again, there are others

who accept that normal

evolution works for all

species, except for

humans! They might

argue, despite the

extensive evidence, that

there is nothing in the

communication systems

of the Great Apes that

23

helps us understand the origin of

human language.

Somewhere in the middle of the

spectrum is ‘Intelligent Design’, referred

to above, that accepts an ancient Earth

and normal microevolutionary

processes – its ‘just that some overall

guidance is required’ – a bit of trial and

error perhaps. Another view, espoused

initially by North American academic

Marxists, was that ‘some major

component was missing’. For example,

they could not accept that competition

would be sufficient for major

evolutionary changes (macroevolution)

– some ‘Great Principle’ (presumably

Marxist) must be missing. The official

Catholic position is that everything is

natural law, apart from two

interventions – one for the origin

of life, and one for the origin of

humans. Individual Catholics

probably vary as much as

everyone else, the previous

sentence refers to the official

position. Finally, the mainstream

Darwinian view is for 100%

natural law (with lots of intersting

things still to discover).

24

My approach in teaching

evolution, after covering the

material here in more detail, is to:

• give this range of views,

• say that I am comfortable with

100% natural law,

• say that you (the students)

should place yourselves where

you are comfortable for the

present,

• and then say that I never ask them

where they are ‘comfortable’.

I do add, that being a science subject, I

expect them to be able to give the

standard evidence from a scientific

understanding. As far as I can gather,

students do not find this approach

threatening, and appear (to me) to

accept such an overview as allowing

them to study the subject without being

challenged beyond their present

comfort zone. The intent is to allow

personal space to consider the

questions, and to allow growth in the

future. Note that all views in Figure 5,

possibly excluding the last, have

advocates with religious persuasion. It

is important to remember than

continued spontaneous generation was

the accepted belief for most of the last

2000 years. The main issue is to see

evolution as perfectly normal science

that makes predictions that can be

tested.

Indeed, in reading Charles Darwin’s

autobiography, he repeatedly

comments on the critical role of theory

in science. He certainly fits into the

scientific approach that Karl Popper

espoused about generating

hypotheses, making predictions, and

testing the hypotheses, just in the way

Popper thought the great scientists

should do. Darwin actively looked for

apparent weak points where his theory

could have difficulties, and sought to

understand the biology better.

Darwin’s theory is excellent testable

science, and continues to generate

interesting and testable ideas.

Figure 5. A range of hypotheses about evolution, ranging from continued spontaneous generation to full acceptance of natural law. Until about 1700 it was assumed forms of living and non-living matter could interconvert. This was followed by a special creation phase that combined a mixture of a separate Creator with Plato’s philosophy that ‘essences’ could not change. There is a range of intermediate steps until a fully naturalist condition is accepted. There is a wide range of views and, in practice, everybody places themselves where they are comfortable. However, all of the views lead to predictions that are testable, and as scientists we must always try to test our favourite ideas.

David PennyResearch Director Professor of Theoretical Biology, Massey University - Palmerston North

This article: D. Penny. (2007). Charles Darwin, evolution simple and testable. NZ Science Teacher (116): 23-27 Can also be downloaded from David Penny’s website at: http://awcmee.massey.ac.nz/people/dpenny/index.htm

For further information: Email D.Penny@massey.ac.nz

25

Recent Publications

Ashton GV, Stevens MI, Hart MC, Green DH,

Burrows MT, Cook EJ, Willis KJ (2008)

Mitochondrial DNA reveals multiple northern

hemisphere introductions of Caprella mutica

(Crustacea, Amphipoda). Molecular Ecology

17: 1293-1303

Bordewich M, and Semple C. 2007. Computing

the hybridization number of two phylogenetic

trees is fixed-parameter tractable. IEEE/ACM

TCBB 4:458-466.

Bordewich M, and Semple C. 2007. Computing

the minimum number of hybridization events for

a consistent evolutionary history. Discrete

Applied Mathematics 155:914-928.

Bruneau A, Starr JR, and Joly S. 2007.

Phylogenetic relationships in the genus Rosa:

New evidence from chloroplast DNA

sequences and an appraisal of current

knowledge. Systematic Botany 32:366-378.

Chan ZSH, Collins L, and Kasabov N. 2007.

Bayesian learning of sparse gene regulatory

networks. Biosystems 87:299-306.

Chen XS, Rozhdestvensky TS, Collins LJ,

Schmitz J, and Penny D. 2007. Combined

experimental and computational approach to

identify non-protein-coding RNAs in the deep-

branching eukaryote Giardia intestinalis. Nucl.

Acids Res. 35:4619-4628.

Chor B, Hendy MD, and Penny D. 2007.

Analytic solutions for three taxon ML trees with

variable rates across sites. Discrete Applied

Mathematics 155:750-758.

Collins LJ, and Lockhart PJ. 2007. Evolutionary

properties of sequences and ancestral state

reconstruction. in Liberles, DA, ed. Ancestral

Sequence Reconstruction. Oxford University

Press.

Convey P, Gibson JAE, Hodgson DA, Pugh

PJA, and Stevens MI. 2007. New terrestrial

biological constraints for Antarctic glaciation.

Pp. Extended Abstract 053 in Cooper, AK, and

Raymond, CR, eds. Online Proceedings of the

10th ISAES. USGS OFR 2007-1047.

Convey P, and Stevens MI. 2007. Antarctic

Biodiversity. Science 317:1877-1878.

Donald K, Sijnja A, and Spencer H. 2007.

Species assignation amongst morphologically

cryptic larval Digenea isolated from New

Zealand topshells (Gastropoda: Trochidae).

Parasitology Research 101:433-441.

Dress A, and Steel M. 2007. Phylogenetic

diversity over an abelian group. Annals of

Combinatorics 11:143-160.

Egel R, and Penny D. 2007. On the Origin of

Meiosis in Eukaryotic Evolution: Coevolution of

Meiosis and Mitosis from Feeble Beginnings. in

Egel, R, and Lankenau, D-H, eds.

Recombination and Meiosis. Springer, Berlin.

Gascuel O, and Steel M. 2007. Reconstructing

Evolution. New Mathematical and

Computational Advances. Pp. 318. Oxford

University Press, Oxford.

Gibb GC, Kardailsky O, Kimball RT, Braun EL,

and Penny D. 2007. Mitochondrial genomes

and avian phylogeny: Complex characters and

resolvability without explosive radiations.

Molecular Biology and Evolution 24:269-280.

Goode MG, and Rodrigo AG. 2007. SQUINT: a

multiple alignment program and editor.

Bioinformatics 23:1553-1555.

Greaves SNJ, Chapple DG, Gleeson DM,

Daugherty CH, and Ritchie PA. 2007.

Phylogeography of the spotted skink

(Oligosoma lineoocellatum) and green skink (O.

chloronoton) species complex (Lacertilia:

Scincidae) in New Zealand reveals pre-

Pleistocene divergence. Molecular

Phylogenetics and Evolution 45:729-739.

Greenslade P, Melbourne B, Davies K, and

Stevens MI. 2008. The status of two exotic

terrestrial Crustacea on subantarctic Macquarie

Island. Polar Record 44:15-23.

Greenslade P, Stevens MI, and Edwards R.

2007. Invasion of two exotic terrestrial

flatworms to subantarctic Macquarie Island.

Polar Biology 30:961-967.

Grunewald S, Steel M, and Swenson MS.

2007. Closure operations in phylogenetics.

Mathematical Biosciences 208:521-537.

Hall R, Oxley J, and Semple C. 2007. The

structure of 3-connected matroids of path width

three. European Journal of Combinatorics

28:964-989.

Hare KM, Pledger S, Thompson MB, Miller JH,

and Daugherty CH. 2007. Low cost of

locomotion in lizards that are active at low

temperatures. Physiological and Biochemical

Zoology 80:46-58.

Hartmann K, and Steel M. 2007. Phylogenetic

diversity: From combinatorics to ecology. Pp.

171-196 in Gascuel, O, and Steel, MA, eds.

Reconstructing Evolution. New Mathematical

and Computational Advances. Oxford

University Press.

Hayward J, Taylor J, and Rodrigo A. 2007.

Phylogenetic Analysis of Feline

Immunodeficiency Virus in Domestic Feral and

Companion Cats of New Zealand. Journal of

Virology 81:2999-3004.

Hoare JM, Shirley P, Nelson NJ, and

Daugherty CH. 2007. Avoiding aliens:

Behavioural plasticity in habitat use enables

large, nocturnal geckos to survive Pacific rat

invasions. Biol. Conservation 136:510-519.

Holland B, Conner G, Huber K, and Moulton V.

2007. Imputing Supertrees and Supernetworks

from Quartets. Systematic Biology 56:57-67.

Hughes J, Kennedy M, Johnson KP, Palma RL,

and Page RDM. 2007. Multiple cophylogenetic

analyses reveal frequent cospeciation between

pelecaniform birds and Pectinopygus lice.

Systematic Biology 56:232-251.

Huynen L. 2007. Revealing the histories of

Maori cloaks using DNA. NZ Sci. Teach 116:19

26

Irimia M, Maeso I, Penny D, Garcia-Fernandez

J, and Roy SW. 2007. Rare coding sequence

changes are consistent with ecdysozoa, not

coelomata. MBE 24:1604-1607.

Irimia M, Penny D, and Roy SW. 2007.

Coevolution of genomic intron number and

splice sites. Trends in Genetics 23:321-325.

Irimia M, Rukov JL, Penny D, and Roy SW.

2007. Functional and evolutionary analysis of

alternatively spliced genes is consistent with an

early eukaryotic origin of alternative splicing.

BMC Evolutionary Biology 7:188.

Joly S, and Bruneau A. 2007. Delimiting

species boundaries in Rosa sect.

Cinnamomeae (Rosaceae) in eastern North

America. Systematic Biology 32:819-836.

Joly S, Stevens MI, and van Vuuren BJ. 2007.

Haplotype networks can be misleading in the

presence of missing data. Systematic Biology

56:857-862.

Knapp M, Mudaliar R, Havell D, Wagstaff SJ,

and Lockhart P. 2007. The Drowning of New

Zealand and the problem of Agathis.

Systematic Biology 56:862-870.

Kneip C, Lockhart P, Voss C, and Maier UG.

2007. Nitrogen fixation in eukaryotes - New

models for symbiosis. BMC Evol. Biol. 7: 55.

Kurland CG, Collins LJ, and Penny D. 2007.

The evolution of eukaryotes - Response.

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Lambert D. 2007. How fast is evolution? New

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Larkum A, Lockhart P, and Howe C. 2007. The

origin of plastids: A shopping bag model.

Photosynthesis Research 91:272-272.

Larson G, Cucchi T, Fujita M, Matisoo-Smith E,

et al. 2007. Phylogeny and ancient DNA of Sus

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Proceedings of the National Academy of

Sciences of the United States of America

104:4834-4839.

Lehnebach CA, Cano A, Monsalve C,

McLenachan P, Horandl E, and Lockhart P.

2007. Phylogenetic relationships of the

monotypic Peruvian genus Laccopetalum

(Ranunculaceae). Plant Systematics and

Evolution 264:109-116.

Lim SG, Cheng Y, Guindon S et al. 2007. Viral

Quasi-Species Evolution During Hepatitis Be

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133:951-958.

Longson CG, Hare KM, and Daugherty CH.

2007. Fluctuating asymmetry does not reflect

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MacAvoy ES, McGibbon LM, Sainsbury JP,

Lawrence H, Wilson CA, Daugherty CH, and

Chambers GK. 2007. Genetic variation in island

populations of tuatara (Sphenodon spp)

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Conservation Genetics 8:305-318.

Martin W, Roettger M, and Lockhart PJ. 2007.

A reality check for alignments and trees.

Trends in Genetics 23:478-480.

Matisoo-Smith E. 2007. Animal translocations,

genetic variation and the human settlement of

the Pacific. Chapter 10. Pp. 147-157 in

Friedlaender, JS, ed. Genes, Language and

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Matisoo-Smith E. 2007. The Peopling of

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Matisoo-Smith E. 2007. Lapita: A genetic

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Archaeological perspectives on the

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Complex. Academia Sinica.

Matsen FA, and Steel M. 2007. Phylogenetic

mixtures on a single tree can mimic a tree of

another topology. Syst. Biol. 56:767-755.

McDowall RM, and Stevens MI. 2007.

Taxonomic status of the Tarndale bully

Gobiomorphus alpinus (Teleostei: Eleotridae),

revisited - again. J. Roy. Soc. NZ 37:15-29.

McGaughran A, Hogg ID, Stevens MI. 2008.

Patterns of population genetic structure for

springtails and mites in southern Victoria Land,

Antarctica. Molecular Phylogenetics and

Evolution 46: 606-618

Meudt HM, and Clarke AC. 2007. Almost

Forgotten or Latest Practice? AFLP

applications, analyses and advances. Trends in

Plant Science 12:106-117.

Michel C, Hicks BJ, Stölting KN, Clarke AC,

Stevens MI, Tana R, Meyer A, van den Heuvel

MR. 2008. Distinct migratory and landlocked

ecotypes in a New Zealand eleotrid

(Gobiomorphus cotidianus) – implications for

incipient speciation and the origin of island

freshwater fish species. BMC Evol.Biol. 8:49

Miller HC, Conrad AM, Barker SC, and

Daugherty CH. 2007. Distribution and

phylogenetic analyses of an endangered tick,

Amblyomma sphenodonti. New Zealand

Journal of Zoology 34:97-105.

Moore JA, Hoare JM, Daugherty CH, and

Nelson NJ. 2007. Waiting reveals waning

weight: Monitoring over 54 years shows a

decline in body condition of a long-lived reptile

(tuatara, Sphenodon punctatus). Biological

Conservation 135:181-188.

Morely CG, McLenachan P, and Lockhart P.

2007. Evidence for the presence of a second

species of mongoose inthe Fiji Islands. Pacific

Conservation Biol.13:29-34.

Moulton V, Semple C, and Steel M. 2007.

Optimizing phylogenetic diversity under

constraints. Journal of Theoretical Biology

246:186-194.

27

Nakano T, and Spencer H. 2007. Simultaneous

polyphenism and cryptic species in an intertidal

limpet from New Zealand. Molecular

Phylogenetics and Evolution 45:470-479.

Nolan L, Hogg ID, Sutherland DL, Stevens MI,

and Schnabel KE. 2007. Allozyme and

mitochondrial DNA variability within the New

Zealand damselfly genera Xanthocnemis,

Austrolestes, and Ischnura (Odonata). New

Zealand Journal of Zoology 34:371-380.

Oxley J, Semple C, and Whittle G. 2007. The

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Penny D. 2007. Charles Darwin, evolution

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Penny D, Holland B, and Hendy M. 2007.

Phylogenetics: Parsimony, Networks and

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Statistical Genetics, 3rd Ed. Wiley InterScience,

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Penny D, and Phillips MJ. 2007. Evolutionary

biology - Mass survivals. Nature 446:501-502.

Perrie LR., Bayly MJ., Lehnebach CA.,

Brownsey PJ. 2007. Molecular phylogenetics

and molecular dating of the New Zealand

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Poole AM, and Penny D. 2007. Evaluating

hypotheses for the origin of eukaryotes.

Bioessays 29:74-84.

Poole A, and Penny D. 2007. Engulfed by

speculation. Nature 447:913-913.

Poole AM, and Penny D. 2007. Response to

Dagan and Martin. Bioessays 29:611-614.

Poss M, Idoine A, Ross HA, Terwee JA,

VandeWoude S, and Rodrigo A. 2007.

Recombination in feline lentiviral genomes

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Virology 359:146-151.

Ramstad KM, Nelson NJ, Paine G, Beech D,

Paul A, Paul P, Allendorf FW, and Daugherty

CH. 2007. Species and cultural conservation in

New Zealand: Maori traditional ecological

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21:455-464.

Robins JH, Hingston M, Matisoo-Smith E, and

Ross HA. 2007. Identifying Rattus species

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Notes 7:717-729.

Rodrigo AG, Ewing G, and Drummond A. 2007.

The evolutionary analysis of Measurably

Evolving Populations using serially sampled

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Roy SW, and Penny D. 2007. Patterns of intron

loss and gain in plants: Intron loss-dominated

evolution and genome-wide comparison of O-

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Roy SW, and Penny D. 2007. A very high

fraction of unique intron positions in the intron-

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Roy SW, and Penny D. 2007. Intron length

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Roy SW, and Penny D. 2007. On the incidence

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24:1579-1581.

Roy SW, and Penny D. 2007. Widespread

Intron Loss Suggests Retrotransposon Activity

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24:1926-1933.

Roy SW, Penny D, and Neafsey DE. 2007.

Evolutionary conservation of UTR intron

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Shavit L, Penny D, Hendy MD, and Holland BR.

2007. The Problem of Rooting Rapid

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Shepherd LD, and Lambert DM. 2007. The

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Slack KE, Delsuc F, McLenachan PA, Arnason

U, and Penny D. 2007. Resolving the root of

the avian mitogenomic tree by breaking up long

branches. Molecular Phylogenetics and

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Spencer H, Waters JM, and Eichhorst TE.

2007. Taxonomy and nomenclature of black

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Star B, Stoffels RJ, and Spencer HG. 2007.

Single-Locus Polymorphism in a

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176:1625-1633.

Star B, Stoffels RJ, and Spencer HG. 2007.

Evolution of Fitnesses and Allele Frequencies

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Steel M. 2007. Tools to construct and study big

trees: A mathematical perspective. Chapter 7.

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Steel M, and Matsen FA. 2007. The Bayesian

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Steel M, Mimoto A, and Mooers A. 2007.

Hedging Our Bets: The Expected Contribution

28

of Species to Future Phylogenetic Diversity.

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Steel M, and Szekely LA. 2007. Teasing apart

two trees. Combinatorics, Probability and

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Stevens MI, Hogendoorn K, and Schwarz MP.

2007. Evolution of sociality by natural selection

on variances in reproductive fitness: evidence

from a social bee. BMC Evol. Biol. 7:153.

Stevens MI, Hunger SA, Hills SFK, and

Gemmill CEC. 2007. Phantom hitch-hikers

mislead estimates of genetic variation in

Antarctic mosses. Plant Systematics and

Evolution 263:191-201.

Stevens MI, McCartney J, and Stringer IAN.

2007. New Zealand's forgotten biodiversity:

different techniques reveal new records for

'giant' springtails. NZ Entomologist 30:79-84.

Stevens MI, Winter D, Morris R, McCartney J,

and Greenslade P. 2007. New Zealand's giant

Collembola: new information on distribution and

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Journal of Zoology 34:63-78.

Storey A.A, Ramirez JM, Quiroz D, Burley DV,

Addison DJ, Walter R, Anderson AJ, Hunt TL,

Athens JS, Huynen L, and Matisoo-Smith EA.

2007. Radiocarbon and DNA evidence for a

pre-Columbian introduction of Polynesian

chickens to Chile. Proceedings of the National

Academy of Sciences 104:10335-10339.

Thatte BD. 2007. A correct proof of the

McMorris-Powers' theorem on the consensus of

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Trewick SA. 2007. Stick insects. Te Ara - the

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Trewick SA. 2007. DNA Barcoding is not

enough: mismatch of taxonomy and genealogy

in New Zealand grasshoppers (Orthoptera:

Acrididae). Cladistics 23:1-15. Trewick SA, Paterson AM, and Campbell HJ.

2007. Hello New Zealand. J.Biogeog. 34:1-6. Contact Us

Allan Wilson Centre for Molecular Ecology and Evolution

Trotter MV, and Spencer HG. 2007. Frequency-

Dependent Selection and the Maintenance of

Genetic Variation: Exploring the Parameter

Space of the Multiallelic Pairwise Interaction

Model. Genetics 176:1729-1740.

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Van den Heuvel MR, Michel C, Stevens MI,

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Whitfield JB, and Lockhart PJ. 2007.

Deciphering ancient rapid radiations. Trends in

Ecology and Evolution 22:258-265.

Woodhams M, Stadler P, Penny D, and Collins

L. 2007. RNase MRP and the RNA processing

cascade in the eukaryotic ancestor. BMC

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