Forward evolution

Evolutionary biologists don’t spend all their time looking backwards. At the Allan Wilson Centre, Kiwi scientists are predicting the future

Evolutionary biologists don’t spend all their time looking backwards. At the Allan Wilson Centre, Kiwi scientists are predicting the future


February 12 marks the 200th anniversary of Charles Darwin’s birth, and 2009 marks the 150th anniversary of On the Evolution of Species

You would be forgiven for thinking evolution is about the past. After all, when most of us think about evolution, we relate it to how our own species journeyed from ape to human.

It seems logical that evolutionary work would be about what has happened sometime before now. The researchers at the Allan Wilson Centre for Molecular Ecology and Evolution can take credit for their share of unravelling old mysteries. Among other achievements, Massey University’s David Penny (one of the centre’s founding directors) conducted work showing that birds and mammals were diversifying long before the giant asteroid strike that has been credited with killing off the dinosaurs. His research proposes that competition between species was probably just as—or more—important than the impact of any meteor. Lisa Matisoo-Smith, a professor of biological anthropology at the University of Auckland and an Allan Wilson Centre primary investigator, researches Pacific prehistory and, using the tools of molecular evolution, her group is leading the charge to finally understand Polynesian migration. And David Lambert, formerly with the centre and now at Griffith University in Australia, was one of the first in the world to work with ancient DNA. Lambert sourced the DNA from the bones of extinct moa and the tissues of Adelie penguins who helpfully preserved their bodies in the freezer that is Antarctica.

So yes, evolutionary biologists do spend a fair bit of their time studying the long-ago. But what happens with much of what they learn takes them firmly into the future.

“The common misconception among the public and many scientists is that evolution is a science that looks backwards—that we effectively look to the past to see how we arose and what happened in our evolutionary history,” says Allen Rodrigo, a director of the bioinformatics institute at Auckland University, and another of the centre’s principal investigators. “But in fact, we think it’s time to put a flag in the sand and say that evolution can also be used to predict things.”

Rodrigo’s work is focused on viruses that mutate rapidly; viruses like HIV, hepatitis and SARS. “The speed with which these viruses evolve is a million times faster than the average gene. And I’m not pulling that number out of a hat—they really are a million times faster.”

While that speedy rate of mutation makes the viruses a challenge to treat (it’s one of the reasons HIV/AIDS patients are typically given a cocktail of antiretroviral drugs: when just one drug is taken, the virus quickly evolves, becomes resistant and stops working), it also creates models for studying evolutionary processes within reasonable time frames. Studying these viruses, says Rodrigo, is watching evolution in action.

When an organism is transported to a new island or continent, over time it expands, fills different niches and mutates to cope with the selective pressures of that new environment. A virus, says Rodrigo, does exactly the same thing: it enters a host, affects different tissues, fights the immune system and evolves to ensure its survival. But viruses do that really, really fast.

Rodrigo is interested in how evolutionary changes in a virus relate to the disease. His research into HIV has shown that the number of mutations that result in changes to the protein of a particular patient’s virus can be used to predict how long the patient will survive. When studying Hepatitis B with collaborators at the National University of Singapore, he showed that the immune system of patients whose virus has a high rate of evolution is able to recognise, control and clear the virus from their system. Not so lucky are patients harbouring a virus with a low rate of evolution—their immune system doesn’t appear to recognise a particular protein of that virus and the virus persists.

Next, he wants to investigate whether the rate of evolution can be used as a diagnostic indicator of the likelihood that someone will be able to successfully battle the virus and clear it. Having that knowledge would be very helpful for clinicians when determining treatment regimes—and it has has clear commercial potential.

Paul Rainey, the director of the Allan Wilson Centre since October 2008, is based on Massey’s Albany campus and, in addition to diseases like Hepatitis B and HIV, is interested in applying the centre’s expertise to other diseases.

“In New Zealand, we have some really interesting—and specific—emerging and persistent diseases that require tackling,” says Rainey. “These problems are often seen as falling in the domain of molecular biology and microbiology, but new diseases and where they come from are primarily questions of ecology and evolution. This is where I think we can make quite a bit of difference.”

There is no shortage of infectious agents to study. New Zealand’s first endemic case of cholera was diagnosed in September and, says Rainey, may be owed to our intensive aquaculture practices. Without even tapping into a list of rapidly evolving diseases faced by the agricultural sector, Rainey reels off Hepatitis C, human papilloma virus, and rheumatic fever as likely targets of research attention.

He’s most keen, though, to get to work on Staphylococcus aureus—the most common cause of staph infections. “It’s an opportunistic bacterium that each year kills several hundred people and disproportionately affects Maori and Pacific Islanders,” says Rainey. “Over the next few years the Allan Wilson Centre expects to develop a research programme providing insight into the New Zealand-specific context of this emerging pathogen.”

Ultimately, he says, it aims to provide the kind of evolutionary framework necessary to initiate a New Zealand-specific vaccine programme.

Established in 2002, the Allan Wilson Centre is one of New Zealand’s seven Centres of Research Excellence (CoRE). The idea behind the CoREs (which are funded by the Tertiary Education Commission) is to encourage excellent—and collaborative—scientific work. It’s based at Massey University with researchers at Massey’s Palmerston North and Albany campuses, as well as the universities of Auckland, Canterbury and Otago, and Victoria University of Wellington. Scientists at Plant and Food Research (the Crown Research Institute newly formed by the merger of Crop and Food and HortResearch) are also part of the team. In all, there are 20 senior researchers, 14 post-doctoral and research fellows and 51 post-graduate students on the centre’s books.

The centre’s full name—the Allan Wilson Centre for Molecular Ecology and Evolution—is quite a mouthful. It commemorates one of New Zealand’s most influential, if not well known at home, scientists.

Wilson, who died of leukaemia in 1991 at age 57, became one of the most controversial scientists in the world when he developed the theory of the molecular clock. Born and raised in Ngaruawahia, he received his PhD from Otago and then joined the faculty of the University of California at Berkeley. It was there in 1967 that he said the timing of evolutionary change can be measured by determining the accumulated number of mutations that occur as one species diverges from another. Using that premise, he estimated that humans diverged from apes as recently as four to five million years ago (rather than the ten to 30 million years as was then believed). He threw his contemporaries into a tizzy.

Twenty years later, Wilson started another biological revolution when he announced the ‘Mitochondrial Eve’ hypothesis. By analysing mitochondrial DNA (which is passed directly from mother to child), he and Rebecca Cann determined that all modern humans could be traced back to one woman who lived in Africa 150,000 to 200,000 years ago.

Wilson’s revolutionary ideas have since been accepted by the scientific community, and he left the legacy of not only being the first to marry biochemistry and biology but also the first to use molecular approaches to study evolution. “Allan broke down the barrier between two disciplines that didn’t talk to each other—the biologists and the biochemists,” says Mike Hendy, professor of mathematics at Massey University. “He recognised how he could bring them together to look at questions that palaeontologists previously thought they were the only ones to know anything about.”

Hendy and David Penny, a professor of theoretical biology, set up the centre in 2002. They’d been inspired by Wilson nearly 30 years earlier when they began collaborating. They first met when a terrified Penny gave a seminar to the Massey mathematics department about evolutionary trees.

“I knew nothing about math,” he says. “How could I talk to them?”

But Hendy, a mathematician who was equally terrified of biology, was in the seminar audience and became intrigued. Coincidentally, Hendy and his wife had attended a public debate pitting evolution against creationism; she asked him why mathematicians couldn’t help solve this dilemma.

“I tried to explain to her how we had nothing to do with it whatsoever and she wouldn’t believe me,” says Hendy. He acquiesced and took the question to Penny. The two struck a deal and started joint meetings with their PhD students and post-docs. Before long, those meetings moved off-campus and included researchers from other institutions (they continue still—in November 2008, over 100 current and former students and collaborators from New Zealand and abroad spent a weekend at Chateau Tongariro talking shop and celebrating Penny’s 70th birthday). Their work began to build an international reputation and in 2001, when the CoRE initiative was announced, the wider group had more than a decade of regular meetings and collaborative work behind it. The centre was funded for an initial six years and Hendy and Penny became its co-directors.

“Evolution is one of those areas where mathematics and biology interact very well,” says Penny. “But there are still very few groups internationally that have a long-term relationship between the two. That’s recognised as a unique feature of our centre.”

Rainey, who took over as director when the centre was funded for a further six years in 2008, agrees. He says the ability to take DNA sequence data and use it to infer something is the basis of much evolution research. But to take data and make inferences requires a great deal of mathematics.

Just as Hendy didn’t think mathematicians could help solve the questions of human evolution, most wouldn’t immediately see their connection with the preservation and management of endangered or iconic species. But consider the work of a researcher like Victoria University’s Charles Daugherty, who specialises in conservation genetics and ecological restoration and spends a lot of his time working with tuatara.

“The majority of the data Charles gets for conservation work is DNA sequence data,” says Rainey. “There are many things you can do with that data … it may just act as a bar code, for example, for a particular individual. But equally, if one has multiple DNA sequences from multiple individuals, it becomes immediately possible to do more with that information.”

That’s where the skills of mathematical biologists come in; these people (who use words that give Google pause) take DNA sequence data, make sense of it and put it in an evolutionary context.

One of the goals of the Allan Wilson Centre, says Daugherty, is to use state-of-the-art molecular genetic information to understand the evolutionary history of New Zealand and its plants and animals, and then apply that knowledge to protecting it. While ultimately there may be unexpected commercial significance of genes the group discovers, not knowing what’s here, how it’s special and how it relates to what exists in the rest of the world is like, he says, “trying to manage a business without knowing the inventory”.

Helping analyse that inventory is Mike Steel, a professor of statistics and mathematics at Canterbury University.

“The data is developing at an incredible speed,” says Steel. “Not just more data, but new types of data. We’re trying to come up with clever ways to exploit that data and answer the questions biologists have such as what is a species’ rate of evolution and how long ago did two species separate.”

Steel’s research with the Allan Wilson Centre has included understanding how much biodiversity is at risk when a species becomes extinct. Tuatara, for example, have no close relatives so extinction would result in much more biodiversity loss than, say, a spider that has many close relatives; likewise, if one or more species depends on another for its survival (say, as a food source) and that source species becomes extinct, the impact on biodiversity could be great. Through a purely mathematical approach, Steel’s group can advise conservationists on how to manage wildlife and which rare species might most need protection.

“One of the great strengths of the CoRES is that they provide a framework within which researchers are encouraged to look outside of their own horizons,” says Rainey.

Looking beyond the horizon. That’s very much what the Allan Wilson Centre is about: studying evolution in order to build New Zealand’s future.

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