Features

A new way of measuring biodiversity, developed at Oxford University, has shown how genetic diversity, as well as population numbers, can plummet due to human activity.

The lost biodiversity is epitomised by a study of the plight of rockfish: ancient species once well-known to California's coast-dwellers.

Mike Bonsall of Oxford's Department of Zoology, along with colleague Sandrine Pavoine, was part of the team reporting their research in a recent issue of Ecology Letters. I asked Mike about rockfish, their decline, and how the new approach might help conservationists:

OxSciBlog: What's been the impact of fishing on rockfish populations?
Mike Bonsall: Awful. First it has to be realised that rockfish are extremely long-lived vertebrates. Some species live for up to 50 years and others have been recorded to live for over 200 years. As the technological ability to harvest fish from the ocean has increased we have overexploited (and collapsed) many stocks.

Rockfish are no exception: by 2003, some species were down to less than 5 per cent of their 1970 levels - so, over 40 years, (and given these harvested species live for more than this time period) we have selectively removed the reproductive cohort and the stocks have no opportunity to recover.

OSB: How has fishing affected the genetic diversity of rockfish?
MB: Sustained fishing affects not only biomass (population size) but also genetic diversity. We have shown that the declining numbers with a rockfish hotspot (off the west coast of California) is accompanied by changes in the phylogenetic (evolutionary) structure of the species assemblage.

For instance, evolutionary-old (basal) species had higher contributions to the diversity and large-bodied species were shown to decline (affecting genetic diversity).

OSB: What advantages does you approach have over other ways of measuring biodiversity?
MB: Our approach allows us to see if changes between communities (either in time or across space) correspond to changes in the different evolutionary lineages (and species that evolve from each lineage). We can weight species differently (depending on their rarity) and allow different classical indices for biodiversity to be used in our ecological-evolutionary analyses. In sum,  our methodology has broad applications that can be used to integrate geographical space, current history (ecological time) and evolutionary history in measuring biodiversity.

OSB: How might your approach be applied to the study of other at-risk species/ecosystems?
MB: It could be applied widely, to many species: We are currently using it to explore how butterfly diversity alters on chalk grasslands and how plant communities are structured in Algerian marshes. However, there is a debate in ecology about whether communities are structured randomly (neutral) or by the evolution of niches. Our approach will allow us to explore a range of different communities where evolutionary histories are well-known to understand the relative contribution of neutral versus niche mechanisms.

The fossilised teeth of ancient rodents suggest that their ancestors found a way to cross the South Atlantic Ocean to colonise South America.

Hesham Sallam, of Oxford University's Department of Earth Sciences, and colleagues report in this week's PNAS new evidence that shows that the ancestors of new world rodents, such as the Capybara, came over from Africa or Arabia in the late Eocene 40-34 millions years ago.

This means that the ancestors of the world's largest living rodent must have found a way to cross the South Atlantic which divided South America from Africa/Arabia at this time.

Rival theories had given Asia, via North America, as a possible origin for the rodent populations [Caviomorpha] that emerged in South America. But this new research shows that evidence from both the fossil and molecular data points to an African/Arabian origin. 

Hesham tells us: 'The caviomorph colonisation of South America evidently occurred via a chance dispersal across the vast South Atlantic.'

'Future paleontological research in the late middle Eocene should not only help to further clarify the later stages of evolution of these rodents but also the evolution of other mammalian groups such as primates.'

A team including Joseph Silk of Oxford University's Department of Physics have dreamt up the biggest particle collider ever: a rotating black hole.

In an article to appear in Physical Review Letters, the team imagine how, once Earth-based machines such as the Large Hadron Collider can no longer provide enough energy to probe deeper into fundamental particle physics, certain sorts of black hole might do the job.

They have calculated that, in middle-weight black holes that are rotating fast enough, particles of dark matter entering at the right angle would be accelerated towards each other at extremely high energy - making for an explosive high-speed collision.

It may even be that enough energy could escape these natural collisions for us to be able to detect them on Earth right now, using the latest instruments such as the IceCube observatory.

Such observations could tell us much about dark matter, gravity, and the beginnings of the Universe - as well as revealing more about the structure of black holes themselves.

Read more about this story in New Scientist.

After his trip to Guyana last year Oxford's George McGavin recently led an expedition to Papua New Guinea as part of BBC One's Lost Land of the Volcano.

The first part of the series went out on Tuesday [watch it on BBC iPlayer] but, with two more episodes still to come, I quizzed George about his latest adventure, the new species the team discovered and how they coped with humidity, leeches and lava bombs:

OxSciBlog: Why is Mount Bosavi such an interesting place to study?
George McGavin: Mount Bosavi, which rises to a height of 2,507 metres (8,225 ft) above sea level, is the collapsed cone of an extinct volcano in the Southern Highlands of Papua New Guinea that last erupted some 250,000 years ago in the Pleistocene.

What makes this area so interesting is that it is remote, relatively unexplored and the difficulty of accessing the crater means that hunting pressure on the animals inside is currently very low. Additionally, the top of Mount Bosavi, being an isolated montane habitat, will harbour species not found in the surrounding lowland forest.

OSB: What species there captured your imagination?
GMcG: The forest is filled with weird and wonderful species from pygmy parrots and giant rats to squeaking beetles and grunting fish. Halfway through the expedition I found and photographed a small group of caterpillars, which I had never seen before. They sat on a branch in a snake-like group and when threatened thrashed around violently.

The only way of finding out what they were was to rear them through to adulthood in a cage. They pupated but nothing happened until the very last morning when we were due to leave. I had transferred them into a small box in the hope that they might emerge - and they did! - I opened the box to see three large and colourful, fruit-piercing noctuid moths (Eudocima iridescens).

OSB: What were the challenges of filming in the crater?
GMcG: Filming in rain forest is tough on equipment and people. Constant high humidity does not go well with sophisticated microelectronics and all the essential camera gear was kept in custom built hotboxes over night to make sure they were dry - even if we were not.

One team filmed inside the 'white water cave' of Mageni on New Britain and had to wade, scramble and climb their way deep into the heart of a mountain. It was like travelling through the world's greatest jet-wash. The enormous quantities of water and spray gave the cameras and sound equipment a hard time but they still managed to film some extremely exciting new passages as well as the cave’s natural inhabitants, bats, leeches and cave crickets.

Another smaller team visited Tavurvur an active stratovolcano near Rabaul in East New Britain. During the time we were filming, Tavurvur became unusually and spectacularly active, throwing up huge plumes of ash and ejecting some large volcanic ‘bombs’ a kilometre into the air some of them flew over and landed near our camp site - forcing a very hasty early morning retreat.

OSB: Why is protecting the wildlife of places such as Papua New Guinea so important?
GMcG: Recent analyses of thirty years of satellite imagery for Papua New Guinea have found that 19.8 million acres of forest was lost between 1972 and 2002. At the rate forest is being cleared or degraded more than 80 percent of the country's accessible forest - and more than half of the total forested area will be gone or severely damaged by 2021.

The loss of what is the world's third-largest rain forest would see the extinction of a unique flora and fauna and have devastating and far-reaching effects on the physical environment, regional weather patterns and the lives of the people that live there.

And it’s not just the forest and its species we will lose. As the process of logging releases huge amount of carbon dioxide into the atmosphere, continuing deforestation make it virtually certain that the world as a whole will not be able to escape the worst effects of global climate change.

The next part of Lost Land of the Volcano will be broadcast on BBC One, 15 September at 9pm, with the third part airing on 22 September at 9pm.

Dr George McGavin is an Honorary Research Associate at the Oxford University Museum of Natural History.

Currently everyone is interested in China – whether its China’s astonishingly rapid emergence as an economic powerhouse, its place as a huge producer and consumer in a globalised world, its role in global politics, its part in climate change negotiations, or as a stage for a fabulous Olympics.

China is also fascinating from a medical and public health point of view. It goes without saying that China has a vast population of over 1.3 billion. But that population is spread between cold northern latitudes and tropical beach resorts in Hainan, and lives both in underdeveloped rural areas and the crowded international cities of Shanghai and Hong Kong.

It’s also an ageing population, as the effects of the rapid improvement in the general health of its population and birth control policies play out.

Changing lifestyles
On top of all that, rapid economic change has led to equally fast changes in many people’s incomes, diets and lifestyles. As a result, disease patterns have altered remarkably over the past 40–50 years so that chronic diseases such as heart attacks, diabetes and cancer are now the biggest killers rather than infectious diseases and diseases of poverty.

Coupled with relatively well established nationwide healthcare infrastructure, this means China is a very good place to carry out large-scale medical research. Clinical trials of new treatments carried out here, as well as observational studies that can reveal risk factors for chronic diseases like heart attacks and cancer, will be useful not only for public health policy in China but also to inform healthcare in both the developing and developed world.

‘There’s much that we can try to understand. In China there’s a huge unexplained variation geographically in many chronic diseases,’ says Professor Zhengming Chen, director of the China Program at the Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU) at the University of Oxford.

‘For example, twenty per cent of adults in rural Sichuan would die in middle age from chronic lung disease back in the 1990s, but deaths from this disease were more than 10-fold lower in many other rural areas. Smoking only accounts for part of this huge variation. Similarly, stomach and oesophageal cancers vary greatly in different regions. There is also a four-or-five fold difference in stroke death rates between different parts of China, with rates in China on average being more than five times as high as in the UK. We’d really like to understand the factors that lead to these differences to inform preventive and therapeutic measures.’

Our news pages announce today that CTSU has just extended and renewed a partnership with Fuwai Hospital of the Chinese Academy of Medical Sciences through the China Oxford Centre for International Health Research. This will further strengthen CTSU’s 20-year long collaboration with medical scientists in China and will provide researchers with dedicated new facilities in China for the next 20 years.

Where it all began
CTSU’s collaborative research with medical scientists at the Chinese Academy of Medical Sciences and the China National Centre for Disease Control started during the early 1980s, initiated by Professor Sir Richard Peto and Professor Rory Collins, co-directors of CTSU.

It began with a landmark study that mapped the regional variation of incidence of chronic diseases, and possible lifestyle and blood determinants of disease rates, at a population level across 69 rural Chinese counties. It grew to include large-scale randomised trials that have resulted in changes to clinical practice worldwide for heart attacks and strokes, and now involves one of the world’s biggest ever blood-based epidemiological studies of the determinants of chronic diseases, involving studying and monitoring the health of over 500,000 people for up to 20 years.

‘We have had the privilege of collaborating with many distinguished medical scientists in China since the early 1980s, probably well before anyone started talking seriously about China,’ says Zhengming Chen. ‘It was not an easy start, and took quite a while to convince many funding agencies and pharma what collaboration with China can really offer.’

That’s changed greatly now that CTSU has demonstrated again and again that you can get collaborative research projects carried out cost effectively in China, with rapid recruitment and high-quality data. These projects have provided clear evidence that can improve clinical practice and save lives. In doing all of this, CTSU has also built up a phenomenal set of partnerships with Chinese research institutions and a network of hospitals across the nation.

One of the early studies that began to change people’s minds was CAST, the Chinese Acute Stroke Trial. Carried out by CTSU and Fuwai Hospital, this looked at whether aspirin as an antiplatelet agent was beneficial if taken soon after the most common type of stroke. Over 20,000 patients from more than 500 Chinese hospitals were randomised to receive either aspirin or a placebo within the first 48 hours of a suspected stroke, at the same time as a similar study was being carried out in the West coordinated by Edinburgh University. This showed definitively that trials could be carried out in China to the same standard as in the West.

‘Even 15 years ago when this was carried out, the number of stroke patients receiving a CT scan in Chinese hospitals was actually higher than in the international study in the West,’ notes Zhengming Chen. The data from both studies were analysed together and showed a clear net benefit for aspirin after a stroke, with the results being published in The Lancet.

More recently, the Second Chinese Cardiac Study (COMMIT-CCS2) involved 46,000 patients from 1250 hospitals in China in investigating the effects of two different emergency treatments for heart attacks. The results, published in 2005 in The Lancet, gave clear evidence for the first time that adding clopidogrel, a new antiplatelet agent, to aspirin can further reduce the risk of mortality for patients after a severe heart attack. The drug is now used in the back of ambulances in many parts of the world.

Biobank reaps dividends
Of all the projects in China involving CTSU, the most impressive so far – in terms of the size, scope and potential scientific significance – is the Kadoorie Biobank Study led by Professor Zhengming Chen at CTSU and Professor Liming Lee in Beijing.

This joint project between CTSU and the China National Centre for Disease Control has $10 million in funding from the Kadoorie Charitable Foundation in Hong Kong, as well as core funding to CTSU from the UK Medical Research Council. It has recruited over 500,000 volunteers over 35 years old from 10 different urban and rural areas across China, and the health of study participants will be closely monitored over the next few decades.

The project started in June 2004 and finished recruiting all half a million volunteers by July 2008. Each of the participants filled out a comprehensive questionnaire on a laptop covering their lifestyle, diet and medical history, completed a range of physical examinations, and provided a blood sample for long-term storage.

This staggering amount of data and the availability of blood samples for later analysis will be an enormously powerful and rich resource in investigating the environmental and genetic causes of many common chronic diseases among Chinese adults over the coming decades. The long-term follow up for deaths and hospital admissions among the 500,000 volunteers has just began, helped by a recent grant of £2.5 million from the Wellcome Trust.

CTSU’s work has shown that high-quality, large-scale medical studies can be carried out in China efficiently, swiftly and economically, providing clear evidence about the efficacy of treatments and revealing risk factors for common diseases. The collaborative centre announced today at Fuwai Hospital will cement this work for the future and add to CTSU’s capabilities in China.