As the rain begins to fall on Tanzania's Tarangire National Park, thousands of zebra, wildebeest and giraffe will begin one of the world's greatest migrations. But many of the herds trampling across the grass at the foot of the Rift Valley highlands are falling in number - and scientists do not know why.

To find out, they are using a new 'photo-fit' system that can recognise individual animals by their unique skin patterns, which are as distinct as a human fingerprint.

The park, dotted with muddy water holes and ancient baobab and acacia trees, has the highest diversity of migratory hoofed mammal (ungulate) species in the world. The animals move out of the park as the wet season begins, in search of new feeding and calving grounds. They will make the return dry season journey in June, to take advantage of the permanent water of the Tarangire river.

Numbers of wildebeest have fallen from 50,000 to 6,000 in the past 20 years, and numbers of antelope species, such as hartebeest and oryx, have declined by 90 and 95 per cent respectively. Confusingly some species - zebra, giraffe, gazelle and buffalo - have remained relatively stable. To understand such contrasting fortunes, scientists from America's Dartmouth and Utah universities are working to determine whether habitat loss, changed food sources, or hunting - or a combination of all - is responsible.

Traditionally animals have been tracked by being captured and tagged, but that is 'expensive and invasive', says Dartmouth's Doug Bolger. The aerial counts conducted every few years by the Tanzanian authorities don't provide comprehensive data. So the scientists have turned to computer-assisted photo identification - the first time the method has been used on such a large scale. 'This new technology allows us to get the best handle on what the population is doing,' Bolger says. 'Is it increasing, declining, is our response sufficient to offset mortality, is high mortality happening in or outside the park, and what should management do?'

The scientists hope that by helping to understand the impact of human activity, and studying birth rates and breeding sites, their research will provide strategies to help wildlife managers to conserve large mammal migrations throughout East Africa.

'What we'd like to understand is why some migratory routes have shut down,' says Bolger. 'By analysing the movement of certain species, we hope to understand what makes a landscape they will pass through and what won't.' Other factors are whether animals always return to the same calving grounds, and what happens when a food source is blocked off.

The team identify an individual animal by its stripe width, colour and shape, the distance between the marks and whether it has unique characteristics such as scars or, in the case of some wildebeest, broken or deformed horns. Only a handful of projects worldwide have used this individual pattern recognition technique so far, on work with marbled salamanders in the US and whale sharks off the coast of Australia.

'Photo mark-recapture hasn't been used on wildebeest before,' says PhD student Tom Morrison. 'There was some scepticism that it would work - but there are lots of animals with natural variability, so there is huge potential for using this technology.'

Large numbers animals are photographed according to strict criteria - a right-facing animal at a right angle to the camera, for instance. To help, the environmental charity Earthwatch provides a stream of volunteers.

Hundreds of digital images are collected in the field each day and the animal's stripe or spot pattern is mapped using a 3D model. Custom-built software then extracts the pattern and compares it with a database of previously photographed individuals. 'What we're interested in is the probability that this is an animal that we "captured" two years ago - if it is, that tells us that it's still alive. And if we don't re-photograph it, then we can estimate what the survival rate is,' says Bolger .

At a later stage the figures will be crunched through another computer program, to generate estimates of population size, survival and reproduction rates. 'We're still at least a year away from being able to use all this data to come up with population estimates and survival rates,' says Bolger.

But as more and more animals are added to the researchers' photo albums, the difficulties the herds face on their trek across the picture-perfect savannah come a little closer to being understood - and protection is a step closer.

Great migrations under threat

Serengeti-Mara

The migration of wildebeest and zebra from Tanzania's Serengeti national park into Kenya's Masai Mara reserve is one of the greatest natural spectacles on Earth. More than 2 million herbivores - about 200,000 zebra, 500,000 Thomson's gazelle and 1,500,000 wildebeest - thunder up to 700 miles northwards across East Africa's plains at the beginning of the dry season in June. Today meat poaching to supply local food markets is considered to be the most serious threat, while agriculture is also encroaching upon the migratory routes.

Bison

The numbers of this 'American buffalo' were once so high that their thundering stampedes across the prairies could be heard from great distances. Hunted almost to extinction during the 19th century by white settlers who wanted their hides, they were also killed for posing a threat to the running of the growing railroad industry. Thanks to conservation efforts introduced after their numbers dropped below 1,000, the American bison now roams freely in protected areas, numbering around 200,000.

Southern Sudan

In 2007 scientists discovered what they believed to be the biggest migration of wild animals on Earth. An aerial survey revealed vast herds of gazelle and antelope on the move in southern Sudan in a region which had been assumed to have been denuded of its wildlife by years of civil war. They put the total number of migratory animals at 1.3 million, but poaching, oil exploration and fighting in Sudan all pose a threat to the survival of the migration and its species.

Monarch butterfly

Every year thousands of these black and tan coloured butterflies fly up to 3,000 miles south from their home in the Rocky Mountains to spend the North American winter in the warmer climates of Mexico and southern California. But illegal deforestation and habitat destruction in the highland fir forests of Mexico that are essential to the monarchs' survival has led to a drop in numbers.

• Visit the Earthwatch website to find out about volunteering in Tarangire National Park