Stools of the trade

Developments in genetics have made DNA a cost-effective and efficient tool in studying wildlife. Poo is a valuable commodity, writes ANTHONY KING

SCIENTISTS studying animals in the wild now have an alternative to trapping: collecting poo in the woods. It’s just one of many ways in which modern genetics has revolutionised wildlife biology.

In India, waste, or “scat”, is brought to the lab, and tigers can be identified through their DNA “fingerprints”, as they can be in forensics. “This way of obtaining information on specific individuals is far less expensive and time-consuming than, say, capturing or recapturing marked individual tigers,” according to US wildlife biologist James Nichols. It’s also safer.

Ten years ago it cost millions of dollars to sequence the DNA of a single individual; today scientists are working towards the $1,000 genome. The gains mean it is now efficient and cost-effective to use DNA to study wildlife.

Irish scientists are ahead of the posse in this regard. An all-Ireland census of pine martens is published in the journal Mammalian Biology this month. The count for this rarely seen carnivore relied on a scat survey and on DNA analyses.

Ecologist Dr Declan O’Mahony reports an estimated population of 2,700 pine martens in the Republic and 300 in Northern Ireland. “It is probably our rarest terrestrial mammal,” says O’Mahony, who adds that the official figures for the Republic of 3,000-10,000 individuals can now be considered unrealistic.

The pine martens’ “favourable conservation” status should be revisited, he says, given the results, and a conservation plan put in place. They are very susceptible to human persecution and are slow to breed, he adds, and common in just half the country.

The geneticist Dr Catherine O’Reilly of the molecular ecology group at Waterford Institute of Technology developed the technique to identify pine martens through scats by looking at a small piece of DNA from the mitochondria, a structure inside cells.

She can also sex them by looking at differences on the X and Y chromosome using a technique called real-time PCR. “With scat, you isolate pine marten DNA from the epithelial cells that are flushed off the gut,” she says.

Trapping mammals can be difficult and time consuming, so O’Reilly has developed DNA tests for otters, foxes and small mammals such as shrews and mice. Last month a volunteer reconnaissance of churches returned bat droppings to her lab. This will allow the resident species to be identified without any disturbance or stress to the animals themselves.

O’Reilly says there are currently 10 pine martens in Portlaw Forest in Waterford. Most people who walk in the woods would be amazed that pine martens are about, she says, and she rarely sees them. “Pine martens love blackberries. At this time of year you will find purple scats all over the place.”

The small mammals that pine martens eat also turn up in their scat, and O'Reilly recently used molecular techniques to identify this prey. She also studies otters and other mammals as part of the Mise project ( miseproject.ie).

Dr Emma Teeling’s bat lab at University College Dublin studies bat evolution in Ireland and overseas, and her work has implications for human health (see panel, below). Teeling first studied zoology and animal behaviour, but soon immersed herself in genetics. “To understand evolutionary biology, you need to study the material it acts on,” she says.

DNA upturned the apple cart in bat biology. So-called “cryptic species” have been uncovered throughout Europe. For example, in the mid-1990s the common pipistrelle bat – often seen feeding around urban streetlights – was found to be two species.

“Human beings are a visual mammal. When we look at cryptic species of bat in the hand, the species look exactly the same,” Teeling says.

Field ecologists were already suspicious of the pipistrelle, because some used sonar calls at a higher frequency (55 kHz) while others used a lower frequency (45 kHz) and had slightly different face colouration.

“When genetics came on board and proved they were two different species, it was a case of ‘I told you so’. But we had no way of proving it up until then,” says the naturalist Conor Kelleher.

A student research project at the University of Limerick aims to identify insects eaten by the two pipistrelles from the DNA in their droppings. Prey eaten by pipistrelles will be compared to see if their diet is the same, says project supervisor John Breen. Traditionally scientists would identify insects as fragments in the droppings.

Ireland’s bat count stands at nine species, but Kelleher believes we probably have a 10th – Brandt’s bat. There has been just one record from Wicklow. It will take genetics to prove he is right. Telling the difference between Brandt’s bat and the whiskered bat is extremely difficult by sight alone. The Brandt’s has a slightly higher cusp on an upper pre-molar tooth, which measures about a millimetre.

Teeling says you can’t possibly mix the two species up once you look at their DNA. They are not even closely related. “It’s just that they found the same solutions to questions of how to inhabit the environment, where to roost, what to feed on,” she says.

The molecular techniques being developed in Teeling’s bat lab will provide hard evidence of a populations health. “If you have to make a conservation choice, you are better off conserving the most variable population,” she says. Similarly, a fall in the genetic variability of a species indicates trouble ahead.

Teelings lab this year published a paper on identifying bats from droppings. “We are going to be able to amplify entire genomes, probably from droppings the size of a full stop, in the next five years,” she says.

Her postdoctoral researcher Dr Sebastien Puechmaille studied the bumblebee bat, considered the world’s smallest mammal. The bat is split into two populations; one in Burma (Myanmar) and the other in Thailand.

The bats are still diverging from one another, with one group evolving a higher sonar pitch. It is open to debate whether they are already two species. Teeling says these bats show evolution in action, signed in their genes.

Long-living old bats

For their size, bats age remarkably well. “Bats don’t age the same way as other mammals. They live a ridiculously long time given their high metabolic rate,” says bat geneticist Dr Emma Teeling of UCD. She is studying how bats halt ageing, with discoveries in this area possibly giving insights into the human ageing process.

Most small mammals run their metabolic engine at full throttle and burn out after a few years. Bats can live for decades.“How do they deal with the metabolic stresses that come from flying?” asks Teeling. Our hearing is often first to go, yet bats’ hearing is critical to their survival and they can live for 10, 20, 30 years and longer.

“Once we work out how they can do this, then we can look within our own genomes and see what we need to do,” she says. For now we don’t even know all the causes of ageing.

“The future ultimate will be gene therapy. But in order to work out which parts we need to correct, we need to understand which parts are going wrong. We still don’t know that. It is only in cross-species comparisons that you can uncover these answers,” says Teeling.

The oldest known bat in the world is a Brandt’s bat, says the naturalist Conor Kelleher; this species may or may not reside in Ireland (see main story). “It was ringed in southern Russia, in 1964, in the wild and then released. And then it was caught again 42 years later. It still had the ring on it. So it was at least 42 years of age.” The life strategy of bats is to live a long time and have just one or two young each year.

A recent European Research Council award will run for five years and allow Teeling to hire five new researchers. Over those years she will capture greater mouse-eared bats (Myotis myotis) in Brittany, France, and take a small sample of blood. With a mere 80 microlitres, she will sequence every gene that is expressed. The bats will then be released and perhaps recaptured. “They have to be released and be happy, fat, healthy bats and stay that way for the course of the project,” says Teeling.

Why do bats live so long? Teeling attributes it to flight. It allows you to lose your predators, especially if you fly at night, and allows you to invest more in genomic maintenance and health. Teeling hopes to uncover the secrets of their longevity and “halted ageing” in their DNA.