Inside New Zealand's ancient DNA lab
Thursday, 5 May 2016
Euphrates Cave is about 1000m above sea level in Kahurangi National Park, northwest of Nelson. It's difficult to reach. Helicopters are generally needed to access the vicinity. Visitors then have to abseil down a buttress cliff to reach the entrance.
Drs Jamie Wood and Janet Wilmshurst were there with colleagues in February 2010. Just inside the cave, they spotted something they thought might be coprolite – or mummified bird droppings. 'They were just sitting there on a rock,' Wood says. Wood and Wilmshurst are palaeoecologists and suspected the find might be from moa bird, extinct for hundreds of years.
Back in the the Long Term Ecology lab at Landcare Research in Lincoln, Wood analysed the 35 coprolite samples from Euphrates, and found they were from upland moa. The oldest were about 7000 years old, the youngest perhaps 700.
So, yes, this is a story about crap, droppings, dung, faeces, egesta, excreta, poop, stools and to some, meadow muffins.
We'll also spend some time on the subantarctic Auckland Islands, revisit the year Polynesians and their rats arrived on these islands, and look at soil samples from New Zealand swamps to figure out what all this means to contemporary New Zealand.
**READ MORE:
* Ancient DNA from Spain's 'pit of bones' could reveal the origin of Neanderthals
* Moa extinction an 'irreplaceable' loss
* Can New Zealand really be pest-free?**
Coprolites are important because there's often no better way to obtain knowledge about the ecology of extinct or endangered species. If you want to know what moa ate, for example, analysing their bones or gizzard stones doesn't get you very far, say Wood and Wilmshurst.
But if you analyse their poop using the latest DNA extraction and analysis techniques, plus things like radiocarbon dating, then you learn that the moa from Euphrates ate 67 different plants. They grazed in southern beech forests and tussock herbfields. These upland moa were one of the smallest of nine species at 1m tall.
You can also get solid data on a bird's diet and range before human arrival if you can collect enough bird stools from enough locations. Which is what Wood, Wilmshurst and others helped do helped do when studying kakapo faeces.
The beloved flightless parrot was once everywhere in New Zealand, from Northland to Southland. By some estimates, kakapo was once the third most common bird on these islands. Today there are 123 alive, after a record-breaking season that saw 46 chicks hatch.
The coprolites the pair found at Euphrates were exceptional. Normally these things are found buried under a layer of dust and debris, often a centimetre or two from the surface. There's often nesting material, bones and feathers as well.
Coprolites are found in caves and under overhangs, the sorts of places that sheep find when the weather's bad, Woods says. Moa and other birds did similar once. These places haven't been wet for centuries. New Zealand's coprolites are not fossils, but rather dried out specimens, Wood says.
So who are these people fascinated by ancient bird dung? Wood and Wilmshurst turn out to be pretty straightforward. They're fit because they get out of the lab and find rock overhangs that are well off the beaten path. For them, a tramp isn't just a tramp but a research expedition that might result in an important find. Their friends and partners have got used to them wandering off in search of caves.
Both are from modest backgrounds. Wilmshurst grew up in Britain and got a degree from Plymouth University, the first in her family to attend university. That led to a Ph.D from Canterbury University in 1995 and then to her current role as director of the Long-Term Ecology Laboratory at Landcare's Lincoln offices. Family and friends back home have been known to ask, 'You study what, where?' She's a good enough scientist to have landed several Marsden grants, considered the most prestigious science funding in NZ.
Wood recalls a boyhood fascination with NZ natural history and birds. He was also the first in his family to attend university. He got a geology degree in 2002 and a palaeoecology PH.D in 2007, both from Otago. He worked in an ancient DNA lab at Adelaide University before returning home to create a similar lab from scratch at Landcare.
Ancient DNA labs have to be scrupulously clean to avoid contaminating old stuff with new stuff. Working in Wood's lab at Lincoln requires full body suits and masks and a hard regime of cleaning. The place carries the permanent odour of bleach. By the time they get home at the end of the day, cleaning isn't a favoured task, Wood says.
Both have a deep interest in NZ natural history and nailing down important dates and events. Like: when did Polynesians arrive and moa die out? Scientific testing of human remains is largely tapu but they've got a proxy species, pacific rats. They can only have reached Aotearoa in Polynesian canoes, as stowaways or passengers, so the oldest rat evidence times the arrival quite rigorously, Wilmshurst says.
She led this early 2000s research and used a novel technique – dating distinctive rat-gnawed seed cases that were preserved in sediment. The result put an end to a long-standing debate about the timing of human arrival in New Zealand and confirmed other lines of evidence numerous findings by other scientists and Maori whakapapa: humans reached Aotearoa in 1280AD, plus or minus 30 years. Moreover, based on the wide dispersal of rat evidence, the arrival (of humans and rats) was sudden and everywhere. That is, there wasn't a slow trickle from Polynesia, but a fast flood.
Wood and Wilmshurst also participated in research dating the extinction of moa. Using radiocarbon dating of moa bones plus rat gnaws and excreta, the team dated effective extinction to about 1430AD and total extinction to about 1480.
Interesting, but what's the contemporary use of this science? In 2015, Wilmshurst led a paper tracing the invasion of a tree daisy on the subantarctic Auckland Islands. Was the tree daisy native to the islands or introduced? If introduced, was it a threat to the islands unique ecosystem? There was another possibility: Could Polynesians have introduced the tree daisy to the Aucklands, which are 360kms south of Stewart Island? Some were there briefly in the 13th or 14th centuries, the farthest south those sailors got, as far as we know.
Using paleoecology and historical records, Wilmshurst and colleagues showed the tree daisy was introduced 1807-10, probably by sealers. The tree daisy hadn't spread far across the islands in 200+ years and probably wasn't a threat. Spending resources on control or eradication was probably unnecessary, Wilmshurst says. There New Zealand, saved you some money.
Another example arises from the pair's work with soil samples taken from swamps on offshore islands in particular. Using a hand-held core device, they extracted soil that represented a 2000-year span of accumulation. Back at the lab, they analysed pollen and DNA and found the pre-human island forests were dominated by palm trees and podocarps. The current forests are largely native but not at all like the pre-human ones and are missing a 'suite' tree species.
The research overturned our view of what was natural vegetation on these islands. Such information can provide an important baseline for 'rewilding' offshore islands – making them predator-free and reintroducing appropriate plants.
For getting this deep into this poo story, you get a joke. Facebook and Twitter don't recognise the word 'coprolite' and both suggest using the word 'profiterole' instead.