From Neanderthals to insects, lifeforms leave traces in dirt

Perhaps a Neanderthal, or several, died in this Spanish cave. Or perhaps they just passed this way, never imagining their scant traces would be discovered 100,000 years later.

It sounds like science fiction – finding the DNA of ancient beings, not in their bones, but in the ground they walked on.

To quote The Atlantic writer Ed Yong: ‘‘Animals have a vast genetic aura that extends beyond their physical bodies into the world around them. Their DNA falls to the ground in balls of dung, zips through the air in blood-sucking insects, and leaches into the soil during decomposition.’’

Environmental DNA (eDNA) is everywhere, and it can reveal the presence of animals from dragonflies to whales, without the need to see them. A ‘‘DNA dipstick’’ can conduct, as Yong puts it, ‘‘a census of the natural world’’; collating and sometimes ruling out. (In 2019, University of Otago geneticist Professor Neil Gemmell used eDNA from the waters of Loch Ness to torpedo the myth of a resident monster.)

And now the method is being used to study our remote ancestors. An excited tweet in April signalled the incredible Neanderthal discovery: ‘‘Today we published a paper where we get Neanderthal DNA from cave dirt, and use that DNA to study Neanderthal history across thousands of years. We’ve worked on this for a few years now, I’m so excited for it to be out!’’

The tweeter was Dr Benjamin Vernot, a bespectacled population geneticist from the Max Planck Institute for Evolutionary Anthropology in Germany, lead author on a paper published in the journal Science.

The DNA found by his group revealed incredible details about individual Neanderthals. It appeared that not one, but two Neanderthal bands lived in one of the caves they studied; the original population replaced by a later group around 100,000 years ago.

‘‘We get human DNA from dozens of sediment samples from three caves,’’ he explained, ‘‘densely sampling the entire 40,000-year history of one site.’’

Vernot’s team found the Neanderthal DNA because they knew what to look for, and had the techniques to find a needle in a genomic haystack of unwanted DNA, from cave bears to bacteria.

Headline-grabbing creatures like penguins, or the super glam Neanderthals, are likely to have their genetic sequence stored in a data bank, ready for ID. But most animal species fall into the spineless (literally) hordes categorised as invertebrates – and only a tiny sliver of these worms, sponges, insects and mollusks can be identified with eDNA, a technique still in its infancy.

In New Zealand, Dr Andrew Dopheide and his team used eDNA techniques to calculate the fauna still living on Little Barrier Island; a sanctuary described by MBIE as ‘‘the most intact ecosystem in New Zealand’’.

Their work, published in 2019, led them to estimate the island was home to some 6800 arthropod species (invertebrate critters); excluding mites; including around 3900 insect species. This suggested over 13,200 insect species might be present throughout New Zealand, including 4000 species of Coleoptera (beetles); 2200 species of Diptera (flies); 2700 species of Hymenoptera (basically wasps, bees, and ants); and 1000 species of arachnid (spiders, mostly). Few of these have been described.

The group’s inventive use of eDNA processes allow us to imagine the once teeming biodiversity of our ancient forests. Poignantly, the single most abundant trace was left by an unknown beetle – an ‘‘undescribed member of the family Salpingidae’’.

As these creatures flutter and scurry from threats like invasive wasps, they are being lost before they can be observed, catalogued, or mourned.

Without genetic testing, we would likely never have known about Oligosoma salmo, a delightful creature a storm away from extinction. The Chesterfield or Kapitia skink was discovered in 1994, although for years no-one understood how special it was. It still clings to a narrow strip of the West Coast only a kilometre wide, just north of Hokitika. There are fewer than 200 left in the wild, and climate change threatens their perch by the sea.

There is something amazing about this tiny, glossy creature, the colour of fallen leaves. ‘‘The prehensile tail was discovered at the beginning of our research project in 2016,’’ says Lynn Adams, technical adviser for biodiversity at DOC.

‘‘As we were handling them, we realised that they were gripping on to our hands with their tails – their tail strength could hold their own weight. That hadn’t been recorded in New Zealand skinks. A prehensile tail [would have been useful] if they lived high in the epiphyte gardens and the wind-sheared vegetation of a coastal forest.’’

This no longer exists – what remained had been cleared for dairy farming.

Since its discovery, the Kapitia skink has lived a somewhat actionpacked existence. After its minuscule habitat was nearly wrecked in 2018 by a cyclone, an airlift to Auckland Zoo established a breeding population.

The Kapitia skink is related to the Alborn Coal Mine skink, found in the Reefton area, although they haven’t shared a common ancestor for at least 2.5 million years. To someone who isn’t a skink expert they look identical.

‘‘This is not uncommon; many skink species, including some which diverged earlier than these, can look very similar,’’ says Adams. ‘‘That’s why we need modern DNA techniques to sort the species out. Once DNA has sorted them into groups it becomes possible to find differences which enable them to be identified in the hand.’’

Some of these differences are subtle, she says. And some less so. Like a marvellous tail, just right for hanging off a lofty twig, in a lost forest by the sea.

‘‘I compare it to having a small new-born baby gripping your finger,’’ says Adams. ‘‘It’s always surprising that such a small delicate creature could have such a strong grip.’’

For years no-one understood how special the Kapitia skink was.