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When the Spanish arrived in South America they caused the catastrophic demographic collapse of indigenous people and their livestock.
This had a major ecological impact which is now preserved in lake sediment, as reported in a new paper published in the Journal of Archaeological Science.
During the rise of the Inca Empire (in modern-day Peru) in the fifteenth century, what is now a small wetland in the mountains was then a small lake known as Marcacocha. It provided a vital stopping-off point along the trade route linking the lowlands of the Amazon to the highlands of the Andes.
Dr Alex Chepstow-Lusty, a researcher at the University of Sussex and first author of the paper, has been examining the tiny organisms that once lived in the lake, in the hope of learning more about the great Inca civilisation.
He has been using a perhaps unlikely scientific tool: llama droppings.
'There is a road passing the lake which was a highway over the mountains,' says Alex.
'It was once used by caravans of up to a thousand llamas, carrying things like maize over into the jungle and bringing back items like feathers and coca leaves.'
As the llamas watered themselves along the edges of the pool, they inevitably defecated. Known as llama beans, their poo provided food for a number of organisms living in the water.
Dr Anne Baker, a mite researcher at the Museum and a co-author of the study, says, 'We think one of these organisms is a tiny aquatic mite belonging to Hydrozetes, a member of the mostly soil-dwelling Oribatida.
'While the mites don't feed directly on the beans, they may well have eaten the broken-down remains of them that ended up in the water. As Hydrozetes feed on rotting plants, they may also have eaten lake edge vegetation damaged by being trampled by the large animals.'
'This indicates that the number of mites in the lake sediment changed in relation to the number of beans that were deposited around and in the water over time,' says Alex.
'The number of mites clearly trace the rise and rapid collapse of the Inca Empire, as reflected in changes in size of the passing llama caravans.
'Hydrozetes even showed a peak when the Spaniards introduced their animals from the Old World - cows, horses and sheep - and a dip when these animals disappeared because there was no one to care for them after smallpox arrived around 1719 and killed nearly all the surviving indigenous people in the area.'
The large volumes of llama beans were also the perfect food for a fungus known as Sporormiella. It was the spores of this microorganism that were of interest to Alex and co-author Dr Mick Frogley of the University of Sussex.
This is because Sporormiella spores found in the sediment of lakes around the world are increasingly being used as an indicator of ancient large mammals such as mammoths. By seeing at what point in the sedimentary lake cores the spores abruptly stop, researchers can use this as an indication of when those large animals went extinct - or so the theory goes.
But Alex, Mick and Anne believe this idea may need a rethink.
'We found that the levels of Sporormiella were not necessarily an indicator of the number of large mammals - in this case llama, and later the livestock introduced by the Spaniards - living in the area,' explains Alex. 'Instead they were reacting to other events, such as lake level fluctuations.'
These ecological changes can create very sudden cut-off points in the record of the fungus, which may then be interpreted as an extinction event. In some cases there could have been a genuine extinction, but in other cases the animals could have survived longer than the lake cores suggest.
It all comes down to how far the spores of the fungus disperse, which evidence suggests is only a few metres from where the faeces are deposited, meaning they are localised around the edges of lakes and rarely make it into the centre. This raises issues for studies that only sample sediment cores from the middle of large lakes.
'This study will help people think about their interpretation of Sporormiella,' says Alex. 'The spores may be saying more about the environmental conditions of the lake at that time, rather than about the herbivores that may have been living around it.'
The researchers hope that what they have uncovered can help bring about a new technique to reveal the numbers of large herbivores that once lived in a landscape, not just by looking at the relative abundance of the fungus but also examining the mites they are found with.
'The identification of the mites was fundamentally important to this project,' explains Anne. 'Putting a name to them allowed us to get a picture of what conditions were like when they were alive, because mite ecology evidently has not changed through history.
'Interestingly, we also found a group of mites in the more recent samples whose identifications showed that they were terrestrial species and so their presence indicated the change of Marcacocha from a lake to wetland.'
Such a technique could also help in uncovering the fate of civilisations that were reliant on livestock but which left few other clues as to their existence.
'Mites live in most regions of the world,' says Alex. 'They could potentially be used to look at the collapse of the Viking colonies in Greenland in the 1350s, for example, as they were dependent on their sheep.'
Similar work now needs to be carried out in other small lakes in Peru and elsewhere to check whether using mites as a technique holds its reliability.
If so, the microorganisms living in ancient sediments could be a very powerful tool indeed.