What is he hiding?

New research examining ancient skeletons aims to tell us more about how lifestyle changes impact our biology

SOMETIMES YOU have to look back to look forward. And a new study is reaching deep into our past, across tens of thousands of years, as our ancestors moved into Europe and their lifestyles changed.

Many questions remain about those early modern humans. How did they live? Did particular groups interact? How did their environments and food sources affect their health? And how did major lifestyle changes – such as the switch to agriculture – help shape their genomes over time and, ultimately, influence ours?

A major four-year project led by Dr Ron Pinhasi at University College Cork has just kicked off, and it will use a battery of high-tech approaches to mine information from hundreds of fossil skeletons discovered around Europe.

“It’s extending back 45,000 years, which is pretty much from the first arrival of anatomically modern humans into Europe,” says Pinhasi, a lecturer at UCC’s school of archaeology who secured funding for the study from the European Research Council.

The study’s time scope encompasses the overlap with Neanderthals, the Stone Age and the switch to agriculture. “Basically the project wants to look at the whole length of this period because it is aiming to target several major historical events in the past, in human evolution and also the transition to agriculture,” he says.

And the particular questions they ask about the fossil remains will vary according to the period in which the individuals lived, according to Pinhasi.

DNA from the earliest fossils will hopefully yield clues about affinities these early Europeans may have had with African populations, and whether genes of interest – such as those involved in nutrition – were already starting to change.

Later on, about 25,000 years ago, the last Ice Age hit. “Most of Europe was covered in ice, and populations mostly existed, for the most part, in the south of Europe,” says Pinhasi.

“This population contraction into pockets had a major effect on genes in human populations – and there was a bottleneck because of the cold, there was a reduction in number. Then 10,000 years ago climate was becoming like it is now and the populations were moving out of these pockets and recolonising Europe. After this, we have the event of the first farmers arriving.”

The project will analyse DNA from the skeletons, and will also use sophisticated computer-based simulations to build up a more complete picture of where and how these humans lived and whether populations interacted with each other.

Aside from the DNA analysis, starch remains on the teeth of skeletons could offer information about plants in the diet, while isotopes in the bones should tell whether the owners ate more land-based meat or marine animals.

The project will also match the dates of individual fossils with existing climate data for the period and look at bone anatomy to see whether the adoption of agriculture and new technologies was linked to changes in robustness and activity.

“Once we put it all together across Europe it’s almost like sampling across the whole continent,” says Pinhasi, who is collaborating with experts in Trinity College, Dublin, York in the UK and Mainz in Germany.

But will they have enough skeletons to cover such a massive period of history?

“We do not have the same amount of material throughout the timeframe, or even throughout space. There are no skeletons at the moment from about 40,000 to 45,000 years ago, so realistically you are starting more about 35,000 years ago,” he says. “It’s not our fault in a sense, this is the fossil record, it gets more patchy as you go back in time. But because of the simulations and the amount of information we can get from any specimen genetically, even one or two specimens can give us a lot of information.”

Ultimately the project will build up a database of genes that can be compared with today’s humans, and if a gene is of interest it can be tracked back over space and time, according to Pinhasi.

“We should have no problem to look back in our data and be be able to say at least whether a particular [gene variant] already existed before the transition to agiculture – maybe for lactose digestion, diabetes or changes in pigmentation, but also perhaps other disease and genetic information that are found in modern humans. We will have all of the genes mapped from different periods,” he says.

“The importance of our project, beyond being blue sky, is that we are doing it systematically and methodically and we can create libraries so we have the code and you can go back and look at it.”

MINING CLUES FROM ANCIENT DNA:

DNA can tell us plenty about a person – if it’s in good condition. But how do you handle DNA extracted from the skeletons of humans who lived thousands or even tens of thousands of years ago?

“The challenges revolve around one issue – that DNA degrades with time,” says Dan Bradley, professor of population genetics at Trinity College Dublin.

He’s collaborating on a project led by Dr Ron Pinhasi at UCC to analyse the genetics of samples dating back through history to when early modern humans appeared in Europe.

But the genetic material that comes from a fossil, or “ancient DNA”, can be tricky.

“If I get a fresh sample of someone’s DNA from a cheek swab or blood sample today, it’s perfect and easy to work with,” explains Bradley. “But if you are dealing with a sample from remains like bone that has been lying in the ground or in a cave for thousands of years, the DNA naturally breaks up and degrades and other types of DNA colonise the bone, like bacteria and fungus. So the DNA you want is a small proportion of what’s there, and it may be damaged.”

Previously, researchers would amplify particular stretches of DNA from the samples, and one of the biggest problems was that ancient DNA could be contaminated with modern material from humans.

“If a bone has been handled by a number of people, their DNA is on the bone. So you could end up a curator or an archaeologist instead of the target person.”

The current project will use next-generation DNA sequencing methods, which makes contamination less of an issue, because it allows researchers to decode lots of DNA and identify the sequences of interest.

The study is in its early stages, says Bradley, but the plan is to look at interesting genes and “put flesh on the bones” of how our ancestors lived, their genetic geography, population structures and how lifestyle changes like the switch to agriculture affected genes.

“It has a grand scope, it looks very promising,” he says of the overall project, which involves other international collaborators. “It has this broad vista . . . it’s very exciting.”