Human evolution

Molecular Archeology Puts Artifacts in Perspective

Buried inside the Earth, lay secrets. Archeologists piece together histories often lost to time as they unearth human remains and their long-lost possessions.

Where archeologists exhume secrets from the soil, molecular archeologists uncover secrets lying inside human remains. By piecing together ancient DNA, molecular archeologists can more definitively answer questions about our past.

“Some people in my field consider themselves to be molecular archaeologists as we tend to work with archaeological remains and use an archeological context to help infer the genetic patterns we see,” said Ripan Malhi, an associate professor of anthropology at the University of Illinois and affiliate of the Institute for Genomic Biology (IGB).

While the day-to-day rigor of being a professor may not seem illustrious, over the course of the year, Malhi’s lab makes amazing discoveries.

Ripan Malhi is a molecular archeologist at the University of Illinois. Photo by Brian Stauffer.

Ripan Malhi is a molecular archeologist at the University of Illinois. Photo by Brian Stauffer. ©

The Golden Era of ancient DNA

“We can do things now that we haven’t been able to do before,” Malhi said. “I like to say that ancient DNA is in a golden era. When I was a graduate student working on ancient DNA, it probably would’ve taken me years to sequence one complete mitochondrial genome and now we can do that in a week or so.”

Today Malhi’s lab studies complete genomes as well as DNA passed down from mothers to their offspring (called mitochondrial DNA) and from fathers to their offspring (called the y chromosome) to infer the evolutionary history of populations and species. Currently, research in the lab is split into two research areas: the evolutionary history of Native Americans and evolutionary genetics of non-human primates.

Last year, his lab found an ancestral link between ancient remains and their living descendants.

“The community members were really happy about the results because their oral histories have said that they’ve been there for a very long period of time as well,” Malhi said. “Now through scientific and DNA data we are able to show this connection in a different way. Being able to show that connection with something that they’ve known to be true was really satisfying.”

While most archeology doesn’t include DNA analyses, they can be vital to distinguish cultural processes from biological processes, Malhi said.

In the past, movement of arrowheads or pottery from one region to another indicated that a population might have moved. But in reality, Malhi said, a number of other factors could explain the distribution of artifacts.

“By combining DNA evidence with this cultural data we can distinguish whether people are moving or cultural artifacts are being traded from one community to the next,” Malhi said. “Using DNA evidence, we can show how genetic variants moved across the geographic landscape after neighboring groups intermarried.”

This work does more than solidify community backgrounds and establish migration patterns. It can also illustrate evolutionary process and show us how we may evolve with other organisms. One of Malhi’s students is studying how infectious diseases brought over after European contact affected Native Americans’ genomes.

How molecular archeology works

First, Malhi works with Native American communities to find out what questions they would like to answer. It’s a first step that scientists have often skipped in the past.

“They know their own history better than I’ll ever know it,” Malhi said. “They can look at the genetic patterns and give us ideas about what those patterns may represent.”

Malhi interacts with Native American communities and museum curators to discuss what the community members hope to learn from DNA analysis, the questions he wants to address, and how best to extract DNA from the ancestral remains.

Next Malhi visits the communities or museums to pick up the remains. Sometimes he has the chance to be onsite during the excavation as the archeologists collect the remains with gloved hands to prevent modern DNA contamination, from their skin cells and microbiome.

At Malhi’s lab, the remains undergo a surface decontamination to ensure that modern DNA is not included in the final analysis. Then they drill out a sample about the size of a cavity from the bone or tooth. The sample is ground up to a fine dust then sequenced and analyzed.

Finally Malhi is able to look for genetic patterns by combining the new results with published results from various databases and combines that information with other anthropological information, such as the community’s oral histories or cultural artifacts from the archeological site.

Today molecular anthropologists like Malhi can turn DNA fragments that are only around 200 or so base pairs in length into a complete human genome made up of about three billion base pairs.

It’s more than a job

From interacting with Native American communities to seeing his students begin successful careers, Malhi said his job is really satisfying.

“It’s always fun to go back to communities and report results and see how people take those results and incorporate that knowledge and then ask new questions,” Malhi said. “I am now at this stage in my career where I have my students presenting at meetings.  They spent years working really hard developing their research. When they put it all together and present it and the audience gets excited about it and the students are excited about it—that’s a really good feeling, too.”

Malhi also values being a part of the Summer Internship for Native Americans in Genomics (SING) workshop, which facilitate discussions about how genomic research is conducted and to create a support network for Native American students in the sciences.

Malhi earned a Master’s degree and a doctorate in anthropology at the University of California at Davis. He also took molecular biology, population genetics, and other biological courses to complement the anthropology curriculum. Today a student interested in this field can pursue graduate degrees in biological or molecular anthropology.

“I recall hearing about a genetic study where an Italian population did not get heart disease because they had a natural genetic variant, and I realized there’s lots of genetic variation out there that can be interesting and useful,” Malhi said. “Then I learned about connections with history and how you can infer human history from DNA variation, and I was hooked.”

The Institute for Genomic Biology (IGB) is dedicated to interdisciplinary genomic research related to health, energy, agriculture and the environment. The Institute’s cadre of world-class scientists, collaborative laboratories, and state-of-the-art equipment create an environment that inspires discovery and stimulates bioeconomic development at the University of Illinois. For more information about the SING workshop, visit http://conferences.igb.illinois.edu/sing/.

Tracing Neandertal Territories in the Mountains of Southeast France

Day of Archaeology 2013 for me means being away on 2 months of fieldwork in the southern Massif Central, France.  I’ve been contributing to DOA since 2011, and if you look back, it’s clear a lot has changed  since then (see my four 2011 posts, and 2012). After my PhD I was searching for a postdoc for several years, ran out of time and money to keep looking, and ended up seredipitously with a contract to write a book about humans and birds in prehistory.

I thought that would be it, and that the 2013 Day of Archaeology would take place without a contribution from me. But it seems that archaeology wasn’t quite done with me…

My workspace at the field station, Laussonne, Haut Loire

My workspace at the field station, Laussonne, Haut Loire

As I wrote in a postscript comment to my post last year, only a few days after writing about the difficult process of changing paths from a research career to one focused on writing and wider communication, an email dropped into my inbox from the European Commission offering the very last postdoc funding I applied for- a Marie Curie Intra European Fellowship to work in at the PACEA lab, Universite of Bordeaux. After a lot of soul-searching on the wisdom of doing another 180 degree turn in my life trajectory, and talking with my husband about him coming out with me, I decided to go for it. And so here I am, in the mountains of the Massif Central!

Laussonne map

Laussonne map

The field station for Archeo-Logis at Laussonne, Haut Loire

The field station for Archeo-Logis at Laussonne, Haut Loire

My postdoc is focused on two elements: training in a new skill (the Marie Curie Fellowships are especially concerned with career development), and applying this method to an archaeological context. I’ve written on my own blog in more detail about my project, which is called TRACETERRE. This stands for “Tracing Neandertal Territories: Landscape Organisation and Stone Resource Management“. It’s part of a larger collaborative project directed by my boss, Jean-Paul Raynal, and Marie-Helene Moncel.

Essentially I’ll be learning a detailed geological technique called petro-archaeology, that allows us to determine where in the landscape Neandertals were obtaining the raw materials to make their stone tools. Specifically, we are especially interested in the flint sources: most of the geology in the area is igneous, which means it comes from volcanic action (the Massif Central is a world famous centre for volcanology, where you can see virtually every type of volcano and lava).

Sancy Massif

Sancy Massif, north of where I am based, showing volcanic formations

It’s possible to make stone tools from these kinds of rocks, but they are often very hard, and can also be coarse. Flint is a sedimentary rock, meaning it forms from the slow accumulation of mineral deposits. Flint is famous for the high quality tools that can be made from it, because of the predictable way it fractures. It’s often associated with Cretaceous chalk deposits, such as the big cliffs in the southern UK, where you can see black bands of flint nodules. So flint forms in marine contexts, but it can also form in other situations such as in lakes.
Although there are few primary sources of flint in the Massif Central (i.e. outcrops of rock containing flint), there are many different secondary sources. These can be eroded outcrops, material washed into river gravels and other kinds of sources. My training will be in identifying these secondary types of sources, based on the way the outer surface of flint cobbles changes during the process of first formation, erosion and later exposure at archaeological sites.

Some of the geological reading I've been getting up to speed on. Volcanoes galore!

Some of the geological reading I’ve been getting up to speed on. Volcanoes galore!

Because there are more than 70 different secondary sources in the region which have been painstakingly identified over more than thirty years (by Paul Fernandes, who will train me), this is too much to try to attempt to learn in two years. So I will be using a source-centred approach, where I look at one flint source, and see how this particular rock has been used by Neandertals. In particular, we are interested in where this rock ends up: which caves or open-air archaeological sites is it found in? And secondly, in what form does it occur: as finished tools, raw blocks, or flakes of stone that have been struck off blocks (cores) but not yet made into tools.

Finding these things out can tell us a huge amount about techno-economics: the way in which Neandertals were choosing to organise their exploitation of resources on landscape scales. For example, working out which types of technology they used to make tools and which stages of tool production occur where can reveal the level of investment of energy: were they making tools quickly, and dropping them soon afterwards? Or were they carefully choosing which kinds of tools to make, and which ones to take with them in toolkits, maintaining them by re-sharpening? Both these strategies can be used as adaptations to different situations, particularly the level of mobility.

A handaxe, one type of tool Neandertals seem to have carried with them as part of mobile toolkits, which could be re-sharpened and used in many tasks. This one is from near Bournemouth, UK

A handaxe, one type of tool Neandertals seem to have carried with them as part of mobile toolkits, which could be re-sharpened and used in many tasks. This one is from near Bournemouth, UK

The question of Neandertal mobility is also a key reason for studying in such detail the different sources of stone used. We want to know where the stone from a flint source was going: which sites is it found in? How far was flint being transported, especially in comparison to other stone types? We can even begin to work out the paths taken through the landscape by Neandertals: did they have to cross rivers, high mountainous areas? Which passes would have been likely to be used? We also plan to excavate at the flint source itself, to see what activities were taking place, and also which tools came from other places in the landscape.

We can then begin, by combining all the geological and techno-economic data, to build up a detailed understanding of the inter-connections between different parts of the landscape that Neandertals were living in. And this is just the stone tools: other parts of the archaeological record, such as animal bones preserved in caves, are studied by other project members. We can use these to determine things like what season people were living at sites, and where they were probably hunting the animals in the landscape.

Gravel bar system, Switzerland- one example of a secondary source of stone. Image used with permission via Creative Commons: " I, Paebi [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC-BY-SA-2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/2.5-2.0-1.0)], via Wikimedia Commons"

Gravel bar system, Switzerland- one example of a secondary source of stone. Image used with permission via Creative Commons: ” I, Paebi CC-BY-SA-2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/2.5-2.0-1.0)], via Wikimedia Commons”

All this creates a web of the palaeo-landscapes that Neandertals were inhabiting. But the impact of sourcing flint tools goes even further, because if we can map the extent of inhabited landscapes, we can start to think about territories. This is crucial because territories are not just regions full of resources- they probably were also involved in defining social interactions between different Neandertal groups. This is something we are still learning how to measure, but it has huge significance because different kinds of territories and social interactions suggests particular cognitive capacities. This is of course one of the key areas of research in human evolution: how did Neandertals differ from us, and how were they similar? Did they have similar webs of social connections, or were they living local, isolated lives in small groups that did not regularly meet? If this was the case, how did they find mates, and prevent huge in-breeding? All these fundamental questions can be advanced by new data and investigations such as the research I am doing.

Right now, I’ve only been here just over a week, and am only one month into a two year postdoc. So there’s a long way left to go. But it’s very exciting, and I hope to start the petro-archaeology training and looking at the flint collections very soon. Meanwhile, there’s always time on fieldwork to have a day off, check out the local wildlife, cuisine and culture, and enjoy some of the lovely sunsets in this region. Very different landscapes to when Neandertals were living here!

 Sunset at Laussonne

Sunset at Laussonne

I am funded through a European Commission Framework 7 Marie Curie Intra-European Fellowship for Career Development, and I work at the PACEA laboratory, UMR-5199, Universite Bordeaux 1.

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