DNA tracks ancient Mediterranean farmers to Scandinavia

Mixing with native foragers led to modern genetic signature.

Geneticists analysing DNA from Neolithic burial sites in Sweden have made a surprising discovery. The genetic make-up of one individual — a female farmer known as Gök4 — bears a startling similarity to that of modern-day Mediterraneans. And the woman's genome provides clues as to how agriculture spread across Europe.

Modern Europeans’ genetic profile may have been partly cultivated by early Mediterranean farmers who moved to what’s now Scandinavia, where they paired up with resident hunter-gatherers.

DNA taken from 5,000-year-old skeletons previously excavated in Sweden unveils a scenario in which agricultural newcomers from the south interbred with northern hunter-gatherers, say evolutionary genetics graduate student Pontus Skoglund of Uppsala University in Sweden and his colleagues. Their findings feed into a picture of many early migrations of farmers into Europe, which often would have included interactions with local hunter-gatherers.

Pieces of DNA extracted from an ancient farmer’s remains buried in southern Sweden display gene variants most like those found in people now living in Greece and Cyprus, the scientists report in the April 27 Science. DNA retrieved from the bones of three hunter-gatherers interred on an island off Sweden’s coast contains distinctive gene variants that most resemble those of native Finns.

Most Europeans today possess genetic arrangements in between those of the long-dead farmer and his hunter-gatherer neighbors, Skoglund’s team finds. Breeding between culturally discrete cultivators and foragers contributed to Europeans’ current genetic makeup, the researchers propose.

“Our data suggest that northern European farmers originated in Mediterranean Europe and were genetically distinct from northern hunter-gatherers some 5,000 years ago,” says study coauthor and evolutionary geneticist Mattias Jakobsson, also of Uppsala University.

Ancient DNA in the new analysis came from cell nuclei, a form of genetic material inherited from both parents. Researchers isolated and studied from 1 percent to 3 percent of the nuclear genome for each excavated individual.

Jakobsson  says the new nuclear DNA evidence challenges a 2010 investigation that traced genes extracted from the remains of members of a 7,000-year-old farming culture in Central Europe to current residents of Turkey and areas just to its east. That study, led by human paleobiologist Wolfgang Haak of the University of Adelaide in Australia, examined maternally inherited DNA from cell structures called mitochondria and the paternally inherited Y chromosome.

Archaeological finds point to several routes into Europe for early Middle Eastern farmers, Haak says. A Mediterranean-based farming group may have reached Scandinavia 1,000 to 2,000 years after an initial expansion of farmers from further east into Central Europe, he suggests.

Farming’s rise “was by no means a uniform process across Europe,” Haak says.

Investigators generally agree that farming originated about 11,000 years ago in the Middle East and reached Europe by around 7,000 years ago. Debate has long revolved around whether waves of advancing farmers chased off European hunter-gatherers or traded cultural practices with native groups that then took up agriculture.

DNA links between the ancient Swedish farmer and nearby hunter-gatherers show that agriculture spread across Europe with the aid of genetic as well as cultural exchanges, Jakobsson says.

The result is strong evidence for the migration hypothesis. "If farming had spread solely as a cultural process, we would not expect to see a farmer in the north with such genetic affinity to southern populations,” says Skoglund.

But Wolfgang Haak, a human palaeobiologist at the University of Adelaide in Australia and a co-author of some of the mitochondrial studies, says that “one farmer from Scandinavia is certainly not enough to explain the spread of farming in places like Spain or Bulgaria and we definitely need more farmers from other parts of Europe”.

Another ancient DNA study, published this week in PLoS One, compares the mitochondrial DNA of Neolithic farmers and hunter-gatherers in northern Spain. The genetic variation amongst the farmers indicates that there was a complex pattern of settlement, with waves of colonization bringing small and different Neolithic groups into the region.

“Given the genetic evidence from studies of both modern-day and ancient DNA, I am convinced that farmers expanded in many different ways and under many different demographic scenarios,” says Haak. But Skoglund's study adds “an important piece to the big puzzle” of how farming became commonplace across Europe, Haak adds.

 “The technical advances in the genomic era now provide us with the necessary tools to tackle the different modes of the Neolithization in every corner of Europe with much higher precision,” says Haak.

There is also the tantalizing prospect that as understanding of the genetic basis of behaviour improves, it might be possible to comb fragments of ancient DNA for signs of behavioural differences between prehistoric populations. “In the future we might know a few genes that affect behaviour and we could go back and look into the hunter gatherers and see what variants of those genes are present,” says Mattias Jakobsson, a population geneticist at the University of Uppsala and a co-author of the Science paper. “But that’s not going to happen in the next couple of weeks at least.”

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The pollen signal of early neolithic farming along a habitation gradient in northern Drenthe

(2005) Bottema, S.; Cappers, R.T.J.; Kloosterman, A. 

ABSTRACT: It is concluded from the uneven distribution of megalith graves (hunebedden) and the presence or absence of surface (settlement) finds in northern Drenthe that the inhabitants of the Funnel Beaker culture were not evenly distributed over the area. Habitation seems to concentrate on the highest part of the Hondsrug and less on the lands to the west. It was studied whether this habitation gradient is reflected in the human impact upon the vegetation.

For this purpose sixteen pollen sites were investigated of which six gave information for the Early Neolithic.
The Early Neolithic was selected by radiocarbon dating and analysed with high resolution. In the pollen analysis the role of the anthropogenic indicators throws doubt upon their value for the archaeological record. Pollen production, distribution and precipitation of Artemisia vulgaris have been studied from modern vegetation. Pollen evidence from the Early Neolithic at various elevations, ranging from three-and-halve to nine metres above Dutch Ordnance Level, demonstrate the differences in vegetation at short distances. No palynological gradient paralleling the archeological record could be found.
Suggestions for prehistoric cattle keeping are compared with the management of nature reserves with primitive breeds. Alder may well have profited from the prehistoric grazing whereas birch may have suffered from it.

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One of Earliest Farming Sites - Vashtëmi, Albania

University of Cincinnati research is revealing early farming in a former wetlands region that was largely cut off from Western researchers until recently. The UC collaboration with the Southern Albania Neolithic Archaeological Project (SANAP) will be presented April 20 at the annual meeting of the Society for American Archaeology (SAA).

Susan Allen, a professor in the UC Department of Anthropology who co-directs SANAP, says she and co-director Ilirjan Gjipali of the Albanian Institute of Archaeology created the project in order to address a gap not only in Albanian archaeology, but in the archaeology in Eastern Europe as a whole, by focusing attention on the initial transition to farming in the region.

"For Albania, there has been a significant gap in documenting the Early Neolithic (EN), the earliest phase of farming in the region," explains Allen. "While several EN sites were excavated in Albania in the '70s and '80s, plant and animal remains - the keys to exploring early farming - were not recovered from the sites, and sites were not dated with the use of radiocarbon techniques," Allen says.

"At that time (under communist leader Enver Hoxha), Albania was closed to outside collaborations and methodologies that were rapidly developing elsewhere in Europe, such as environmental archaeology and radiocarbon dating. The country began forming closer ties with the West following Hoxha's death in 1985 and the fall of communism in 1989, paving the way for international collaborations such as SANAP, which has pushed back the chronology of the Albanian Early Neolithic and helped to reveal how early farmers interacted with the landscape."

The findings show that Vashtëmi, located in southeastern Albania, was occupied around 6,500 cal BC, making it one of the earliest farming sites in Europe. The location of early sites such as Vashtëmi near wetland edges suggests that the earliest farmers in Europe preferentially selected such resource-rich settings to establish pioneer farming villages.

During this earliest phase of farming in Europe, farming was on a small scale and employed plant and animal domesticates from the Near East. At Vashtëmi, the researchers have found cereal-based agriculture including emmer, einkorn and barley; animals such as pigs, cattle and sheep or goats (the two are hard to tell apart for many bones of the skeleton); and deer, wild pig, rabbit, turtle, several species of fish and eels. What seems evident is that the earliest farmers in the region cast a wide net for food resources, rather than relying primarily on crops and domesticated animals, as is widely assumed.

Allen was awarded a $191,806 (BCS- 0917960) grant from the National Science Foundation to launch the project in 2010.

Albania: Agriculture Goes Beyond Its Roots

Anthropology professor earns NSF grant to dig in Albanian wetlands.

Date: 10/11/2010
By: Ryan Varney
Phone: (513) 556-0142
Photos By: Susan Allen
Susan Allen, field service assistant professor in the Department of Anthropology, researches paleoenvironmental issues in Southeastern Europe and the Eastern Mediterranean among other areas.

This summer, she received a National Science Foundation grant of $191,806 to visit Albania and study the widespread dispersal and adoption of agriculture beyond its roots.

Professor Susan Allen and UC anthropology senior Kathleen Forste (left) visited the Vashtëmi dig site in southern Albania.

Your project is titled “Wetlands and the Transition to Agriculture in Europe: The Southern Albania Neolithic Archaeological Project.” Can you provide a little background on the purpose of this project?

I noticed in the literature that scholars commonly cited wetland environments in explanations for why agriculture developed in key centers around the world, such as Mesoamerica, East Asia and the Eastern Woodlands of North America. But they had largely ignored their role in shaping the adoption of farming in other areas. 

So what I am really interested in is addressing this question by looking at the transition to farming in Europe, which is not one of the centers of “pristine” origins. The site we are excavating, Vashtëmi, is at the leading edge of the shift to agriculture in Europe, in an area of the southern Balkans that was once part of a series of vast wetlands that stretch into present-day Greece and Macedonia. 

Now that you’re back from Albania and have had some time to reflect, what stands out most clearly about your experience?

What stands out most clearly is the urgent need for projects like this one, due to the rapid pace of development and the ineffectiveness and lack of enforcement of the recently implemented Albanian heritage laws in the current political climate. I was devastated to see that someone had started to build a house right on the site itself. Thankfully, the owner agreed to delay construction and allowed us to excavate in a small area within the house. 

The research team studied the Vashtëmi site for clues about agricultural migration.

So, were you able to draw any conclusions regarding the shift to agriculture in Europe?

I have to say that what I have now are more questions than conclusions! One of the very interesting discoveries is the diversity of meat-eating represented on the site. In the trash deposits we excavated, we found a surprisingly high diversity of wild animals—turtle, red deer, roe deer, boar, hare and fish—recovered only because of the specific methodology that we are using, as well as a possible lion bone. The domesticated animals we identified include sheep, goat, pig, cow and dog. 

One issue that really intrigues me is the role of cattle in the southern Balkans and the question of the beginning of dairying, which has recently been placed slightly later (around 5500 B.C.) in the Central Balkans according to DNA evidence. At present, what is clear is that the earliest farmers in the area were not wholly reliant on domesticated plants and animals, but also made use of wild resources from a diversity of habitats. So the transition, whether local or by colonization, was neither abrupt nor immediate.

Is there a similar habitat here in the U.S. that might help us better visualize your dig site?

Well, people hear about the project and they expect something totally different on the ground than the reality. One of the tragic environmental legacies of the Communist period throughout the Balkans is the widespread drainage of wetlands. The Maliq wetland, where we are working, suffered the same fate. So today, you’d need to picture a Midwestern cornfield, but place it in a broad agricultural valley surrounded by beautiful mountains on all sides. When it was first occupied around 8,500 years ago, the site would have been located in an area with a mosaic of streams and marshes, a short distance from a broad open lake filled with a great abundance of eels, other fish and waterfowl.

One of the goals of the project was to offer environmental archaeological training for young Albanians. How was your experience working with Albanian students?

It was fantastic! I got to know some of these students as participants in an Environmental Archaeology course that I taught in Albania in 2006-07 while there on a Fulbright Fellowship. The students who worked with us have a remarkable passion for archaeology, despite limited prospects for career advancement or economic gain. They worked very hard and were thrilled to learn a lot of new skills and approaches that they can take with them to any excavation—in Albania or elsewhere. I should also add that the American students—including three from UC—also did really well in the field.

Were any of these items a part of your dig apparel:  fedora, bullwhip, revolver, leather satchel?

Only when absolutely necessary of course, but only my wardrobe specialist knows for sure!

Report on the symposium on Modern Human Genetic Variation

The following text is taken from the http://dienekes.blogspot.com/

Joshua Akey summarizes the talks of a recent symposium at the Swedish Royal Academy of Sciences. Two bits of information stand out from his report. 

The first:
In another talk focused on demography, Mattias Jakobsson (Uppsala University, Sweden) presented novel data on the impact of the agricultural revolution on the genetics of contemporary European populations. Specifically, Jakobsson and colleagues obtained nearly 250 Mb of sequence from three 5,000-year-old remains of Neolithic hunter-gatherers and one Neolithic farmer excavated in Scandinavia. Analysis of these sequences in the context of the present day European gene pool suggests that the spread of agriculture involved the northward migrations of farmers. Thus, these data provide the most direct and compelling support for the demic diffusion model of agriculture (as opposed to cultural diffusion) described to date.

It seems I have my answer to the what's next question. Jakobsson has been doing some interesting work on the demography of human emergence and dispersal, so it will be interesting to see not only the novel sequences from these Neolithic Scandinavians, but also how they fit into existing models of demic diffusion.

The second bit of information:

Similarly, Jeff Wall (University of California San Francisco, USA) described a novel method for inferring archaic admixture, which he applied to publicly available whole-genome sequence data generated by Complete Genomics. Provocatively, he finds higher rates of introgression in Asians compared to Europeans. An advantage of Wall’s method is that it does not require an archaic genome to infer introgression, and thus he was able to also test the hypothesis that contemporary African genomes have signatures of gene flow with archaic human ancestors. Strikingly, Wall indeed did find evidence of archaic admixture in African genomes, suggesting that modest amounts of gene flow were widespread throughout time and space during the evolution of anatomically modern humans.

I guess that I shouldn't throw explanation #1 out the window yet. Wall was involved in the recent paper on archaic African admixture, which only looked at a small subset of the genome, so it is nice to see that he is now working with full genomes, and that the race to data mine complete genomes for archaic admixture is afoot.

The book of abstracts is online at the symposium site. The Jakobsson paper does seem to agree with our emerging picture of a non-local origin of northern European farmers as well as greater survival of pre-farming populations in the northern periphery of Europe, but it will be interesting to see where exactly extant populations fall on the farmer-hunter/gatherer continuum.

Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Northern Europe
Mattias Jakobsson
Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden

The prehistoric spread of farming in Europe has garnered intense interest for almost a century, and was one of the first questions to which population genetic data was used to investigate demographic hypotheses. However, the impact of the agricultural revolution on the European gene pool remains largely unknown. We obtained 249 million base pairs of quality-filtered human autosomal sequence data from some 5,000 year-old remains of three Neolithic hunter-gatherers and one Neolithic farmer excavated in Scandinavia, the northernmost fringe of agricultural practice at the time. Applying novel methods to study population structure based on low genome-coverage data, we find that Northern European Neolithic farmers are most similar to modern-day southern Europeans, contrasting sharply to Neolithic hunter-gatherers who are most similar to extant individuals from northern Europe. With most extant European populations appearing genetically intermediate between the two Neolithic groups, our results suggest that migration from the south by a genetically distinct group of humans accompanied the spread of agriculture to geographic regions where hunting and gathering was the mode of subsistence, but that admixture eventually shaped modern-day patterns of genomic variation.

Archaic admixture in the human genome
Jeff D Wall
Department of Epidemiology & Biostatistics, University of California, San Francisco, USA

We describe a method that uses patterns of linkage disequilibrium in extant human populations to identify regions of the genome that were inherited from ‘archaic’ human ancestors, such as Neandertals, Homo erectus or H. floresiensis. We validate this approach using two recently published archaic human genomes, and show that several ancient admixture events must have occurred, both within and outside of Africa. We also explore differences in the amount of archaic admixture across different contemporary human populations.


Finally, here is the meeting report:

Investigative Genetics 2012, 3:7 doi:10.1186/2041-2223-3-7

Understanding human evolutionary history: a meeting report of the Swedish Royal Academy of Sciences symposium of modern human genetic variation

Joshua M Akey

Neolithic farmers brought deer to Ireland

The origins of the iconic Irish red deer was a controversial topic. Was this species native to Ireland, or introduced?

In a new study that was published 30 March 2012 in the scientific journal Quaternary Science Reviews, a multinational team of researchers from Ireland, Austria, UK and USA have finally answered this question.

Comparing DNA

By comparing DNA from ancient bone specimens to DNA obtained from modern animals, the researchers discovered that the Kerry red deer are the direct descendants of deer present in Ireland 5000 years ago. Further analysis using DNA from European deer proves that Neolithic people from Britain first brought the species to Ireland.
Although proving the red deer is not native to Ireland, researchers believe that the Kerry population is unique as it is directly related to the original herd and are worthy of special conservation status.

A link to the past

Fossil bone samples from the National Museum of Ireland, some up to 30,000 years old, were used in the study. Results also revealed several 19^th and 20^th century introductions of red deer to Ireland, which are in agreement with written records from the same time. At present there is no evidence of red deer in Ireland during the Mesolithic period, 9000 years ago, when humans first settled there.

Neolithic house, Irish National Heritage Park. Image: David Hawgood (Geograph, used under a CC BY-SA 3.0)

The investigation’s findings are in agreement with archaeological evidence, which also suggests a special relationship between humans and red deer during later prehistoric times. Antler fragments and tools are frequently found in Neolithic, Bronze Age and Iron Age excavations.
Dr Ruth Carden, working as a researcher in the National Museum of Ireland, who led the study, said “The Kerry red deer represent a unique population within an Irish context and therefore should be given special conservation and management status within Ireland.”
The genetic analysis also showed that some of these herds were descended from animals imported from Britain in the 1800s and 1900s, matching the historical records.
The DNA showed that the reds away from Kerry have started to “hybridise” or cross-breed with Sitka deer, a species introduced here in 1860. There is however no such interbreeding for the Kerry red population, Dr Carden added. Sitkas also live in the forests of Killarney but the DNA analysis showed no interbreeding had yet taken place.
Dr Allan McDevitt, from the School of Biology and Environmental Science, University College Dublin, one of the lead geneticists said “We have very few native mammals in Ireland but certainly those that arrived with early humans, such as the red deer, are every bit as Irish as we are.”
Source: School of Biology and Environmental Science, University College Dublin

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More information:

R F Carden, A D McDevitt, F E Zachos, P C Woodman, P O’Toole, H Rose, N T Monaghan, M G Campana, D G Bradley, C J Edwards (2012). Phylogeographic, ancient DNA, fossil and morphometric analyses reveal ancient and modern introductions of a large mammal: the complex case of red deer (Cervus elaphus) in Ireland. Quaternary Science Reviews. doi: 10.1016/j.quascirev.2012.02.012
School of Biology and Environmental Science, University College Dublin
The Heritage Council, Ireland
Woodman P.; McCarthy M.; Monaghan N., (1997) The Irish quaternary fauna project: Quaternary Science Reviews, Volume 16, Number 2, 1997 , pp. 129-159 http://dx.doi.org/10.1016/S0277-3791(96)00037-6

Spread of Impressed ware - Adriatic

Here I present map, on the base of the Radiocarbon dates, possible route of neolithisation of the East Adriatic coast. My area of interest is Dalmatia (Croatia) and it's neolithisation around 6 000 BC.

On all of the sites presented on this map Impressed ware was found as a clear indicator of early Neolithic on the East Adriatic coast

This dates clearly indicate that neolithic package reached East Adriatic coast by marine route (arrow  #1). Impressed ware as a clear indicator of early Neolithic, here I don't argue about it's origin, shows that it started to spread from somewhere around south Adriatic/Ionian sea coast into the Adriatic basin within just a few hundred years or less.

A dramatic climatic transition at ~4000 cal. yr BP and its cultural responses in Chinese cultural domains

A dramatic climatic transition at ~4000 cal. yr BP and its cultural responses in Chinese cultural domains

From the text:

Our review of published archaeological literature shows that six of the seven well-documented Chinese Neolithic cultures collapsed at ~4000 cal. yr BP with the exception of the Henan Longshan Culture that evolved to the more advanced Erlitou Culture.

Full TEXT

Transitions in the Mediterranean or how hunters became farmers (Epipaleolithic, Mesolithic, Neolithic) [International Symposium on 14-15 April 2011]

On the occasion of last years "Prehistory", the Natural History Museum of Toulouse, in collaboration with Centre for Prehistory and Early History of the Mediterranean organized an international symposium on the theme of transition Epipaleolithic - Mesolithic - Neolithic in the Mediterranean. 

The Mediterranean is a privileged space to study the mutation that made the old switch from hunter-gatherers in the sphere of food producers.

Here I present J.-F. Berger; G. Matallinou and J. Guilaine "The Mesolithic and Early Neolithic site of Sidari (Corfu)" paper from the conference.

From the text: 

"This costal neolithic site, established in a small valley cut into detrital marine formations of Pliocene age, is an important milestone to explain the modalities of neolithisation in the Adriatic area...."

There are no dates in this paper but you can find dates that authors gave (hand written - last page) at the conference since they were not available when the paper was in the print.

It is very interesting paper because it's results shine a new light upon neolithisation process of this area.

Paper LINK 

Neolithic Farming in Central Europe: An Archaeobotanical Study of Crop Husbandry Practices

Neolithic Farming in Central Europe examines the nature of the earliest crop cultivation, a subject that illuminates the lives of Neolithic farming families and the day-to-day reality of the transition from hunting and gathering to farming.

Debate surrounding the nature of crop husbandry in Neolithic central Europe has focussed on the permanence of cultivation, its intensity and its seasonality: variables that carry different implications for Neolithic society.

Amy Bogaard reviews the archaeological evidence for four major competing models of Neolithic crop husbandry - shifting cultivation, extensive plough cultivation, floodplain cultivation and intensive garden cultivation - and evaluates charred crop and weed assemblages.

Her conclusions identify the most appropriate model of cultivation, and highlight the consequences of these agricultural practices for our understanding of Neolithic societies in central Europe.

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 From 1st April to 15th May 2012 free access to all content in the Journal of Field Archaeology from the last 3 years !


LINK

Cranial variation and the transition to agriculture in Europe

Abstract

Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centred on two opposing models; a 'demic' diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities and an 'indigenist' model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East, but with little or no gene flow. The extreme versions of these dichotomous models have been heavily contested primarily on the basis of archaeological and modern genetic data. However, in recent years there has been a growing acceptance of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data have been particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships amongst Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.

LINK