About 10,000 years ago, the prehistoric hunter-gatherers of Europe began meeting some new neighbors.

These farmers spread gradually at first, expanding from the Near East through Anatolia and the Balkans. Then agriculture exploded, reaching present-day Britain within a few thousand years. The farmers settled into houses, which soon evolved into villages, towns and eventually cities.

The archaeological record tells us that much. But what it doesn’t reveal is how agriculture spread. Did it spread like a fad, as hunter-gatherer groups saw what their neighbors were doing and imitated their ways? Or was it more of an invasion, with subsequent generations of farmers advancing across the continent and overwhelming indigenous hunter-gatherer populations as they went?

Some genetic studies suggest the former. But in the September 3 issue of Science, the first study to directly compare ancient DNA (aDNA) from prehistoric burials of hunter-gatherers to that their agricultural neighbors suggests migrants spread farming through Europe.

The research team, led by Barbara Bramanti of Mainz University, sequenced the mitochondrial DNA (mtDNA) of just under 50 individuals unearthed from various prehistoric burial sites across central and eastern Europe. Half the individuals came from hunter-gatherer societies, and the other half from communities based around farming. As a comparison, they also sequenced the mtDNA of nearly 500 modern Europeans from the same parts of Europe.

The authors’ first task was to compare the hunter-gatherer mtDNA to that of the farmers. Upon doing so, they found both groups to be so different from each other that there is no way the two could be closely related. There was absolutely no overlap in the kinds of mtDNA lineages – known as haplogroups – between the hunter-gatherers and the farmers. This stark difference suggests the earliest farmers were not related to the hunter-gatherers, and most likely came to the region by migration.

And how do these two groups compare to the modern-day Europeans? The hunter-gatherers had little in common with modern people. Haplogroup U, the most common lineage among the hunter-gatherers, is one of the least common haplogroups among modern Europeans.

But the authors also found little to connect the farmers to modern Europeans. Other studies have pointed to a substantial genetic component from the Near East among Europeans, but the authors found many genetic differences between the two groups.

Based on these results, the authors have proposed an alternative theory. The unexplained component to the genetic make-up of modern Europeans may be explained by later migrations that post-date the skeletal remains examined here. It could have been a later expansion of farmers from the Near East, or perhaps an influx of hunter-gatherers from the west. The exact details remain unclear, but the authors are confident that, with additional DNA analysis, they can hope to unravel the increasingly complex story of the peopling of Europe.

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Over the past decade, there has been no shortage of studies focused on the relationship between Neanderthals and our own species, Homo sapiens. Researchers have dug deep into the fossil record and our genomes to uncover how closely related we are to the Neanderthals, whether we interacted with them, and even whether our two species shared offspring.

But what about the Neanderthals themselves? We know that beginning around 400,000 years ago, they occupied over 3 million square miles of Europe and Western Asia, from Spain to Iraq.  We know that they developed a unique tool technology and that they buried their dead.  But what we really don’t know is how they compared to each other:  were there in fact distinct Neanderthal sub-groups, shaped by the vastly different environments in which they lived?  Or can they all be considered a single, genetically similar population? These questions are addressed in the most recent issue of PLoS One by anthropologists from the Université de la Méditerranée in France, using a method that is both unique and comprehensive.

This study is of interest not only because it attempts to understand Neanderthal diversity, but also because it utilized data from a various sources.  First, the researchers collected data from the mitochondrial DNA sequences of 12 separate Neanderthal skeletons. These skeletons ranged in age from 29,000 to 100,000 years and were uncovered in various parts of the Neanderthal homeland, from Siberia to Spain.  The researchers then took physical measurements of the skeletons themselves. Finally, they developed and ran complex computer simulations based on the genetic and skeletal data, in an attempt to discover the most likely scenario for how Neanderthals evolved and spread across much of Eurasia.

The authors concluded that the most likely scenario for how the Neanderthals populated Europe and Western Asia involves three Neanderthal sub-groups: one centered in Western Europe, another in Southern Europe, and the final group in the Levant/Western Asia.  They propose that the Neanderthals within each of these sub-groups were more genetically — and perhaps physically — similar to each other than they were to members of another sub-group.  This is contrary to the idea that the Neanderthals were a single, uniform population.

This result begs the question of cultural distinctions between the sub-groups.  After all, if they were genetically and physically different from one another, it is entirely plausible that cultural differences, such as tool technologies, between the sub-groups also existed.  The authors hope to understand cultural differences between Neanderthal sub-groups in the same way as they’ve understood genetic and physical differences.  And, as more fossils are found and more DNA extracted, we will hopefully develop — with even more confidence — a clear picture on the origins and movements of Neanderthals.

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Early human history was characterized by many rapid, long-distance migrations. But despite our beginnings as travelers, genetic evidence published online last Sunday in Nature indicates that after expanding to all corners of the earth people (at least those in Europe) tended to stay close to home.

Close on the heels of similar research published just a few weeks ago (and covered in The Spittoon), John Novembre and colleagues have created a genetic “map” of Europe that closely mirrors the geographic map. Their results will allow scientists to better understand how geography contributes to genetic variation, which is important for both genome-wide association studies and ancestry analyses.

Figure 1: The genetic map of Europe using PCA, with the geographic map of Europe for reference. Figure 2: The same map, but zoomed in on Switzerland. Swiss individuals tend to cluster with countries that speak the same language. (Courtesy: John Novembre, UCLA)

The researchers used a mathematical technique called principle components analysis (PCA) to collapse large amounts of SNP data for 3,192 people drawn from throughout Europe into a two-dimensional “map” of their genetic distances from one another. (Figure 1)

When the researchers looked at the DNA of any two individuals, they found that the number of genetic differences between them was proportional to the geographic distance that separates their respective home countries. Even within countries the researchers saw that groups with similar cultural histories shared similar genetics. For example, Italian-speakers from southern Switzerland tended to cluster together with other Italian-speakers and apart from other Swiss groups. (Figure 2)

Using only genetic data, the researchers were able to assign, on average, 50% of European individuals to within 400 kilometers of their correct country of origin. But there was one caveat: all four grandparents of an individual had to come from the same European country for the assignment to be correct. People with mixed European ancestry tended to show up between the locations of their ancestors.

The accuracy of assignment varied greatly from country to country: some people, like the Swedes and Portuguese, were placed on the map with less precision than other groups like the Polish and Belgians.

As in earlier research that constructed a genetic map of Europe, the results of this study show that genetic variations between people tend to follow a northwest to southeast path. This may reflect an ancient migration after the Last Ice Age when glacial sheets extended down from northern Europe. Human groups (not to mention grasshoppers, hedgehogs, etc.) were forced to take refuge in warm southern locations like the Italian and Iberian Peninsulas. But after the glaciers melted about 15,000 years ago, humans began to re-colonize Europe, moving from south to north.

In the past, genome-wide association studies have been hampered by the effects of geography on genetics. For example, a study looking for DNA variants associated with height found spurious evidence of linkage to SNPs that are actually linked to lactose tolerance, because both traits vary along the same NW/SE axis in Europe. The results of this study current study and others like it will help scientists make corrections in their data and increase their ability to detect true associations.

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It should be no surprise that in general, we are more genetically similar to our neighbors than to people living far away. The reason is fairly simple — until recently in human history it was fairly rare for people from widely separated geographic regions to even meet, much less reproduce.

This pattern, known as isolation-by-distance, has been observed in a number of studies over the past several decades. This week, it has been confirmed in Europe by the largest study of its kind to date.

The researchers produced a two-dimensional map, like the one below, that preserves the genetic similarities between individuals as far as possible; in other words, the closer two dots (people) are on the map, the more closely related they are genetically.

Two dimensional genetic similarity map of Europeans showing the northern and southern clusters. Each colored symbol in the plot on the left represents a single person’s genotype. Note the similar placement of symbols on the plot to the left and the geographic legend to the right. Adapted from Tian et al., Plos Genetics, (2008).

In the figure above, each individual was labeled with their country of origin after the mapmaking procedure was run. If Europe were genetically homogeneous, you would expect the different nationalities to appear in a jumble. Instead, they  separate into clusters that, remarkably, roughly recapitulate the geography of Europe.

Northern vs. Southern Europe

Even though Europe has been occupied for only a relatively short time compared to other parts of the world, different populations within the continent have had time to differentiate from one another. Scientists have known for a long time that certain traits, like lactase persistence and light-colored eyes and hair are more common in northern than in southern Europe. Likewise, there are certain diseases such as sickle cell anemia that, although rare across Europe, are found more in the south than in the north. Height and skin color also vary from northern to southern Europe: both vary gradually with latitude rather than in quick jumps.
Early genetic studies (such as those in the landmark population genetics text History and Geography of Human Genes) showed that this north-south cline was also a genetic one: even though Europeans of different nationalities did not fit into simple clusters, there was an overarching north-south difference. Newer studies have increased the number of people typed, and the number of markers, to approach the genome-wide level of hundreds of thousands of SNPs we use here at 23andMe — which brings us to this week’s paper.

A summary of genome-wide findings

The Lao et al. study out this week obtained genotypes from more than 2,500 individuals of known European ancestry. Each of the genotypes consists of about half a million SNPs typed on the Affymetrix 500K, a chip similar in size to the Illumina 550K used here at 23andMe. They confirm the findings of several recent but smaller European studies (Seldin et al, PLoS Genetics (2006); Bauchet et al, AJHG (2007); Tian et al, PLoS Genetics (2008); Price et al, PLoS Genetics (2008); Paschou et al, PLoS Genetics (2008)), namely:

• Over all SNPs, Europeans are very genetically similar.
• There is a small set of SNPs that does allow European populations to be distinguished — at least when used among people whose ancestors are all from the same part of Europe — and they are surprisingly effective.
• Most of the genetic variation in Europe is found along the north-south axis, which is consistent with archaeological knowledge. The next most prominent axis of genetic variation runs roughly east-west.
• More isolated populations tend to exist at the extremes of these plots. In the case of this current paper the Finns are the only nationality completely distinct from the rest of the European samples. The Finns speak a different kind of language from much of the rest of Europe, and are the only Scandinavian population represented.

There’s plenty of action in the blogosphere on this one. For more discussion check out dienekes’ anthropology blog, anthropology.net, gene expression, and genetic future.

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The question of how agriculture first arose and spread in Europe has perplexed archaeologists and geneticists alike for decades. Evidence for farming communities in Greece, Crete, the Balkans, Southern Italy, and Mediterranean France and Spain first appears in the archaeological record eight to nine thousand years ago with the appearance of domesticated wheat, barley, sheep, goats and cows, and a related culture featuring pottery and anthropomorphic figurines. Before this period, most of the indigenous people of Europe fished, hunted small game or foraged for their livelihood.

But how did farming get to Europe in the first place? We know that 2,000 years before agriculture hit Europe, just after the end of the Ice Age, people living in the Near East had already developed farming, with the domestication of wild species of grasses, goats and cattle likely beginning in the fertile river valleys in present-day northern Iraq, Syria and southeastern Turkey. Near Eastern farmers also settled in villages and produced pottery and ceramic human figurines similar to the ones later found across Mediterranean Europe.

So did the first farmers of the Near East hop into boats with their domesticated plants, animals and artistic motifs and colonize Mediterranean Europe? Or did native Europeans learn about farming through trade with the Near East and decide to adopt this agricultural economy too?

Genetic studies are starting to provide answers to this enduring question. Not only do genetic studies of sheep, goats, cows and wheat demonstrate that the European varieties are subtypes of the species found in the Near East, but data from the human Y chromosome suggest that people currently living in Southern Europe are descended in large part (at least through the paternal line) from the Near East. This suggests, at least for the Mediterranean areas of Europe, that the most probable scenario is that Near Eastern farmers did actually move into Europe, bringing farming with them.

23andMe has a Y chromosome marker on its custom chip, rs34126399, which captures the spread of agriculture from the Near East to Europe. The G state at rs34126399 is found in most individuals carrying paternal haplogroup J2a, whose origin can ultimately be traced to Turkey 15,000 to 20,000 years ago. Southern Turkey is the likeliest source for the initial domestication of wheat.

In the millennia after its appearance in Turkey, rs34126399G then experienced a population growth and spread westward into the eastern Mediterranean and eastward into Mesopotamia, Iran and northern Egypt. The map to the right shows the present-day distribution of rs34126399G in Europe and the Middle East.

In addition to its high frequency in the Near East, rs34126399G is present in 10 to 25% of the population of southern Greece and Italy, Crete, Sicily, Bulgaria and Romania. The concentration is an indication of the early spread of farming to these regions, where the climate of wet winters and hot dry summers suited the varieties of winter wheat that were first domesticated.

Since the initial movement of people associated with the origins of agriculture nearly 10,000 years ago, there has been persistent contact and trade throughout the Mediterranean. Just think of the Mediterranean diet — rich in olive oil, goat cheese, and red wine — all of whose origins can be traced to these regions. One archaeologist described the Mediterranean Sea figuratively as a giant bathtub that for millennia has permitted easy seafaring transit from one area to another. The genetic evidence appears to support that analogy.

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