When scientific research is published, the authors often confess that they wish they’d collected more data. Critical reviews of research studies often say the same thing. Indeed, if there’s anything scientists love, it’s more data.

Which is why the members of an international team of genetic anthropologists led by Sarah Tishkoff of the University of Pennsylvania are probably quite pleased with themselves. In a new study published this week in Science, the team took the concept of “more is more” to heart by collecting and analyzing the DNA of thousands of people, mostly from Africa, so that they might uncover more clues to not only the genetic make-up of modern Africans, but also the genetic history of Africans and non-Africans alike.

The scientists’ first step was to collect DNA from a diverse set of Africans. Africa is the most culturally and linguistically diverse place on Earth, so it was important to take a wide sample of individuals from all corners of the continent. In total, they collected 2,432 DNA samples from 113 diverse and distinct groups of people from across the African continent as well as 60 non-African groups. They sampled everyone from the Mozabite Berbers of Morocco to the hunter-gatherer San of the Kalahari Desert, and many in between.

But the hard work didn’t stop there. The scientists then examined 1,327 genetic markers across the human genome for each individual studied. While many studies focus on a particular part of the genome such the mitochondrial DNA or the Y chromosome, this study took a comprehensive approach. Finally, the researchers used sophisticated statistical techniques, piecing together how these populations from Africa and around the world were the same, and how they were different.

The results confirmed that Africa has the highest genetic diversity of any continent, as many scientists have proposed. In fact, the authors found genetic diversity to decrease the further one traveled away from Africa. Genetic diversity is often used as a measure of how long ago humans inhabited a region — conventional wisdom places the earliest humans in East Africa, which had exceptionally high genetic diversity according to this study, though an analysis by the researchers put the origin of the human expansion farther south near the border of Namibia and Angola.

The study also shed light on the incredible genetic diversity among African populations, said Roy King, a professor of psychiatry and anthropological geneticist from Stanford University:

Not only did farming and pastoral communities differ from hunter-gatherers, but within the broad range of agricultural populations of West and West-Central Africa — from which many African Americans derive their ancestry — the authors also found some genetic diversity. For example, the Dogon of Mali, although geographically near the Mandinka of Senegal, cluster with North African Berber populations. Thus, this study supports the notion that not only is Africa varied in culture — art, music, religion and language — but also harbors a rich genetic diversity across its multitude of ethnic groups.

The authors also found a loose connection between the genetics of a population and its language. However, there were a few exceptions, most often the result of a population adopting a new language within the last few thousand years.

The sheer size and diversity of the DNA samples collected allowed the researchers to construct a human family tree based on their analyses. Not unexpectedly, the tree they constructed fits well with current theories on the genetic relationship between Africans and non-Africans; namely that all non-Africans are descended from a particular group or groups of people who were the first humans to migrate out of Africa tens of thousands of years ago.

This study is important for a multitude of reasons. It has been able to confirm theories from the archaeological, cultural, and linguistic records on the origins and movements of Africans and non-Africans.

“It fits nicely with earlier genetic studies, while subverting the early 20th century colonialist idea of sub-Saharan Africa as constituting a homogeneous genetic an cultural unit,” King said.

It also creates a new resource that historians, linguists, archaeologists and scientists from a range of other disciplines can use in their own work. If we are lucky, this study will bring forth a flurry of activity surrounding the origins and history of the African continent, and the people who live there.

Credit: istockphoto/Erie

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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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There has been plenty of research in both genetics and archaeology recently trying to figure out how the New World was colonized. Was it by boat or via the frozen wasteland of the Bering Strait? Was it a fast trip down to South America, or did these first inhabitants take a more leisurely stroll? And when did all this happen anyway?

As each new study is published we are learning vital information on the peopling of the Americas. Ideas and theories continue to be retooled as new evidence comes to light.

This will certainly be the case with regards to a paper in the May 2008 issue of PLoS Genetics. In this article, researchers from Oxford and Cornell Universities report on a new computer model they have developed to trace prehistoric human migrations across the globe.

Using genetic information from various populations alive today, the authors estimated how those groups may be related to one another. Then they used those relationships to piece together the prehistoric movements of early humans.

As expected, their analysis showed a single migration out of Africa that eventually populated Eurasia and the Americas. However, the results for the Peopling of the Americas were more surprising.

The conventional wisdom states that the first inhabitants of the Americas came from Asia in a single wave more than 10,000 years ago. But when the authors compared the genetic data of two Native American groups (one in Colombia and one in the American Southwest) to groups in East Asia, what they found supported a two-wave migration.

The Colombian sample of Native Americans was actually more closely related to the East Asian sample than it was to the American Southwest sample. That suggests the two populations come from independent sources – and that there were at least two separate migrations of humans into the New World. Clearly, one of these migrations would have come from East Asia and made its way into South America. However, the data suggest a separate migration, probably from a different part of Asia or Siberia, came at a different time, and this time only made it to North America. This conclusion is significant, as it contradicts current theories on the topic, which argue a more constant flow of migrants from an original source somewhere in Asia.

There are still plenty of questions regarding this research, especially with regard to how it compares to the archaeological record and to previous genetic studies. The answers to these questions can only come with additional research, which, thankfully, is always forthcoming on the peopling of the Americas.

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