Take a look at the second installment of 23andMe’s Human Prehistory 101 series.  23andMe’s creative team (led by chief illustrator Ariana Killoran) recently released “Out of (Eastern) Africa.”  With this new installment, we pick up where the previous video left off, when humans were starting to take their first tentative steps beyond the shores of Africa and into the unknown.

We begin this second episode around 60,000 years ago, when early human groups were exploring Africa for food and other resources. Just a few thousand years later, a few people journeyed even farther, heading east into the Arabian Peninsula, Asia, Europe and beyond. The common theme here? Things were changing for our human ancestors, who had previously stayed relatively confined to their homeland but now they were on the move. Around the time they first set foot in Asia, humans in Africa began creating sophisticated stone tools and art the likes of which had never been seen before.

As humans ventured into uncharted territory, they may have encountered other species who bore some resemblance to themselves.  In Asia, they may have run into Homo erectus, a distant relative that had journeyed into Asia from Africa almost 2 million years earlier.  In Europe humans likely came across the Neanderthals, another related species that had been braving the cold northern latitudes of Europe and western Asia for hundreds of thousands of years.

Our story continues as we see where various human populations settled over the next several thousand years, and gives us a peek at the difficulties that awaited them as the harsh Ice Age approached. Subsequent episodes will document how our human ancestors survived the harsh Ice Age conditions and how the innovation of agriculture and development of language laid the groundwork for the genetic diversity we see today.  Enjoy this latest installment and stay tuned for future episodes of Human Prehistory 101!

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In 1974, scientists digging in the dry lake bed of Lake Mungo in southeastern Australia uncovered the skeleton of a man preserved in the deep layers of sand and clay. Dating techniques eventually revealed that this individual died about 40,000 years ago.

Scientists and the popular press dubbed the individual “Mungo Man.” Why did he make such a splash?  Not only because he was – and remains – one of the oldest and most complete skeletons of the earliest Australians, but because his appearance shattered the previously held notion that humans had first set foot in Australia less than 10,000 years ago. It was so far from where humans arose in Africa, and so remote.  So of course humans arrived there so much later than everywhere else, many experts reasoned. With the discovery of Mungo Man, this idea lost support, and scientists now concede that Australia was settled much earlier than many other parts of the world, including the Americas and parts of Europe.

While this discovery initially answered many questions regarding the peopling of Australia, it left many more unanswered — especially how people could have reached an island continent so soon after humans first expanded beyond Africa about 60,000 years ago.

The thinking is that after leaving Africa, one or more groups of humans journeyed from their homeland in East Africa into Arabia via the Red Sea. Over the next several thousand years, their descendants continued along the coasts of Arabia and India, eventually heading south into present-day Indonesia and finally to Australia, which was joined with the island of New Guinea at the time.

There has been some archaeological and genetic evidence of such a migration, but most of it has been indirect or circumstantial. Some scientists remain unconvinced because researchers have not been able to show a direct link between modern Australian Aborigines and modern people living along the coastal route from Africa. But now, in a new study led by the Anthropological Survey of India, geneticists believe they’ve found the first concrete evidence of such a link. Their results are reported in the July 21 issue of BMC Evolutionary Biology.

The team, led by Satish Kumar, reasoned that if the hypothesis of an ancient migration along the Indian Ocean coast toward Australia was accurate, there would be evidence in the DNA of modern people living along that path. So they compared the DNA of modern Australian Aborigines to that of tribes from India, such as the Baiga of central India and the Birhor of eastern India. These groups are often called “relic populations” because they are believed to share many cultural, linguistic, physical and genetic features with the region’s ancient inhabitants.

Experts have long noticed that the Baiga, Birhor and other relic populations share physical similarities with native Australians. Kumar and his team reasoned that there could be DNA similarities too.

Kumar led the extraction and analysis of mitochondrial DNA (mtDNA) from nearly 1,000 individuals from Indian relic populations. For comparison, they used Australian Aboriginal DNA data that had already been analyzed and published by colleagues. After comparing the two groups, they came to a startling conclusion: two specific genetic mutations on the mtDNA of the Indian and aboriginal samples matched perfectly. Not only that, but these particular mutations do not exist elsewhere in the world; they are shared exclusively between a few isolated tribes in India and native Australians.

Kumar and his colleagues concluded the two groups must share a common ancestry. To lend further credence to their theory, they calculated the date when the ancestors of the Indian tribes and Aborigines must have split.

Their calculations produced a date of 55,000 years ago, a time when early humans in India were probably hunting wildlife and gathering plant foods. Some of their descendants eventually formed tribes like the Baiga and Birhor; others moved eastward, traversing southeastern Asian and then using maritime technology to cross nearly 60 miles of open ocean between Indonesia and New Guinea.

After arriving in Australia, they moved into the heart of the Australian Outback. A few thousand years later, a direct descendant of these ancient explorers was laid to rest along the shores of Lake Mungo.

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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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In the world of genetic anthropology, mitochondrial DNA and the Y-chromosome are the major players.  They are regions of our genome scientists use most frequently when tracing both ancient and historical human migrations, and are an important tool for genealogists using DNA to piece together their family trees.

But another part of the human genome has recently started to prove itself as a window into our species’ past: the X-chromosome.  Like both the mtDNA and the Y-chromosome, the X is passed from parents to children in such a way that scientists can use it to to trace the deep ancestry of our species. But it is only recently that the X-chromosome has been used this way, and some of the early research has been rather inconsistent.

Now, the authors of a paper published in this week’s Nature Genetics believe they have perfected a way of using the X-chromosome to unravel details about the initial migration of humans out of Africa tens of thousands of years ago. Their results suggest that more men than women were involved in the exodus that initiated the peopling of the entire globe.

One of the reasons analysis of the X-chromosome has not proven straightforward compared to the mtDNA or the Y-chromosome is that the way the X is passed down from one generation to the next differs depending on the sex of the child. Fathers pass on their X-chromosomes to their daughters, but not their sons, while mothers pass one X-chromosome to their children of both sexes. So while any person’s X-chromosome came down to them along a specific lineage — just like their Y-chromosome and mtDNA — that path is impossible to trace.

But the X-chromosome does have one distinctive quality. Since men have one and women have two, any population with a 50/50 sex ratio will have three X chromosomes for every four of the 22 paired chromosomes. And that means that all other things being equal, genetic diversity on the X-chromosome should be about three-quarters as much as it is on the non-sex chromosomes.

To see if all has been equal in the history of the human species, researchers from Harvard, the Broad Institute and the National Human Genome Research Institute analyzed the genotypes of people from around the globe and looked for differences among the populations of Africa, Europe and East Asia. Though they found the expected 75% X-chromosome diversity ratio within Africans, there was considerably less diversity among European and East Asians on the X compared to their 22 non-sex chromosomes.

What could all this mean?  First of all, a decrease in genetic variation is usually a sign of decreased population size.  Because it shows up in East Asians and Europeans but not Africans, the authors believe the decreased variation is a signal of a population bottleneck that occurred after humans left Africa for the first time nearly 60,000 years ago — but before the non-African populations diverged from each other.

But the decreased genetic variation only seems to show up on the X-chromosome.  This, the authors speculate, may be due to some sort of sex-biased migration.  In other words, when humans first ventured outside of Africa and into Europe and Asia, there may have been more men on the move than women.  Scientists have long observed the same phenomenon when comparing the Y-chromosome to mtDNA; now researchers are seeing the same phenomenon here, with the X.

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Neanderthal and Homo sapiens skeletons side by side. The thicker femurs, different eye sockets and barrel-shaped chest of our distant relatives are prominent in this comparison.

Mining the past: The Neanderthal Genome Project
The first invited speaker at the SMBE 2008 conference was Svante Pääbo of the Max Planck Institute for Anthropology in Germany. Pääbo and colleagues continue their incredible project to sequence the Neanderthal genome. Neanderthals are especially interesting in understanding our own history; they were another animal that walked upright, hunted with weapons, used clothes, and had culture, traits we consider very “human.” Pääbo presented some new findings that may change the way we think about our own history and that of our distant cousins, who went extinct around 25,000 years ago.

So far, the project has sequenced more than 3 billion Neanderthal DNA base pairs. The figure sounds impressive, and it is. However, sequencing ancient DNA is subject to contamination and in fact more than 99% of the DNA Paabo’s group extracts from Neanderthal bones is from bacteria, fungi or other organisms – including modern humans.

Scientists have debated for decades whether Neanderthals and humans interbred. So far, the Neanderthal genome does not show any evidence of having human ancestry. But the recent split between humans and Neanderthals has resulted in some sharing of genetic material between the species. That is, some people may share versions of SNPs with Neanderthals, but this sharing traces to a common ancestor who lived before the two species split about 800,000 years ago.

One especially interesting finding by Paabo’s group was in the so-called “language gene,” FOXP2. Humans have a very different version of FOXP2 than most other mammals, birds, and reptiles. Rare deletions in the gene cause people to have trouble with speaking and comprehension, providing support that the gene is important for language. Interestingly, other verbal mammals also have changes in FOXP2.
Scientists had thought the “human” version of FOXP2 arose within the last 200,000 years, since the origin of Homo sapiens and long after the human lineage split from Neanderthals. However, it turns out Neanderthals share the human version of FOXP2. These results indicate that something else happened in human history to make FOXP2 appear younger than it really is; and that this may not be related to the unique version of the gene shared by humans and Neanderthals.
So, is FOXP2 the gene that makes us unique from other animals? No. But could it still have played an important part in our own history? Probably. Just one of the many mysteries that evolutionary geneticists hope to answer.

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