Africa is home to a number of dwindling hunter-gatherer populations, most of them living deep in the rainforests that stretch from western Africa’s Atlantic coast to the eastern edge of the Democratic Republic of Congo. Known as “Pygmies” because of their short stature, previous studies (including one funded by 23andMe) have shown that these forest-dwelling groups are descended from populations that arose 20,000 to 50,000 years ago.

But today populations such as the Mbuti, who live in the eastern forest, speak radically different languages from those spoken by the Biaka and other groups who live in the west. In fact, the Biaka speak a language belonging to the Niger-Congo linguistic family, which is associated with the expansion of agriculture throughout sub-Saharan Africa less than 5,000 years ago.

How did a hunter-gatherers in the African rainforest end up speaking less like their distant cousins and more like their farming neighbors? A paper published last month in Current Biology offers an explanation by genetically modeling the population history of the western African Pygmies and their farming neighbors using autosomal DNA, which is inherited from both parents.

Verdu and colleagues suggest that for most of the last 50,000 years western Pygmy groups were a single population, exchanging marriage partners and migrating through large tracts of the western forest. They also suggest that, contrary to earlier studies, the western African Pygmies were isolated from non-Pygmy populations until about 2,800 years ago, when they began exchanging marriage partners with neighboring farming populations.

Today, social taboos discourage Pygmy men from taking wives belonging to neighboring farming groups. But farming men and Pygmy women can marry, and sometimes the children of these unions sometimes return to their mother’s natal group in the forest. These cultural taboos and the resulting sex-biased gene flow probably began after western Africans invented farming techniques and began expanding through the rainforests about 5,000 years ago.

The research by Verdu and colleagues is the first to put a date on the breakdown of western Pygmy migration patterns due to the expansion of farmers — about 2,800 years ago. The integration of western Pygmy groups and farmers is also reflected in the linguistic similarity between the groups; both speak Niger-Congo languages. It is generally assumed that this linguistic shift occurred as farmers and hunter-gatherers intermarried.

The original languages of these western Pygmies have now been lost. But because Pygmy women have been marrying into farming groups for millennia, their genetic signature is well preserved in both populations. Using mitochondrial DNA, which is passed down from mother to child, genetic researchers discovered that over 80% of western Pygmies carried lineages derived from haplogroup L1c1a. About 20% of farmers from neighboring villages in western Africa carry the same haplogroup as evidence of their Pygmy maternal ancestry.

Could you have Pygmy ancestors? That’s difficult to say. About 12% of African Americans carry mitochondrial DNA lineages belonging to haplogroup L1c, which indicates maternal ancestry somewhere in the Congo basin and surrounding areas, but not Pygmy ancestry per se. Absent a confirmed assignment to L1c1a, the odds are that the maternal ancestry of an African American individual in haplogroup L1c traces back to farming rather than Pygmy populations.

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One of the reasons genetics is such a powerful tool for telling us about the past is that mutations that accumulate over the generations can be used as a clock, allowing scientists to calculate when different events occurred in the prehistoric past.

By counting the number of mutations differentiating one person from another, we can determine when in the past they shared a common ancestor. Each mutation is like a genetic tick of the clock, equivalent to a certain period of time. But figuring out how frequently mutations occur, and thus how long each tick of the genetic clock takes, is a major enterprise.

In a new paper appearing this month in Molecular Biology and Evolution, scientists from 23andMe propose that the genetic clock may have started running faster after the Ice Age ended about 15,000 years ago. If so, they may have resolved a discrepancy that has perplexed researchers for a number of years.

DNA mutation rates are estimated in two different ways. Geneticists can either count the number of mutations that occur in one generation (the changes between parents and their children), or they can count the number of differences between human and chimpanzee DNA and calculate a mutation rate based on the number of years since the two species diverged — about 6 million years.

It turns out that mitochondrial DNA mutation rates measured by these two methods described differ almost 10-fold. This difference is seen not only in humans, but also in species such as birds and fish. The discrepancy hints at the possibility that what we are measuring might be more complicated than we previously thought.

Working with Marcus Feldman of Stanford University, 23andMe scientists set out to find a new way of estimating the human DNA mutation rate by comparing the genetic diversity of lineages derived from the first human inhabitants of various continents and islands with archaeological finds that give precise information about when those colonists arrived (such as Polynesia).

We focused our studies on mitochondrial DNA data because there are a large number of mitochondrial sequences available in databases and the mutation rate of this DNA is known to be higher than in the autosomal DNA found in the 23 pairs of chromosomes,

What we found was surprising. Younger lineages (i.e. groups of people that have more recent common ancestors) had higher rates of mutation than older lineages, meaning that the molecular clock is not constant for human mtDNA: it slows down as lineages get older.

But why?

In our study the estimated mutation rates dropped off quickly around the end of the Ice Age — 15,000-20,000 years ago — suggesting that population history may play an important role in explaining the reduction in genetic diversity, and thus the changing pace of the DNA clock.

Prior to 20,000 years ago, humans lived in small hunter-gatherer groups that likely experienced boom and bust cycles: periodic climatic shifts or food shortages probably caused frequent and sudden population collapses. When populations decrease in size, or “bottleneck,” some genetic lineages are lost, which decreases the genetic diversity of the population. Since mutation rates are calculated using genetic diversity, the mutation rate estimates from these older lineages are slower.

After the climate warmed about 15,000 years ago and humans subsequently invented agriculture, populations grew dramatically. This resulted in more stable genetic diversity and faster mutation rate estimates.

More research needs to be done before we can determine whether population history or other factors, such as natural selection changing mutation rates, are primarily responsible for the human molecular clock slowdown. For example, we could simulate genetic diversity changes when a population size decreases and see if this matches the empirical mutation rate estimates.

Using our new data, which trace the slowdown in mutation rate back in time, scientists can identify the number that is most appropriate to use for studies of particular population events.

To date, the timing of most population events in human evolutionary genetics was estimated has used a rate close to the slower one we see for older lineages, before the end of the Ice Age. So our understanding of the genetic history of early human evolution shouldn’t change very much. But the timing of the splits between mitochondrial lineages associated with relatively recent events, such as agricultural expansions, may need revision. Using our newly calibrated mitochondrial mutation rates, researchers will be better able to correlate genetic, archaeological and linguistic data, leading to a more accurate understanding of human prehistory.

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A Nilotic-speaking pastoralist from Tanzania / Sarah A. Tishkoff

Genes are just one component that children inherit from their parents. Throughout much of human history, especially when populations consisted of small hunter-gatherer groups, the language and lifestyle of a people were also inherited from generation to generation. This is why genetic patterns and cultural traits are often correlated. So, when scientists see cultural similarities between two populations, they can ask whether there are genetic similarities between the two groups as well. For many cultural traits, such as pastoralism and agriculture there is still a debate: did people actually migrate into new regions, bringing their genes and culture with them, or did the language and lifestyle simply spread by word of mouth to new lands?

In this week’s Proceedings of the National Academy of Sciences, scientists from Stanford University (several of whom are also associated with 23andMe, including myself) have used the principle of genetic and cultural exchange to find the first genetic evidence of a prehistoric migration of people from Tanzania to southern Africa. We discovered a mutation (aka ‘SNP’) on the Y-chromosome that originated about 10,000 years ago in eastern Africa and is now most common among people from two regions: Tanzania and southern Africa.

Pastoralists (people who rely heavily on animal husbandry for food) such as the Datog and Burunge of northern Tanzania carry the newly discovered SNP. In fact, it is present among 30-40% of men from these populations. Unexpectedly, the click-speaking Kxoe of southern Africa carry the same SNP at similar levels to the Tanzanian populations, indicating that these people are closely related to the Tanzanian pastoralists. The evidence indicates that men from southern and eastern Africa shared very recent common ancestors between about 1,200 and 2,700 years ago.

With this genetic evidence in hand, we then turned to archaeologists to see if the fossil record indicated an ancient migration around this time.

As it turns out, the current thinking among archaeologists is slightly different than what this new genetic evidence has revealed. Archaeologists currently favor a model in which the cultural practice of pastoralism spread from an unknown eastern African group into southern Africa about 2,000 years ago, perhaps without any sort of movement of people (i.e. genetic exchange). Our new genetic study, while still supporting the archaeological record for the timing and place of the origins of pastoralism in sub-Saharan Africa, puts a new twist on the current thinking. It suggests that a small group of men actually migrated into southern Africa about 2,000 years ago. These men probably married into local hunter-gatherer populations, contributing their livestock and cultural knowledge of pastoralism. These migrants were probably closely related to the modern day Datog and Burunge groups of Tanzania.

A shift to pastoralism was a fundamental change for the hunter-gatherers of southern Africa during the last couple thousand years. It caused a dramatic change in the culture and belief systems of these people. As pastoralism became more widespread in southern Africa, so did the beginnings of a sense of ownership of animals and the emergence of chieftans. These changes can still be seen today in the practices of people throughout Namibia, Botswana and South Africa. For example, the Nama of Namibia began practicing pastoralism not long after its arrival in southern Africa and continue to do so today.

The question of whether the shift from hunting and gathering to agriculture was the result of cultural exchange or actual migrations between groups is one of the most important debates among archaeologists and geneticists. With this new genetic evidence, we think we have answered this question, at least in southern Africa. Future studies will further examine the relationhip between genes and culture, and how this relationship has influenced the genetic and cultural makeup of modern African populations.

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