The Maasai and their Diet

The Maasai are a pastoralist tribe living in Kenya and Northern Tanzania. Their traditional diet consists almost entirely of milk, meat, and blood. Two thirds of their calories come from fat, and they consume 600 – 2000 mg of cholesterol  a day. To put that number in perspective, the American Heart Association recommends consuming under 300 mg of cholesterol a day. In spite of a high fat, high cholesterol diet, the Maasai have low rates of diseases typically associated with such diets. They tend to have low blood pressure, their overall cholesterol levels are low, they have low incidences of cholesterol gallstones, as well as low rates of coronary artery diseases such as atherosclerosis.

Even more remarkable are the results of a 1971 study by Taylor and Ho. Two groups of Maasai were fed a controlled diet for 8 weeks. One group – the control group – was given food rich in calories. The other group had the same diet, but with an additional 2 grams of cholesterol per day. Both diets contained small amounts of a radioactive tracer (carbon 14). (You’d never get approval for a study like this today, and for good reason.) By monitoring blood and fecal samples, the scientists discovered that the two groups had basically identical levels of total cholesterol in their blood. In spite of consuming a large dose of cholesterol, these individuals had the same cholesterol levels as the control group.

Here is how the authors concluded their study:

This led us to believe, but without direct proof, that the Masai have some basically different genetic traits that result in their having superior biologic mechanisms for protection from hypercholesteremia

Motivated by these results, we set out to identify genes under selection in the Maasai as a result of these unusual dietary pressures. We scanned the genome looking for genetic signatures of natural selection at work.

The Data

Our data comes from the International HapMap Project, a collaborative experimental effort to study the genetic diversity in humans. The HapMap Project has collected DNA from groups of people from genetically diverse human populations with ancestry in Africa, Asia and Europe. Their anonymized data is publicly available for free. One of the HapMap populations is a group of Maasai from Kinyawa, Kenya  (n=156), and this is the population that we focus on.

HapMap does not sequence full genomes, as this would have been prohibitively expensive at the time of data collection. Instead, they employ a shortcut. If you take my DNA sequence and line it up against yours, the two sequences will be about 99.9% similar. But every once in a thousand letters, or so, there will be a difference. You may have an A where I have a C. The HapMap group measures the DNA sequence at these very locations, where humans are known to vary from each other. In essence, they’re sampling the genome, looking only at sites where we expect to see variation. In the jargon of the field, this method is called looking for Single Nucleotide Polymorphisms, or SNPs (pronounced snips).

Hunting for signatures of selection in genetic data

Once you have the data, what can you do with it? We wanted to detect signs of natural selection. The basic idea behind detecting selection in genomic data is quite simple, and it has to do with sex. Every sperm or egg cell that you produce contains a single genome, which is formed by shuffling together the two sets of genomes that you inherited from your parents. Viewed this way, the role of sex is to shuffle together the genomes in a population into new combinations. If you compare the DNA sequences of a group of people, you will see signs of this shuffling.

Now lets add natural selection to the mix. What happens if an individual is born with a new mutation that benefits their survival? Over time, you’d expect to see this mutation rise in frequency. Descendants of this individual will be over-represented in the population, as the fraction of people with this beneficial mutation goes up. In essence, the fingerprint of such selection is a reduction of genomic diversity. (I’m describing a particular model of selection here, known as positive natural selection. Some other types of selection can increase diversity, such as the selection on viruses to evade recognition by their host’s immune system.)

Eventually, new mutations will creep in again, and generations of sexual reproduction would build back the diversity. However, if the loss of diversity was sudden enough (strong selection) and not too long ago, you can still detect it today. There are statistical tests (Fst, iHS, XP-EHH) that can formally detect if the reduction in diversity at a given region is sufficient to infer selection. Sabeti et al have a nice review paper that discusses the different methods available to detect selection using genomic data.

Our Results

We used three different methods to detect selection, and our top candidate regions under selection are considered significant by at least two of the methods.

The strongest signal of selection was a region on Chromosome 2 that contained the LCT gene producing lactase, the enzyme that breaks down the lactose in milk. Interestingly, the default state in all adult mammals is to stop producing lactase in adulthood – our ancestors were all ‘lactose intolerant’. This makes sense from an evolutionary point of view, it forces children to wean from milk, and frees up the mothers resources. It turns out that different sets of mutations arose that gave European and African pastoralists the ability to digest milk. Those of us whose ancestors weren’t pastoralists still have trouble digesting milk.

This is a classic example of a selective sweep – a mutation confers an advantage (the ability to digest milk), and then sweeps through a population like wildfire. This result has been previously described in European populations, and also in African populations (including the Maasai) by Sarah Tishkoff and collaborators. Given that the Maasai consume large amounts of milk, it is not surprising that we see a very strong signal at this locus. We sequenced DNA in this region to confirm this result and, sure enough, we found that one of the lactase persistence conferring mutations identified by Tishkoff was present in the HapMap Maasai samples.

Two of the tests for selection that we used require that you make comparisons with another population. We chose the Luhya of Kenya as a our reference population. Among all the protein-altering mutations present in the data, the one that showed the largest population difference between the Maasai and Luhya (as measured by Fst) sits in the gene for a fatty acid binding protein FABP1. This protein is expressed in the liver, and the variant that occurs at higher frequency in the Maasai is associated with a lowering of cholesterol levels in Northern German women (n = 826) and in French Canadian men consuming a high fat diet (n = 623). Furthermore, studies in mice fed a high fat, high cholesterol diet showed that deactivating the FABP1 protein leads to protection against obesity, and lower levels of triglycerides in the liver, when compared to normal mice on an identical diet. These results suggest that this protein plays a role in regulating lipid homeostasis, and its selection in the Maasai may be diet-related.

On Chromosome 7, two of the methods we used to detect selection identified a cluster of genes that fall in the Cytochrome P450 Subfamily 3A (CYP3A). This family of genes is involved in drug metabolism, in oxidizing fatty acids, and in synthesizing steroids from cholesterol.

What’s next?

Computational methods can only take you so far. We have identified genes in candidate regions undergoing positive natural selection in the Maasai, possibly arising due to their unusual diet. But the case for selection can only be definitively made with an experimental study targeted to address the role of these genes in maintaining cholesterol homeostasis. We’re hoping to collaborate with experimental biologists to take these hypotheses forward and investigate their role in the evolutionary history of the Maasai.

So head over to PLOS, check out the paper, and let us know what you think.

Update: Here’s another blog post that discusses the paper, focusing more on the mixed genetic makeup of the Maasai.

References:

Kshitij Wagh, Aatish Bhatia, Gabriela Alexe, Anupama Reddy, Vijay Ravikumar, Michael Seiler, Michael Boemo, Ming Yao, Lee Cronk, Asad Naqvi, Shridar Ganesan, Arnold J. Levine, Gyan Bhanot (2012). Lactase Persistence and Lipid Pathway Selection in the Maasai PLOS ONE, 7 (9) : 10.1371/journal.pone.0044751

If you’d like to read more about selective sweeps, you may enjoy my post Why moths lost their spots, and cats don’t like milk. Tales of evolution in our time.

And death is not just the end of the individual, it’s the end of a lineage. Organisms that die before they can reproduce deny their genes a road to the next generation. In this simple fact lies the engine of change. For example, genes that make a prey more camouflaged will end up increasing their reproductive success, whereas genes that make them more noticeable are not going to get very far. In this way, natural selection is driving prey to become better hiders, and predators to become better seekers.

Nowhere is this evolutionary race more evident than in the case of the peppered moth. This is a species of moth that is found all across England and Ireland. When people first studied them in the early 1800s, almost all the moths looked something like this:

As you can see (if you’re looking closely), the white and black speckles are effective camouflage. For ages, these moths have hidden on light colored trees and lichens. Over time, they have evolved this distinctive pattern to help them evade the notice of the birds that prey on them.

But just fifty years later, things were beginning to change. By the 1850s, moths of the same species had stumbled upon a new color. These new moths were called carbonaria after their carbon-black color, to distinguish them from their salt-and-pepper colored relatives with the dull name typica.

By the end of the nineteenth century, the change was drastic. In 1895, a study in Manchester showed that 95% of the peppered moths were now of the black type. So what was going here? What could cause such an incredible change in appearance in just a hundred years?

They key lies in a major event in the history of humanity that took place during the nineteenth century – the Industrial Revolution. During this time, a large number of factories were being built in England, and they burned a mind boggling amount of coal. From 1800 to 1900, annual coal production went up in the UK from about 10 million tonnes to 250 million tonnes.

This had a drastic effect on the environment. The trees in the woods between Manchester and London were covered in soot. And the increased levels of sulphur dioxide was killing the lichen. All of a sudden, the peppered moth was losing its camouflage. It stood out like a sore thumb against the sooty black barks of the trees, while the rare black form of the moth became an instant success.

In a new study in this week’s issue of the journal Science, researchers in Liverpool and the Czech Republic were able to trace down the genetic signatures of this extreme evolution. They did this by looking at the variation in letters of DNA between the 2 types of moths.

At the heart of the idea is sex. The genetic role of sex is to shuffle together different genomes in a population. This has the effect of creating more types of genomes, and thus increases diversity.

When the Industrial Revolution comes along, it paints the world of the moth black. Most of the genomes in the population get wiped out as they are no longer fit. A few rare ones contain a gene that protects their possessor by coloring them black. These genomes quickly begin to dominate in the population, and so there are now fewer kinds of genomes around – the diversity begins to plummet (think of 1895, when 95% of these moths were now black). This is known as a selective sweep, where a set of genes rapidly sweep through a population.

Over time, as these moths mate with others, the diversity builds back. But just as it takes many shuffles to completely randomize the order of cards in a deck, it takes many generations of sexual reproduction before all trace of the past is lost in the genome. By tracing down regions of the genome with unusually low diversity, we can uncover the signals of natural selection that must have acted on our ancestors. This method of detecting natural selection works best if the selection was strong (so that it wiped out the diversity), and if it happened recently (so that sex hasn’t had enough time to bring the diversity back).

This is just what the authors did. They first compared the genomes of 68 typica and 64 carbonaria moths (the offspring of two pairs of parents) and found that a particular region on one of the chromosomes was responsible for the difference in moth color. But this is a coarse-grained picture, as the region that they identified is over a million letters in length. The next step was to probe the diversity at a finer scale.

To do this, they looked at 6 variant letters of DNA that were spread out in this region, and measured how the carboneria and typica moths vary with respect to these letters. At each of these positions, there are 2 possibile letters that any moth can have. So if the genomes were properly shuffled with the maximum level of diversity, there would be 32 64 possible possible 6 letter words that could be formed here.[1] The spotted moths were found with many different words in this region, a sign of diversity. The black moths, on the other hand, all had small variations from just one sequence: CAGGTA. The scientists inferred that this must be the ancestral sequence of the black moths that thrived in the Industrial Revolution.

By comparing our DNA, we are actually looking back in time. We can use these techniques to infer the pressures that our distant ancestors faced. A cool example of this kind of DNA archeology is the story of lactose tolerance in humans.

Here’s a counter intuitive fact – mammals typically can not digest milk in adulthood. Of course, all mammals love milk as infants (that’s what gives them their name). That’s because they can produce a chemical called lactase, which breaks down the lactose in milk. But once infants reach the age of being weaned, the body switches off production of lactase. We all like to think of cats as cute pets that love a saucer of milk, but in reality this is more likely to give them indigestion and diarrhea. Lactose intolerance is not a disease, it’s actually the norm.

This makes sense from an evolutionary point of view. Milk is a nutrient rich food for infants, but it is costly for a mother to produce. At some point, the growing infant needs to move on, or it will become too great a burden for the mother. This digestive ‘switch’ in mammals ensures that this happens.[2]

So why is it that some us can digest milk? The answer takes us from one cultural revolution to another, to a time  8000 years ago when some of our ancestors had begun to rear cattle. This was happening in the Middle East and in Africa. Through sheer chance, anyone who had a mutation that disabled this lactase switch suddenly had an advantage over their peers. They had access to a reliable and nutrient rich source of food – milk from cattle.

The same process that changed the color of the moths is at work here. As was shown by a team led by Sarah Tishkoff in 2006, cattle herders in Africa and in the Middle East independently evolved different mutations that allowed them to drink milk, an example of what is called convergent evolution [3]. This is why lactose tolerance is very prevalent in Europeans. Many of their ancestors were cattle herders who originated in the Middle East. Similarly, northern Indians are more likely to be able to digest lactose than southern Indians, perhaps due to closer contact with the pastoral Sindhi tribes of north India.

And those of use who can digest milk carry the signs of this cultural revolution in our DNA. To date, the region surrounding the lactase gene has a remarkably low diversity in populations that descended from cattle herders.

We usually think of adaptations as occurring in response to changes from within nature. But I find it fascinating that our culture can also be a driving force of evolution. It has happened time and again, without our explicit knowledge of it. During the dawn of agriculture, we evolved wild grains into harvestable varieties like wheat and rice. In the birth of pastoralism, we modified our cattle to produce more milk, while also evolving ourselves to be able to consume it. And in the Industrial Revolution, our pollutants ended up driving evolution in moths.

As we look further out into space, we learn more about the origins of our universe. But at another extreme, by looking inwards to our DNA, we are also learning more about our place in it. We are unraveling the lives and cultures of our prehistoric ancestors, as well as the effect that we have had and continue to have on our surroundings.

Incidentally, the story of the moth has another surprising twist. Eventually the air quality improved in the UK, and the lichen began to grow back. The trees were restored to their lighter colors. And this meant that the carbonera moths have once again started to get noticed. They are now at a great disadvantage and have become extremely rare. In this way, the ebb and flow of genes are echoing the waves of cultural changes.

Footnotes

The kind of evolutionary genetics discussed in this article is the subject of my research. I have spent the last year and a half working on a project that studies how certain African pastoral tribes have evolved protection to their extreme diets, a case of culture and gene flow being intricately woven together.

[1] There are 2^6 = 32 64 combinations in all. The reason for there being 2 possible letters at these variant locations and not the usual 4 (A, C, T and G) has to do with biology. The variants arise through mutations (for example, an A gets flipped to a T) in somebody. It is incredibly unlikely that two mutations in the recent past (say, A to T and A to C) will occur at exactly the same place.

[2] However, if this lactase disabling switch was only useful to the mother, than it wouldn’t evolve. But such a switch also benefits her genes, as she can now invest the resources that she gains on caring for her offspring or on rearing more children.

[3] Incidentally, the peppered moth also occurs in North America, and there are reports that a similar adaptation towards darker moths arose along with the rise in pollution in the nineteenth century. If true, than this is another neat example of convergent evolution.

References

Van’t Hof AE, Edmonds N, Dalíková M, Marec F, & Saccheri IJ (2011). Industrial Melanism in British Peppered Moths Has a Singular and Recent Mutational Origin. Science (New York, N.Y.) PMID: 21493823

Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M, Ibrahim M, Omar SA, Lema G, Nyambo TB, Ghori J, Bumpstead S, Pritchard JK, Wray GA, & Deloukas P (2007). Convergent adaptation of human lactase persistence in Africa and Europe. Nature genetics, 39 (1), 31-40 PMID: 17159977

Image Credits

Creative Commons Licensed: Peppered moth (typica) by Andy Phillips. Black moth (carbonia) by naturalhistoryman. Cat and milk by Sunfox. Maasai herder Kamaika Kingi by Oxfam International.

Wikimedia Commons Licensed: Light and dark moth (typica and carbonia)