Saturday, April 28, 2012

Beyond Ötzi: European Evolutionary History and its Relevance to Diet. Part I

In the previous post, I explained that Otzi descended in large part from early adopters of agriculture in the Middle East or nearby.  What I'll explain in further posts is that Otzi was not a genetic anomaly: he was part of a wave of agricultural migrants that washed over Europe thousands of years ago, spreading their genes throughout.  Not only that, Otzi represents a halfway point in the evolutionary process that transformed Paleolithic humans into modern humans.

Did Agriculture in Europe Spread by Cultural Transmission or by Population Replacement?

There's a long-standing debate in the anthropology community over how agriculture spread throughout Europe.  One camp proposes that agriculture spread by a cultural route, and that European hunter-gatherers simply settled down and began planting grains.  The other camp suggests that European hunter-gatherers were replaced (totally or partially) by waves of agriculturalist immigrants from the Middle East that were culturally and genetically better adapted to the agricultural diet and lifestyle.  These are two extreme positions, and I think almost everyone would agree at this point that the truth lies somewhere in between: modern Europeans are a mix of genetic lineages, some of which originate from the earliest Middle Eastern agriculturalists who expanded into Europe, and some of which originate from indigenous hunter-gatherer groups including a small contribution from neanderthals.  We know that modern-day Europeans are not simply Paleolithic mammoth eaters who reluctantly settled down and began farming. 

OK, so Europeans are a mix of early agriculturalist and local hunter-gatherer genes, including neanderthals and perhaps other non-human hominids.  What fraction of the collective European genome derives from each?  This is where the evidence gets contentious.  Early studies indicated overall that European ancestry derives primarily from local hunter-gatherers that had been in Europe for thousands of years before the domestication of plants (1, 2, 3).  However, recent studies with more sophisticated methods, and larger sample sizes of modern and ancient genomes seem to be painting a different picture.  Here are a couple of quotes from a recent paper on mitochondrial DNA (4):
The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers.

The [mitochondrial DNA] data thus suggest that the pre-Neolithic populations in Europe were largely replaced by in-coming Neolithic farming groups, with a maximum [mitochondrial DNA] contribution of around 20% from pre-Neolithic hunter-gatherers.
This paper has been criticized by people more knowledgeable about genetic anthropology than myself (5).  However, different methods, including approaches based on skull morphology rather than genetics, have yielded similar results (6).  Here's a paper from 2010 on the Y chromosome (7):
Taken with evidence on the origins of other haplogroups, this indicates that most European Y chromosomes originate in the Neolithic expansion. This reinterpretation makes Europe a prime example of how technological and cultural change is linked with the expansion of a Y-chromosomal lineage ...
The genetic contribution from Middle Eastern agriculturalists may decrease as one moves Northwest throughout Europe, and thus further from the Middle East.  A brand new paper attempted to estimate the proportion of the genome that derives from incoming Neolithic farmers in different European populations (8).  In the following image from the paper, the proportion of the genome derived from Neolithic farmers in different modern European populations is represented in red:

This is the authors' best guess, based on a very limited number of ancient Paleolithic and Neolithic DNA samples from archaeological sites.  The picture will certainly change as more data come in.  However, I think it illustrates the overall points clearly that a) modern Europeans are a genetic mix of indigenous Paleolithic and incoming Neolithic farmer populations, and b) the proportion of Neolithic genes generally decreases with increasing distance from the Middle East.

The story of human evolution is a story of population expansions that displace and assimilate surrounding populations.  For example, humans expanded and replaced the non-human hominids neanderthals and denisovans in Europe and Asia (although some human populations also assimilated a portion of their genome into our own, so they aren't genetically extinct).  Europeans expanded into North America and Australia, and today represent the majority of the human genetic material on those continents.  Han Chinese expanded and assimilated surrounding populations in China, and continue to do so today.  African Bantu expanded and assimilated surrounding cultures in a large swath of Africa.  There is some evidence for similar events occurring in Native American history before the arrival of Europeans.  This is due in large part to cultural and genetic adaptations that favor the expansion of certain populations.  Like it or not, this is the story of human evolution, and this expansion/assimilation scenario is a plausible explanation for what happened in ancient Europe when agriculturalists arrived. 

Do the Proportions Even Matter for Our Purposes?

The issue of how much modern European DNA comes from local hunter-gatherers, and how much comes from Middle Eastern agriculturalists, is still hotly debated, and I won't pretend to be an authority on the matter.  It will certainly vary by population.  However, I'm going to argue that for our purposes, it doesn't even matter, because the majority of modern Europeans probably carry the most important genetic adaptations to agriculture regardless of the proportion of our genome that has Middle Eastern agriculturalist ancestry.  Why?  Natural selection.  If there has been a significant amount of early agriculturalist genetic material in the European gene pool for thousands of years, which we know at a minimum to be the case, even if that amount is relatively small, natural selection would have favored the propagation of the specific genes that increase reproductive success in an agricultural environment.

Take the example of lactase persistence, a genetic mutation that allows adults to digest the milk sugar lactose.  The mutation that's most common in Europeans arose in a single individual about 7,500 years ago, shortly after the introduction of dairying, and today is present in 590 million Europeans (80 percent).

Here's a hypothetical example to illustrate the point.  You have a group of 90 hunter-gatherers eating large game in Europe 5,000 years ago.  10 Middle Eastern agriculturalists who have been farming for the last 5,000 years come along, teach the hunter-gatherers how to farm, and have children with them.  This newly agricultural population is now 90 percent hunter-gatherer, and 10 percent agriculturalist, genetically speaking.  We know that early adopters of agriculture had serious health problems that must have exerted major selective pressures on them, favoring genetic adaptations over time.  The offspring from this hybrid hunter-gatherer-agriculturalist population would be subject to the same damaging effects of the agricultural diet and lifestyle.  Over time, if the agriculturalists carried any significant genetic adaptations to an agricultural diet and lifestyle, these would be favored by natural selection and increase in frequency, just like lactase persistence.  Fast forward 5,000 years, and you could end up with a hypothetical population that's overall 88 percent descended from European hunter-gatherers, 12 percent descended from Middle Eastern agriculturalists, but nevertheless carries all the key genetic adaptations to an agricultural diet and lifestyle that the early agriculturalists brought along with them when they immigrated to Europe, not to mention any new ones they acquired in the meantime.

In the next post, I'll explain that this process of rapid genetic adaptation is not only plausible, it has already been convincingly demonstrated in humans.  


Eimear said...

Hi Stephan, I didn't look back to see if there was any more discussion on your previous blog post. I just read your comment that it wasn't an assumption but only half the story. So this is the post that answers my questions:)

Tyler said...

So when did these middle eastern immigrants start relying heavily on agriculture?

Nyx said...

We always seem to think of agriculture like some sort of invention that spread, but given how many different places where it was independently "discovered," and that many hunter-gatherer societies know how to cultivate plants but don't make that their preferred lifestyle -- isn't it at least as likely that agriculture is itself an adaptation? is it not possible that agriculture is what happens when other resources become too scarce? and is it not also possible that what spread was not agriculture but oppression? Maybe I'm wrong, but I can't help but suspect that this giant grain-production machinery depended on the ability to force a large number of people to do the bidding of others. I look at my little kids who would live off of grains if I let them and I know that grains are a high reward food. Let somebody get a taste of that (literally) and then notice that they need an army of fieldworkers to supply them with it, and ....

allison said...

Great post. I was under the impression that the search for evidence of Neanderthal genes in modern humans yielded negative results. One account I read speculated that Cro-Magnons and Neanderthals were genetically incompatible. They probably interbred, but their offspring were sterile, as when a horse breeds with a donkey.

Nyx said...

@Allison, I think the Neanderthals were much longer ago than what we're talking about now. Also, I think more recent evidence is that there WAS some interbreeding, and most people, or maybe it's just most non-African people, have a small amount of Neanderthal genes.

Pieter said...

Fascinating stuff! Very curious to where this will lead you re: diet. Natural selection is all about replication of genes, and thus reproduction. But enhancing reproductive fitness does not necessarily mean enhancing individual health.
Do you think genetic changes to agriculture could have had reproductive advantages, but negative implications for health, especially for the second half (or second third) of live?

Peter said...

I posted my initial comment on the wrong section so I do it again.

Nice job Guynet. Atleast when it comes to Scandinavia, there's no connection with hunter-gatherers and the present day Germanic-speaking population.

Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians

"Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia" w947

I find it very funny that the parts of Europe (Sweden) where these fad Fred Flinstone diets reign are regions where the contemporary population show the least amount of any genetic input from actual hunter-gathers. To make it even more puzzling the above study discloses that genetic refuge of hunter gatherers is North-East Europe, Finland whose population is internationally well known to be very susceptible to heart disease (and being equally known for showing staggeringly high high serum cholesterol levels)

Ed said...

I encourage those interested in this narrative to read Jared Diamond's Guns Germs and Steel. He goes into quite a bit of detail around the domestication of plants and animals around the world. I'm about halfway through the book right now and the synergy between it and these posts is interesting.

One thing that I feel continues to be under-discussed is food preparation techniques. I recognize that food preparation techniques are probably tangential to Stephan's intended story arc, but I hunger for more discussion here. It's one thing to say, perhaps, that modern humans are somewhat adapted to, say, wheat. But I always wonder: prepared exactly how? To what from of soaked, fermented, cooked etc wheat are we best adapted? How did food preparation techniques change over time? Or even dietary mixes of various foodstuffs?

Jude said...

Agriculture is something that began before man. Man met it here on earth and it is something that we can't do without.

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Puddleg said...

Agriculture can also mean specialised animal herding as well as crop growing.
Nomadic horse and reindeer peoples are virtually paleolithic in diet despite being agricultural in culture.
Genghis Kahn's genes are everywhere today, apparently.
Descendants of mediterranean grain cultures mixed again and again with nomadic herders from central asia. The last such invasion was only a few hundred years ago.
Many other admixtures in more recent migrations would have a further diluting effect on the long-term grain eaters.
10,000 years is only a long period in evolutionary time if we assume that grains are toxic and sterilizing enough to amount to a significant selective pressure.

As I'm sure they are.

Eva said...

Nyx, good point, humans weren't stupid and it doesn't take too many brain cells to notice which plants can be eaten and start thinking about getting more of those to grow and to grow nearer to your location. I suspect one main driving force behind agriculture would be scarcity of resources. When we have just a few of us in a big lush environment, it is often easy to find food and game, but as our numbers increase, we tax the local resources. One answer is to spread out and go further, but those on the inside of the circle will soon find that all surrounding areas are taken.

Another answer is to start pulling out weeds and start planting more edibles. And to start cultivating more edible animals as well. We either change our environment or we alter it. Those two of the main options to support continuing population growth and it doesn't take a genious to figure either of them out.

Since we probably didn't have effective birth control and the urge to have sex is natural, then that mostly rules out the third option of controlling population, unless you consider killing which does seem to also happen but not quite the extent of often really solving the problem enough. Agriculture is less miserable than killing and less miserable than abstaining from sex, so it's a natural first line plan of action when you realize your food is starting to run out and all the surrounding territories are also full of hungry people. It's also a safer option as you can stay closer to your territory in a more packed in and defensible situation than if lone hunting parties are out in the boonies by themselves.

Miki said...

That we have genetically adapted to consuming grains is obvious. We are here to testify. Does this means that consuming plenty of grains contribute to longevity? not really. Evolutionary design is a game of compromises. Our consumption of a large amount of starch is unique in the animal kingdom as the presence of starch in nature is quite rare. It is quite conceivable that we compromised longevity in the process of adaptation to significant starch consumption. Cynthia Kenyon's findings re insulin and longevity hints in this direction.

Boomka Music said...
This comment has been removed by the author.
Boomka Music said...

It's an article of faith to say that it's simply elementary that "Natural Selection" necessarily whould have selected for grain consumption amongst European populations. We'd to know the sum and discreet effect(s) of all selection pressures on those populations to even begin to make conclusions as to which of them had any meaningful impact on reproduction. Of course, as Miki points out above, just because you're eating it doesn't mean you ought to.

Also, we'd need to account for all political, social and economic factors which could've forced the "obsolescence" of hunter-gatherer genes in those populations. Have a look at the case of European agriculturalists overtaking hunter-gatherers in the Americas. The "selection" - if you will - had far more to do with a patently non-genetic ability to resist small pox and certain strains of influenza than just about any other factor. It's not as though there was clear competition between the genes governing grain tolerance, or any other dietary factor, for that matter.

Don! said...

I'm very confused by the scenario a couple of commenters seem to be positing. How and why does agriculture arise when resources are scarce? This just isn't making sense to me.

If you have water and fertile soil then there are going to already be lots of plants growing, and there will be lots of animals showing up to eat those plants, so any halfway competent hunter would be able to get some.

On the other hand, if you don't have water or fertile soil, growing things is going to be extremely difficult, and certainly not something to be undertaken by people who are weak from starvation and/or dehydration. So I can't imagine a scenario in which agriculture would arise - successfully - out of desperation. Can someone elucidate?

Skookum said...

It seems to me, on thinking about it, that the arrival of Europeans in the Americas may provide a bit of insight here. Didn't we see that disease wiped out large numbers first, upon first contact. The few who survived the wave of diseases then forced to engage in armed conflict with the new arrivals. Only those that survived all that were around to succumb to dietary, cultural and genetic changes... Doesn't seem to far of a stretch to me that it may have happened similarly in Europe thousands of years before.

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gunther gatherer said...

Hi Stephan,

"...10 Middle Eastern agriculturalists who have been farming for the last 5,000 years come along, teach the hunter-gatherers how to farm, and have children with them."

I think we're leaving out some cultural hurdles here that would have made it unlikely that another group could just integrate into another like that. HGs we see now fight for territory and have marked cultural clashes and don't necessary mix this way. The two sides seem to hate each other and each is always claiming the other ruins the first's subsistence strategy.

It seems more likely that they fought and one just wiped the other out or at least diminished its numbers enough to marginalize it and leave them no choice but to assimilate or die off.

Galina L. said...

Having genes from agricultural ancestors doesn't mean you are immune to a celiac disease and doesn't give you a warranty that are not gluten sensitive. If your ancestors ate grains during last 10000 years, does it mean you will not benefit from an Archevore Diet, for example? So far it looks like the populations similar to the Aboriginal people in Australia or Native people in the North America are getting more sick on a Standard Western diet then the people whose ancestors came from Europe, but the difference doesn't mean much for health-considered people.

Anonymous said...

We should address the elephant in the room. The wheat we are consuming today is also genetically different than the wheat man ate 10,000 years ago. Even a difference of a few amino acids can change the way the immune system responds, and is perhaps sensitized, to certain areas of wheat proteins.

Just like our genetics have changed, so have the genetics of the plants themselves, a concurrent variable that cannot be ignored, and makes the picture much more complex.

Perhaps the problems we are having with wheat today have to do with the genetic modification of these plants. Indirectly, altering the genetics of a food that is a staple of our society is also altering the adaptive environment, changing the course of evolution, and favoring only those whose immune systems are not sensitized to the new proteins.

Jane said...

Was it really the grains that made early farmers less healthy than the hunter gatherers?

'This paper examines the puzzle that human beings adopted agriculture independently at least seven and perhaps up to ten times independently in different parts of the world around ten thousand years ago, in spite of the fact that skeletal evidence suggests that the first farmers suffered worse health and nutrition than their hunter gatherer predecessors. It proposes an explanation based on investments in defence, which would have been more necessary for farmers (who being sedentary would have had more resources to defend), but which in turn made them an increased threat to their neighbours. This would have made adoption more attractive among communities whose neighbours had already adopted, leading to a snowball effect of adoption but not necessarily making the first farmers better off than they were before.'

Nyx said...

@Don!, I didn't mean to imply that my comments were particularly well informed, so I'm just speculating out loud. But I could imagine a situation in which first off, people practice a "little bit" of plant cultivation. I think that's fairly common among hunter gatherers. but then maybe they become increasingly reliant upon whatever food that is because other more preferred food becomes less available. as population increases, I would assume that would be the more sought after things, so perhaps we're talking about game animals here. this forces them to rely more upon the cultivated stuff, and to gradually cultivate more and more of it. also, it seems like you would have pressure on their range of territory. if people are living in tribes and there are more tribes, it will be harder to move around as much without running into someone else's territory, so the smaller territory could also create a different kind of pressure, it seems to me. I see that kind of pressure easily incentivizing a people to increasingly try to manipulate the environment they're in, once they are unable to leave it. You have more incentive to try to catch and tie up the animals also if you need to keep them from running into someone else's territory where you cannot pursue them. but I also see power dynamics coming into play as more vulnerable and timid individuals seek protection with stronger more dominant ones and perhaps begin to cultivate specific food items as a kind of tribute. then control of surplus desirable food stuffs becomes a symbol of prestige and power on top of everything else, and presto!

Jane said...


'..altering the genetics of a food that is a staple of our society is also altering the adaptive environment, changing the course of evolution, and favoring only those whose immune systems are not sensitized to the new proteins..'

If I might make a suggestion, according to my understanding this is not how things work. The gut immune system is organised in such a way that ANY food protein can elicit 'oral tolerance'. Nowadays lots of people are sensitive to one protein or another, and this seems to be because their gut immune system is not working properly and oral tolerance is not established.

The oral tolerance system is very complex and the details are still being worked out. Still, it can be said with confidence that the same micronutrients are required for gut immune system health as for the health of any other system. Stripping out the micronutrients from grains is asking for trouble.

Have a look at this paper entitled 'Successful oral tolerance induction in severe peanut allergy' to get an idea of how it all works.

fr said...

>If you have water and fertile soil then there are going to already be lots of plants growing, and there will be lots of animals showing up to eat those plants, so any halfway competent hunter would be able to get some.

Have you ever hunted? Most animals are NOT easy to catch. Even today, armed with high-power rifles and scopes and all sorts of other high-tech gizmos, most deer hunters have a hard time bagging a deer. Catching animals with primitive weapons is much more difficult. Meanwhile, even where animals are not hunted, such as national parks, there is usually plenty of plant food for the taking at certain times of years. Berries and nuts, in particular, are extremely abundant in places. Agriculture doesn't neessarily mean using plows and whatnot. It could simply mean burning down some trees and scattering berries seeds and then coming back in a year or two to collect newly growing berries. Dittos for nut trees. Girdle and thus kill the other trees but leave the nut trees alone. Very easy. Wild grains are also abundant in parts of the world. So abundant, that all it takes is a few weeks of work to collect enough to provide food for a year. The competitors for this abundance are birds, which are not always easy to catch, but can be easily chased away.

Puddleg said...

Just because you adapt to some novel food, it doesn't follow that you will quickly loose your adaptation to everything that came before.
You will likely still be better adapted to the more primal foods as long as they stay in the diet; and animal foods are highly conserved in human diets.
Also, you probably don't really need much adaptation to digest foods that dont contain toxins and closely resemble your own body composition.

Don! said...

In a good rainy year, I've seen a geriatric arthritic dog catch squirrels. When the animals are that abundant, they're easy prey. Are you suggesting early humans were less adept hunters than a 12-year-old dog?

And LOL at just scattering seeds, and birds being easy to chase away. You can just scatter seeds and grow stuff if there's fertile soil and enough water. I've sowed seeds that didn't sprout until years later because there just wasn't enough rain. As for the birds, they're easy enough to chase away if they have abundant food sources elsewhere. If there's not much other food around, they're not going to leave that easily. If you're such a skilled bird whisperer, please, come and help me out so I can maybe get a few figs from my tree this year.

Don! said...

Nyx, I'm just bewildered by people who seem to think growing food is easy. Even if you do get the soil and water conditions right and get the food growing, you have to put so much effort into keeping the animals out that it makes more sense to eat the animals. They provide more calories per unit of effort. But now that I think about it, perhaps humans did originally grow plant food to use as bait to lure in animals, and then started eating the plants for whatever reason.

gallier2 said...

Also most people forget that the biggest source of meat comes from trapping. Rabbits, squirrels, birds, hedgehogs are rather abundant and not really difficult to catch. Let's not even start on seafood, musles, oyster, urchins, snails, crayfish, shrimps are really easy to catch (as children we went often to shrimp collecting in the North Sea shores, the most difficult was to get up at 5 in the morning when the tide was low).

allison said...

I have noticed that when it comes to diet, the interpretation of the data from the burgeoning field of genetics falls into familiar odeological patterns. Ambiguities tend to be resolved according to one's ideological sensitivities. The vegans and vegetarians see it one way and the meat-eaters see it another. From what I can tell, the classification of Europeans by haplotype is complex and inconclusive as to optimal diet. The best advice for an optimal diet may remain the simplest: don't consume more calories than you can burn, get off your duff and exercise and avoid manmade foods.

x1r said...

So when did these middle eastern immigrants start relying heavily on agriculture?

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fr said...

@don: the reason you have problems growing things is you are using delicate plants. Blueberries, blackberries, oaks and other nut-bearing trees grow NATURALLY. As for squirrels being easy to catch, that is because you aren't hunting them regularly. Start trying to live off the wild game and suddenly the wild game becomes quiet scarce. Trapping is easy for a very short while, then you exhaust the game and it isn't so easy anymore unless you have unlimited amounts of land at your disposal. Regarding birds, again, this is because you are talking about delicate plants. Wild grains grow naturally. For example, the American indians harvested natural wild rice. Birds are a competitor for wild rice, so why didn't the birds eat it all up? Because, unlike humans, birds can't harvest and store a year's worth of food at once. All they can do is migrate from feeding ground to feeding ground, and inevitably this leaves lots of areas underutilized. And they learn quickly that humans can shoot arrows and thus tend to avoid anyplace that has humans present. The net result is that humans can typically grab a substantial proportion of any plant food they want, in most places of the world, regardless of competition from birds or other animals.

There are only two situations where hunting is easy. The first is when there is a low supply of other humans, since humans can usually wipe out the other top predators (using dogs and weapons). That's when hunting and trapping is easy. However, within a very short period of time, human population will rise to where either humans are limited by starvation (same limit as is imposed on other top predators) or the humans will turn to eating plants.

The second situation is one where no top predator is able to be very successful and thus there is always a surplus of prey. The sea fits this description. Before modern times, the sea always had an essentially unlimited supply of fish. The limiting factor was the danger of the fisherman lifestyle. For whatever reason, other ocean top predators (big sharks, killer whales) were never abundant enough to make a dent in the vast supply of prey fishes.

Asim said...

All of these assumptions totally negate the fact that the gut flora is part of the digestive system. The traditional humans weren't as excessively clean and when they ate, they ate the bacteria that possessed the enzymes to digest a particular 'food' that people above are claiming these traditional people do not have a genetic pre-disposition to. There is a reason why fermented dairy product would create less issues for a person than non-fermented.

Also, the same genetic pattern can express itself differently depending upon the tissue or environment. To correlate these alleged genetic 'signatures' with food toleraces seems to be a stretch of imagination. Things tend to sound more impressive when you classify them in scientific terms, but classifying something in this terminology doesn't make it truth or more impressive for that matter.