January 22, 2014

Lactase persistence and natural selection (Sverrisdóttir et al. 2014)

The big question is: did the present-day high allele frequency in Europeans happen because of natural selection or because of admixture with a population that was already lactase persistent?

For example, the lactase persistence allele occurs at a non-trivial frequency in present-day inhabitants of the Americas, whereas it was zero there a few thousand years ago, with the culprit being post-1492 European colonization. The frequency change in the Americas didn't happen because of natural selection, but because a new population (Europeans) moved in.

If admixture with a lactase persistent population L is at play, then the question remains how L became lactase persistent in the first place. However, this transforms the problem from (a) seeking something in the European cultural or natural environment acting as an agent of selection, into (b) seeking something in the cultural/natural environment of population L. I don't know what L might be, but seeking a population with lots of cows is a good place to start...

Mol Biol Evol (2014) doi: 10.1093/molbev/msu049

Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe

Oddný Ósk Sverrisdóttir et al.

Lactase persistence (LP) is a genetically determined trait whereby the enzyme lactase is expressed throughout adult life. Lactase is necessary for the digestion of lactose – the main carbohydrate in milk – and its production is down-regulated after the weaning period in most humans and all other mammals studied. Several sources of evidence indicate that LP has evolved independently, in different parts of the world over the last 10,000 years, and has been subject to strong natural selection in dairying populations. In Europeans LP is strongly associated with, and probably caused by, a single C to T mutation 13,910bp upstream of the lactase (LCT) gene (-13,910*T). Despite a considerable body of research, the reasons why LP should provide such a strong selective advantage remains poorly understood. In this study we examine one of the most widely cited hypotheses for selection on LP – that fresh milk consumption supplements the poor vitamin D and calcium status of northern Europe's early farmers (the calcium assimilation hypothesis). We do this by testing for natural selection on -13,910*T using ancient DNA data from the skeletal remains of eight late Neolithic Iberian individuals, whom we would not expect to have poor vitamin D and calcium status because of relatively high incident UVB-light levels. None of the 8 samples successfully typed in the study had the derived T-allele. In addition, we reanalyse published data from French Neolithic remains to both test for population continuity and further examine the evolution of LP in the region. Using simulations that accommodate genetic drift, natural selection, uncertainty in calibrated radiocarbon dates, and sampling error, we find that natural selection is still required to explain the observed increase in allele frequency. We conclude that the calcium assimilation hypothesis is insufficient to explain the spread of lactase persistence in Europe.

Link

41 comments:

Fanty said...

At this topic I usualy recall one paper on LP development in Germans, that technically claimed LP in Germans spread only like between 1000 and 1500 AD and not in the ancient or even the stone ages. (assumtion based on LP allele tests on German corpses from the medival period, wich was something like 20% in 900AD, 40% in 1300, 50% in 1500 and 80-90% at present day.

It oracled around, it may have something to do with changed food during the middle ages and stuff like that, but was puzzled about the "extreme" speed in wich the allele apeared to have spread.

Unknown said...

Dienekes wrote
"I don't know what L might be, but seeking a population with lots of cows is a good place to start..."

Is it that goat's milk is not a candidate?

I'm not sure how natural selection (or for that matter artificial selection) favors milk drinkers, but I guess if there is nothing else to eat or drink, lactase persistence would win out. Until somebody figured out how to make cheese. It would seem to be a very old or very isolated situation.

Maju said...

As far as I know, the earliest known sites with the T allele at rs4988235 (causing lactase persistance among most Europeans in dominant Mendelian way) are three early Chalcolithic sites: two nearly contemporary ones in the southernmost Basque Country and another one in Götland.

In Götland (Pitted Ware culture) only 1/20 alleles was T (i.e. 1/10 persons had the CT combo, all the rest being CC and therefore likely lactose intolerants).

In Longar (Navarre, dated to c. 4500 BP) 1/7 individuals was TT, while the other six were CC (intolerant). There were no CT cases.

In San Juan Ante Porta Latinam (SJAPL, Araba, dated to c. 5000 BP), 4/19 were TT, 2/19 were CT, while the remaining 13 were CC.

What I found most interesting in the two Basque southern border sites (see here) was that there are too few cases of CT, strongly suggesting that the two populations (the TT and the CC carriers) were just beginning to mix at that point.

Both sites were war cemeteries it seems (mostly adult males, arrow injuries and arrow points) and their mtDNA is somewhat different from the Basque genetic pool of the Neolithic-to-Modern times (less H and U and more K, J and T/X). Their genetic pool, at least judging on the frequency of K and T/X, did not make it to the overall Basque genetic pool of later times.

It's hard to make extrapolations for the generality of Europe but, in the local context, my impression from this Basque data (one of the two European areas best sampled for aDNA, along with NE Germany) is that two populations were meeting at those military cemeteries of the Chalcolithic Age: a foreign one carrying CC (lactose intolerant) and a local one carrying TT (tolerant). The presumption of who were foreign and who local is made based on the relative discordance of their mtDNA pool with previous and later Basque pools (lots more of K and T/X, most likely T, also modern Basques have very high frequencies of lactose tolerance) but is of course somewhat uncertain.

IF there was at least some level of population replacement triggering the spread of the T allele in much of Europe it may well have begun in the Chalcolithic (all tested Neolithic farmers lack it). After that there may have been some strong selective pressure in the Metal Ages but, like the authors, I find difficult to discern which was it.

frog david said...

Fanty, this is interesting, do you have a reference? To me it feels like such rapid changes would not even be possible unless the population size was ridiculously small. I would be curious to read the paper describing this.

Ned said...

Given the unsanitary environment of mediaeval towns and the regularity of plagues milk and beer drinkers would survive whilst cold water drinkers would have died!

Gabriella Kadar said...

Fanty, if that is the case, then maybe the bubonic plague had an effect.

Grey said...

@Unknown

"Is it that goat's milk is not a candidate?"

IIRC some Arab populations have LP for camel's milk in Arabia so it's not so much a question of what kind of milk but how *critical* it is in the diet of a particular people at a particular time.

Assuming LP is a random mutation then the difference in the selective pressure to spread it through the population rather than just disappear must be proportional to how important it is to survival and/or reproduction.

Given how rare fixed LP is in the world I'd say this must mean an environment where crops were relatively unproductive and at the same time where cattle were relatively favored over other domesticated animals.

(I think the Atlantic coast, Swiss Alps and Dinaric Alps fit this because of the very heavy rainfall.)

.

The more cattle are favored by a culture the more critical their food products become.

.

Famines and long winters are the obvious negative selection mechanisms but I wonder if there could also be a founder effect.

If you take a coastal hunting/fishing culture like Ertobolle on the frontier of LBK and add cattle and other domesticated animals to the package to turn it into Funnelbeaker the benefit might not be new sources of food but *extra* food i.e. if you add cattle but it's the *children* who herd them and milk them and do most of the work then the males can carry on hunting and fishing.

So as a family unit if cattle or other domesticated animals means the children are more productive that might lead to a dramatic increase in total food production and a dramatic population increase.

Once you have a large population unusually (from a historical point of view) reliant on cattle and milk products you have a favored environment for the spread of a random LP mutation.

Fanty said...

"Fanty, this is interesting, do you have a reference? To me it feels like such rapid changes would not even be possible unless the population size was ridiculously small. I would be curious to read the paper describing this."

I am sure, I found this here on Dienekes Blog, not all that long ago (maximum 1 or 1,5 years ago?)

The population size WAS "riduculousy small".

Old, maybe outdated estamination (1960 or so):

Germany 100AD: 1 Million
Germany 900AD: 3-4 Million people. Germany 1200AD: 7 Million people
Germany 1300AD: 12 Million people
BLACK DEATH WAS HERE
Germany 1400AD: 6 Million people
Germany 1600AD: 11 Million
30 years war: "Kills 50% of all Germans. So what does mean? Bombed back to 6 Million?
Dont have stats for the time after.

;-)

No estaminations but real numbers:

Germany 1834: 23 Million
Germany 1871: 41 Million
Germany 1900: 56 Million
Germany 1910: 65 Million
Germany 1919: 61 Million
Germany 1939: 79 Million
Germany 1946: 65 Million
Germany 2013: 82 Million

Estamination for 2040 (low child birth rate): 50 Million

Maju said...

For what I've read in the Middle Ages, the main source of milk were goats. So what "Unknown" says makes good sense to me.

The question is that, other than for calcium, milk is not such an important source of nutrients, provided that alternative foods are available. One has to assume that either a lactose-tolerant population expanded massively OR that being able to drinking raw milk (cheese, etc. are OK for lactose intolerants) became a matter of life and death for an extended period of time in much of Europe.

And unless there was a milk-drinkers cult who murdered everybody else, I can't really imagine how that happened.

eurologist said...

I have previously speculated that antibodies and even bacteria and viruses in the milk could help protect against diseases. For example, as we all know, cowpox infection protects against smallpox.

mikej2 said...

The place of mutation and how it came to NW-Europe is not the question if we look only the high diversity of the allele T in NW-Europe. Much more relevant question is the environment, livelihood and natural selection. We are missing the point if we don't see the consequence of random mutation and it's effect in different environments.

mikej2 said...

Sorry if I wrote in my previous message "high diversity", should be "high distribution in NW-Europe.

So the message was that mutations are random, but how it survives depends on the environment. Mutation can be negative, neutral or positive. If it is neutral it can still survive and wait for better opportunity in some other place and under different condition. In a big view it doesn't matter where single mutations occurred first time. This is my answer to the question about the high distribution of LP variant in NW-Europe.

mm said...

Could You please suggest any good genetic paper arguing against out of Africa theory?

Unknown said...

Grey wrote:
“Given how rare fixed LP is in the world I'd say this must mean an environment where crops were relatively unproductive and at the same time where cattle were relatively favored over other domesticated animals.”

But it says here that: “Goat’s milk is tolerated by only 40% of CMA (Cow’s Milk Allergic) children.”

http://www.allergyclinic.co.nz/guides/21.html

I’m not sure exactly how this works. But it seems like goat’s milk could have caused the same kind of problems. And encouraged lactase persistence.

And because goats appear to have been domesticated earlier and in drier places, maybe it was goats and goat’s milk that started this whole thing off. Later on, it just applied with more force to people who had to or choose to rely on cows.

There’s also again a problem with using the static population analysis.

One scenario is emigration. Goat herders go north to herd cows. All could handle goat’s milk. But, according to the stat I quoted above, about half can’t handle cow’s milk. So the ones who can’t handle cow’s milk move back south and go back to goat herding.

Emigration causes the genetic change in the “population.” Cow milk drinkers are the only ones left. Selection is accomplished by people moving, not by a kill-off.

I’d suggest again that it’s important to remember that people are not dumb about these things. They can observe these factors like other animals can’t and can alter the environment (stop herding cows) or leave it (go where there are no cows).

This is not strictly speaking natural selection. But it is selection. Maybe what Darwin called artificial selection.
Also, in the case of LBK, it is becoming clear that they were heavily cattle herders and less dirt farmers. Way back when, Andrew Sherratt in forming the Secondary Products Revolution, postulated that the giant vats LBK used were for storing milk. (Later he decided they were probably beer-making vats.) Maybe LP arose in some isolated situation and very slowly made its way into much later populations.

http://www.ucl.ac.uk/mace-lab/gallery/lactase

Gnarlodious said...

Goat's milk is typically much lower in lactose but higher in fat.

Grey said...

@Maju

"For what I've read in the Middle Ages, the main source of milk were goats."

If the percentage of milk in a population's diet is 5% does it matter if it is goats or cows?

What matters is the percentage of milk in the total diet (or the percentage at critical times like winter).

.

"One has to assume that either a lactose-tolerant population expanded massively"

The only thing you need to assume for that to occur is that compared to the *alternatives* available at the time in certain regions at a certain time that a cattle-centric milk drinking package produced more calories.

Given the location of the main LP regions that is extremely easy to believe especially when you take into account we are talking about a forager type population density becoming shifting herders.

.

"The question is that, other than for calcium, milk is not such an important source of nutrients, provided that alternative foods are available."

1) Yes, *provided* that alternative foods are available. That is the critical point. You need an environment where cattle are favored and other alternatives aren't both at the same time.

2) Iodine.

.

@Unknown

"But it says here that: “Goat’s milk is tolerated by only 40% of CMA (Cow’s Milk Allergic) children.”"

The selection pressure will be proportional to the total percentage of milk in the diet - hence LP for camel milk among Arabs in Arabia *and* the availability of alternative calories, again hence Arabs in Arabia and camel milk.

.

mikel2

"The place of mutation and how it came to NW-Europe is not the question if we look only the high distribution of the allele T in NW-Europe. Much more relevant question is the environment, livelihood and natural selection."

Agree. The mutation itself could have come from Mars. The critical point is how strongly it was obviously selected for in certain regions of Europe at a certain time because of the environmental conditions in those regions at that time.

Grey said...

@Unknown

"Also, in the case of LBK, it is becoming clear that they were heavily cattle herders and less dirt farmers."

Again, it's not the presence of cattle it's how critical milk is to the total diet. If the LBK farmers diet was 70% crops, 20% meat and 10% dairy then the selection pressure is different to a northern shifting agriculture population where the diet is 30% crops/foraged, 40% meat, 15% dairy and 15% milk (for example).

The areas with very high LP would need to have been areas where milk was plentiful but other food was not - which is obviously the case as otherwise the LBK farmers would have expanded there themselves.

If the LBK package didn't work in those northern reaches then if the options were:

A) Foraging

or

B) Shifting forager / herders

then all you need to explain the LP distribution is that at a particular point in time option (B) produced more calories than option (A) and a large percentage of those calories were in the form of milk.

Maju said...

"If the percentage of milk in a population's diet is 5% does it matter if it is goats or cows?"

What matters is that focusing on cows when most of the milk of Europe was produced by goats is absurd.

"What matters is the percentage of milk in the total diet (or the percentage at critical times like winter)".

That's true but hard or even impossible to measure without statistical data or, in most cases, even a sloppy historical annotation.

For whatever is worth, oral accounts say that here a poor person's meal often was
"acorn bread and goat's milk". So maybe it was a matter of poverty, being goat's milk almost always available (but not meat or even bread). And that would be indeed a matter of life and death: drink milk or starve.

That would add weight to goat's milk importance, because poor people could not afford cows but goats are cheap and hardy and even the poorest farmer surely had some.

Maybe it's less a matter of ethnic ways of life and more of a social class way of life. If so, it makes all sense that lactose tolerance got fixated only since the Chalcolithic, when social stratification began.

"The only thing you need to assume for that to occur is that compared to the *alternatives* available at the time in certain regions at a certain time that a cattle-centric milk drinking package produced more calories".

Cattle (cows) was not (judging on medieval data) for dairying in most cases but for traction and meat. Also since the Chalcolithic (and more so in the Metal Ages) in many social realities it would have been owned by a growingly reduced class of privileged people.

"Given the location of the main LP regions that is extremely easy to believe especially when you take into account we are talking about a forager type population density becoming shifting herders".

The LP concentration region of Europe (considering only this allele, there are others less well known) is very large and includes all West and Northern Europe. Many of those areas (Britain, Basque Country, for example) were not particularly dedicated to cattle but to sheep herding instead. However, given that sheep only produce milk in certain seasons, it's doubtful that they are the real cause.

"Yes, *provided* that alternative foods are available. That is the critical point. You need an environment where cattle are favored and other alternatives aren't both at the same time".

Again: cattle is expensive and would not be available for the masses. If milk was to be a staple, it had to be goat milk.

...

Besides:

"Unknown" said: "Goat’s milk is tolerated by only 40% of CMA (Cow’s Milk Allergic) children."

Milk allergy and lactose intolerance are different things. Allergies are developed immune reactions, lactose intolerance is a genetic inability BY ADULTS (not children) to digest lactose (milk's sugar) and to a large extent a very normal thing (why would adults need to be able to digest milk before domestication?)

Grey said...

@Maju

Fair enough. There are two arguments.

1. Does Funnelbeaker represent a shift from forager/fisher to shifting forager/farmer which led to a dramatic expansion of the native forager population in northwest Europe around 5000-6000 years BP.

2. When and where LP took off.

I do tend to jumble the two arguments together.

andrew said...

"Blogger mm said...
Could You please suggest any good genetic paper arguing against out of Africa theory?"

There are none. The universal consensus among published authors of genetics papers is that modern humans originate in Africa. The only dispute among published authors of genetics papers is when modern humans left Africa which range from about 120,000 years ago on the early side to about 60,000 years ago on the late side.

Maju said...

@Grey: Funnelbeaker only affected Northern Europe and parts of Central Europe. Everything West of the North Sea cannot be explained by it. Anyhow Funnelbeaker (other than in Denmark and maybe some nearby areas) was rather a "fashion" affecting several different cultures (late Danubian and early Kurgan alike).

If anything it might explain the LP phenomenon in its very specific area: Northern Europe senso stricto, but never in the Atlantic Islands, SW Europe, etc.

War Lord said...

"The question is that, other than for calcium, milk is not such an important source of nutrients, provided that alternative foods are available."

LOL You are walking around a big elephant and you don't see him. Milk is a source of the best natural proteins that are available. It is a nutrient that has the most profound effect on physical growth. Nothing can't match it - only pigmeat comes close. It would be incredible, if lactose tolerance didn't mean a huge advantage for all populations, who bear this gene. And indeed, the sudden expansion of the Corded Ware folk must have been a direct consequence of this adaptation. You should see the comparison of stunted dwarfs from the Linear and Lengyel culture with Corded Ware people - it would open your eyes.

I think that acknowledging these relationships will mean one of the last nails to the grave of Marija Gimbutas' Kurgan theory, because we can't suppose an overwhelming migration from the steppes to Central/North Europe just in a period, when lactose tolerant populations started to exploit their massive genetic advantage.

Maju said...

You're partly right, War Lord, milk is a great source of proteins and fat, much like meat. I realized the "elephant" in my second comment (some time after the one you quote), I believe, when I suggested that if milk was about the only decent source of calories and proteins available, then the positive selection makes sense.

That implies sustained food scarcity, what brought me to the hidden (taboo?) issue of social classes, which arose precisely in the Chalcolithic, when we begin to spot some LP alleles.

The rich would have generally no trouble in getting the best food, be it milk or whatever else, but for the impoverished masses of agricultural workers (the vast majority of the population until very recently) maybe their main source of protein and fat was goat milk (cows would have been to expensive to buy and keep for them, at least in many cases).

Oat meal with milk, bread with milk, walnut bread with milk, acorn bread with milk... that was often the staple food for most people in the past. And in most cases the milk was produced by goats.

"I think that acknowledging these relationships will mean one of the last nails to the grave of Marija Gimbutas' Kurgan theory".

Not at all. One thing has no relation with the other: IEs did not bring the LP allele most likely and they did not cause such a massive genetic impact, especially in the West - their influence was in essence of cultural and linguistic assimilation by means of aristocratic domination, as corresponds to the barbarian conquerors of all times (think Mongols or their Turkic relatives for example, or Arabs too). The Kurgan model of IE expansion is extremely solid on archaeological grounds: this issue most likely has no relation with the LP allele, which shows rather the opposite cline (peaks to the West, not to the East).

Chad Rohlfsen said...

http://www.sciencedaily.com/releases/2009/08/090827202513.htm

http://www.sciencedaily.com/releases/2013/08/130828092010.htm

Maybe some of this will offer some insight. Yogurt would've helped the transition to a diet with large amounts of cow milk.

Chad Rohlfsen said...

The Brits and Scandinavians have the highest skin reflectance and lactose tolerance. Vitamin d is needed to digest calcium. There may be some kind of connection.

Maju said...

@Chad:

The first study is a mere simulation. I have meet it a couple of times but I fail to see the merit or at least the evidence that could back the simulation. The later is a letter speculating around the cheese-making sieve of Poland found last year and makes some blatantly unfounded claims, notably:

"By the late Neolithic and early Bronze Age, around 5,000 years ago, the LP allele was prevalent across most of northern and central Europe"...

Where's the evidence of that claim? I mentioned ago the first known aDNA instances of the T allele (not at all prevalent yet, at least in the sampled sites) and these are already deep in the Chalcolithic (sometimes confusingly lumped into Late Neolithic or Bronze Age in English). All Neolithic samples we know of, very especially in Central Europe, are LP negative. The only "evidence" is the abundance of cattle bones but nobody really knows if these were used for traction, meat or dairying (and if dairying if the produce was raw milk or rather cheese, a friendly food for most lactose intolerant people).

Also:

... "milk may have helped (...) because of its relatively high concentration of vitamin D"...

What is a blatantly false claim: milk has only small amounts of vitamin D (unless industrially enriched). If that would be the reason, people would have focused on fish, not milk, because fish is the only relevant dietary source of vit. D.

So I think that all these scholars are very much confused, like trying to hit a piñata many meters away from the target but still believing they are right on it (to the hilarity of the spectators).

They say that "just because it's published in Nature, it does not mean it's wrong". But it does not mean it's right either. Certainly not in this case.

Chad Rohlfsen said...

@Maju

I had questions on the vitamin D in the milk. I know that vitamin D is important in absorbing calcium. Maybe the pressure to drink milk as necessity, brought about even lighter skin to absorb the calcium, or it was sorely lacking in their diet.

I'm not sure how it all plays together, but the links between the lightest skin and highest lactose tolerance are there.

Maju said...

@Chad:

There are two main known effects of vitamin D, one is bone formation and has been known for long, its lack producing rickets. However in the last years a key role of vitamin D in early brain development has been highlighted as well, and I'd dare say it has been even more important in evolutionary terms, leading to "white" pigmentation at latitudes far away from the ancestral tropics.

I have been collecting in my blogs some of the relevant links:
→ http://www.sciencedaily.com/releases/2008/04/080421072159.htm
→ http://www.sciencedaily.com/releases/2010/06/100621125137.htm

Other recently understood roles of vitamin D are:

· Disease prevention and recovery: → http://www.sciencedaily.com/releases/2009/08/090821211007.htm
· Cholesterol control: → http://www.sciencedaily.com/releases/2009/08/090818182053.htm
· Prevention of urinary infections: → http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015580
· Prevention of allergies: → http://www.sciencedaily.com/releases/2011/02/110224103244.htm

I don't know if calcium absorption is linked somehow to all these effects or only to the issue or bones (as I would say on shallow inspection) but what is clear is that vitamin D is crucial for much more than the classical issue of rickets.

So, unless it can somehow be demonstrated that calcium is key in all these aspects, I would focus on proteins and fats instead, which is what natural milk actually has to offer to people with limited access to food (typically poor people).

And that's why I emphasize goats, because these hardy "cheap" animals would have been available to nearly all people, unlike cows most likely. However the ability to digest milk, whatever its source, was available only individually on random genetic basis.

Unknown said...

Deprivation and poverty.

Milk is all that’s left. I guess you already ate the last goat or cow.

That certainly could have happened to Corded Ware folk.
Compared to what was going on in the south, it looks like at least
some of them were impoverished and living on the edge.


https://www.academia.edu/1347342/A_Revision_of_Corded_Ware_Settlement_Pattern_-_New_Results_from_the_Central_European_Low_Mountain_Range

Corded ware would certainly be a candidate...
“...in famine conditions, such as when crops fail, they are likely to have eaten all the fermented milk foods, leaving only the more high-lactose products. This would have caused the usual lactose intolerance symptoms such as diarrhea. Diarrhea in in healthy people is not usually life-threatening, but in severely malnourished individuals it certainly can be. So famine could have led to episodes of very strong natural selection favoring lactase persistence.”
http://www.uu.se/en/media/news/article/?id=3154&area=2,10,16&typ=artikel&na=&lang=en

But around the same time there were lactase persistent people in Iberia,
who would probably pass that mutation along to Celtic-speakers and western Germans who followed them. 27% of a population is a huge number when everything else is coming up zip.

And BTW I don’t agree with much David Anthony says, but I have to agree that “Kurgan Culture” is an outdated and useless term that does nothing for the question of Indo-European language origins or archaeology in general.

eurologist said...

Light skin color (relative to received sunlight) is only possible with sufficient folate intake. Milk contains 5-10 microgram per 100 g:
http://www.ncbi.nlm.nih.gov/pubmed/10759136
so, an individual consuming 1l of milk a day (not unusual in Central and Northern Europe) receives 50-100 micrograms a day. While recommended intake is 300-400 micrograms, ill effects clearly are produced at a much lower rate of intake. Drinking milk can prevent this. Conversely, given a certain amount from other sources, milk intake allows for a lighter skin color, and thus better vitamin D production.

Folate-binding proteins in milk may also play a role, and may help avoid destruction by sunlight in the skin.

See also:

http://ajcn.nutrition.org/content/80/6/1565.full

"Meals prepared for the milk group contained three 245-mL servings of skim milk daily...

erythrocyte folate concentrations declined only in the nonmilk group and remained unchanged in the milk group"

Simon_W said...

Maju's first comment is quite interesting; it reminds me of this paper showing that  the cultivation of cereals in Britain did not last, and that between 3300 and 1500 BC Britons became largely pastoral, reverting only with a major upsurge of agricultural activity in the Middle Bronze Age:

http://dienekes.blogspot.ch/2012/10/the-winding-road-to-agriculture.html

These first documented instances of the T allele Maju mentioned occured at about the same time frame, 3000 and 2500 BC. The foreign population in those war cemeteries in the Basque country appears to have been more Early Farmer-descenced, judging from their mt-DNA. Yet, I think, it may have been them who introduced the T allele to the Basque country – possibly they didn't bring their women along, so their mt-DNA didn't have much of an impact on the Basque gene pool – the T allele on the other hand was afterwards favoured by selection.

Maju said...

@Simon:

Not sure if you understood well the situation in those Chalcolithic "military" necropolis of the southernmost Basque Country: not only the T allele is found in some individuals (not most) but it is almost always found in the diploid TT form (while the C allele is found almost only in the CC diploid form). So in essence those "soldiers" included two almost unmixed populations: a TT one and (the majority) a CC one, with only rare instances of admixed individuals (CT).

I titled that entry "caught in the act" because it really underlines the existence of two different and mostly unadmixed source populations for those cemeteries, based on the linkage disequilibrium of the LP allele.

I can't know which populations are, I just more or less arbitrarily described the majority CC group as "foreign" because it does not fit with modern Basque LP frequencies and because, overall, the cemeteries seem rather different from the (pre-)historical Basque sequence of mtDNA pools, with much greater frequencies of haplogroup K and other "Neolithic" ones, like J and "T/X" (sic) and lower ones of H and U. Following the same logic I considered the smaller TT subpopulation to maybe have local origins. But I could be completely wrong in my assessment, especially considering that the Atapuerca farmer was CC.

In any case the central point is that, because of the strong linkage disequilibrium found, at that moment, some 5000-4500 years ago, there was already somewhere a TT population, apparent as the smaller subpopulation in those two military sites.

Maju said...

@Eurologis:

Effectively folic acid (folate) is almost certainly the main factor in the dynamic equilibrium of human skin color leading originally to dark skin and later to the retention of at least the ability to tan in most "white" people. Skin cancer may be a co-factor but it would seem to weight less. My reference was other (http://www.pnas.org/content/107/suppl.2/8962) but same result.

Anyhow folic acid is readily available in many foods, notably green leaf vegetables, fruits, nuts, legumes, meat, eggs, fish, grains, etc., as well a milk and various dairies. Considering the ability to tan in summer (and get paler in winter) and the general availability of this nutrient, I'd say that attributing the massive genetic swap to just folates looks quite unlikely.

Your nutritional link only makes sense provided that the availability of folic acid was low. You just have to read the abstract:

"Design: Thirty-one young women were fed low-folate diets"...

...

@"Unknown":

Your link seems interesting but we have to understand that, while in Central Europe the percentage of LP phenotype is rather high to very high, the rs4988235-T variant is quite lower, so at least part of the Central European LP phenotype must be explained by some other unknown gene.

The areas of highest rs4988235-T are Scandinavia, Britain, Ireland, the Basque Country, Brittany and other parts of SW France. Of these only Scandinavia was affected by Corded Ware.

Ref.: http://www.biomedcentral.com/content/pdf/1471-2148-10-36.pdf

Grey said...

a lot of interesting posts - ty all

Chad Rohlfsen said...

I apologize if this is a double post. I lost my connection a bit ago.

Vitamin D is important in absorption of calcium.

http://ods.od.nih.gov/factsheets/VitaminD-HealthProfessional/

There certainly is a link with the lactose, folate, and skin coloring. Grains sure appears to have made a big difference in the skin color. I wonder what color Europeans might be today if they did not give up the strict meat and fish diet.

There has been a four to five fold increase in Rickets in Britain since 1997. I believe that most of it was in the darker complexioned immigrants though. It is on the increase in America as well.

eurologist said...

Your nutritional link only makes sense provided that the availability of folic acid was low.

Maju,

Well, you are the one who brought famine into the discussion. If milk played any role at all, you could think of a scenario where beans, peas and lentils had failed or become scarce enough to only be available to the ruling class or male soldiers. Grains are not particularly high in folic acid, and people who don't have much to eat but grains and milk might not be so smart and vary their diet with greens (not available in the winter) or nuts (not available outside the fall and not if forest harvesting like hunting is, as often was the case, only allowed by the ruling class).

So, perhaps, women had milk and grains available, but not much else. The ones who only had water and grains certainly did not produce many healthy children.

Maju said...

@Eurologist: I can think of an scenario in which the main staple food for the farmer masses was acorn bread (or similar: oat meal, regular bread, chestnut dishes) and goat milk. This is actually for all I know a historical scenario in fact, just that I'm extrapolating it to earlier but very much comparable times. In such conditions much of the caloric intake would come from the bread-equivalent but it's aminoacid quality would be very poor. This is a well known problem in vegan diets which has to be managed but is non-existent in ovo-lacto-vegetarian diets, where milk and eggs provide good quality proteins and other nutrients less common in vegetals sources (assimilable iron for instance, vitamin B12, possibly other stuff). Additionally milk also would have provided extra fat (more calories in essence).

A diet that would also include legumes would be much less risky but I'm not sure if legumes were available in all situations and seasons. That's something to research but, for what I have read about old style basic diets in Western Europe, legumes were not staple, while goat milk was instead. Often even cereals were scarce, being replaced with wild nuts like acorns or chestnuts, but goat milk was there readily available all year long for almost nothing, and hence for all, even the poorest ones.

In such situations, lactose intolerant people would have suffered a severe disadvantage, as they could not drink the most readily available food, a good quality one incidentally.

Of course episodes of famine (in addition to likely severe class inequality in food access) may have been punctual episodes of acceleration of the selective sweep.

... "greens (not available in the winter)"...

I am pretty sure that several greens like lettuce and dandelion (edible), as well as other "herbs", are available year long in Atlantic climate. We have lost a lot of traditional such wild vegetable foods but they were once common.

... "nuts (not available outside the fall and not if forest harvesting like hunting is, as often was the case, only allowed by the ruling class)"...

I have on good account that acorn and chestnut bread (or puree) were eaten often instead of the preferred cereal bread by poor people in Spain and the Basque Country respectively. I can only imagine that "privatization" of forests happened only rather late, as they became rarer.

"So, perhaps, women had milk and grains available, but not much else."

That's in essence my point. Other foods (other than greens) were available for many only occasionally, if at all, not enough to provide a healthy diet without the milk supplement. But that would not affect just women but the general population (not sure why you say "women", I guess that's because they provide for the nutritional needs of babies with their body, what would have a multiplying effect).

Chad Rohlfsen said...

Study of Medieval Europeans with high lactose tolerance; indicating that the Plague had nothing to do with the increase in lactose tolerance, as medieval and modern rates are similar.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0086251

Maju said...

@Chad: a most interesting reference for this discussion, thanks.

Not only shows that in Central-West Germany (there are several towns named Dalheim in Hesse and Rhineland, not sure which one it is) modern-like LP alleles were already established c. 1200 CE, but, by citation of Nagy 2011, it reminds us that further to the SE, in Hungary, LP prevalence was still low just a few centuries before (although higher than among Neolithic farmers).

Therefore there may have been various different localized processes leading to the prevalence of LP alleles and phenotype, each with its own chronology.

eurologist said...

Maju,

All of what you state is perfectly true for the SW/ W Atlantic region - including a diet of acorns in famine, as well as (almost) all-year-round greens. So, that's important to contemplate considering early high adult lactose tolerance, there.

On the flip side, in C to N Europe, Acorns historically play less of a role; sometimes roasted beechnuts were used as a substitute to grain. And due to the generally wet climate, cows were much more common than goats, and cow's milk a staple (while goats milk and seasonal sheep's milk was almost always made into cheese but very rarely drunk).

My emphasis on women is due to the known detrimental effect of folate deficiency on successful pregnancies and healthy children, combined with the numerous additional nutritional benefits of milk. A multiplier, of sorts - especially if it turns out that my hunch that the immune system is also involved, proves correct.

Simon_W said...

@ Unknown

Your link to the study on the Corded Ware site of Wattendorf-Motzenstein is certainly interesting, so thank you for providing this. However, I don't think that it suggests that the Corded people were impoverished and living on the edge. At least not more than other Neolithic cultures.