Sunday, April 29, 2012

Tishkoff on the origins of patoralism in Africa

Convergent adaptation of human lactase persistence in Africa and Europe
Tishkoff et al
(Link)

"Archeological evidence suggests that cattle domestication originated in southern Egypt as early as ~9,000 years ago but no later than ~7,700 years ago and in the Middle East ~7,000-8,000 years ago28, consistent with the age estimate of ~8,000-9,000 years (95% c.i. ~2,200-19,200 years) for the T-13910 allele in Europeans. The more recent age estimate of the C-14010 allele in African populations, ~2,700-6,800 years (95% c.i. ~1,200-23,000 years), is consistent with archeological data indicating that pastoralism did not spread south of the Sahara and into northern Kenya until ~4,500 years ago and into southern Kenya and northern Tanzania ~3,300 years ago28,29. The ability to digest milk as adults is likely to be adaptive owing to the increased nutritional benefits from milk (carbohydrates as well as fat, protein and calcium) and also because milk is an important source of water in arid regions2,28,30,31. Considering the symptoms of lactose intolerance, which includes water loss from diarrhea, individuals who had the lactase persistence–associated alleles and could tolerate milk could have had a very strong selective advantage2. This is supported by our high estimates for the selection coefficient (s = 0.035-0.097). Because the selective force, adult milk consumption, is associated with the cultural development of cattle domestication, the recent and rapid spread of the lactase persistence–associated alleles, together with the practice of pastoralism in East Africa, is an excellent example of ongoing adaptation in humans32 and coevolution of genes and culture3."

"We observe the oldest age estimates of the C-14010 allele, ~6,000-7,000 years (95% c.i. ~2,000-16,000 years), in the Kenyan Nilo-Saharan and Tanzanian Afro-Asiatic populations (Table 1). We also observe an old age estimate in the Tanzanian Sandawe, but its low frequency suggests it was introduced via recent gene flow (Supplementary Discussion). However, we cannot distinguish with certainty whether this allele first arose in the Cushitic-speaking Afro-Asiatic populations, who are thought to have migrated into Kenya and Tanzania from Ethiopia ~5,000 years ago33 and practice a mixture of agriculture and pastoralism, or in the Nilotic-speaking Nilo-Saharan populations, who are thought to have migrated into Kenya and Tanzania from southern Sudan within the past ~3,000 years33 and are strict pastoralists28. These results are consistent with both linguistic34 and genetic data (F.A.R. and S.A.T., unpublished data) indicating cultural exchange and genetic admixture between these groups. The absence of C-14010 in the southern Sudanese Nilo-Saharan–speaking populations suggests that this allele either originated in or was introduced to the Kenyan Nilo-Saharan populations after their migration from southern Sudan. Regardless of the population origins of the C-14010 allele, it spread rapidly throughout the region along with the cultural practice of pastoralism, consistent with a demic diffusion model of genetic and cultural expansion35."

13 comments:

  1. It'd be most interesting if it could be demonstrated that cattle was first domesticated in Egypt and not Anatolia/Kurdistan as most papers on the matter claim. Sadly, the references mentioned in this paper are not available online what makes more difficult to contrast their evidence and logic.

    IF that would be the case, a plausible model for the emigration of E1b lineages to West Asia and Europe could be inferred. I wouldn't be too surprised but I'd like to know more about the relevant archaeological and how it contrasts with the archaeological evidence for the domestication in Anatolia. 9000 years ago anyhow, seems a bit too late for first domestication events, which are typically in the 11 Ka ago zone, right?

    9000 years ago Neolithic had already penetrated into SE Europe and 7500 years ago it had arrived to coastal Iberia. So, based on these dates, I would rather think of diffusion from West Asia and not independent local evolution.

    As for the lactose tolerance alleles, the relativeness and clinality of its influence in the various East African groups fit better with what I would expect of a less important adaptive allele, as it is (you can always eat something else, including some dairies) than the extremist claims that are invoked for its much more dramatic hegemony in parts of Europe, where it seems more a founder effect fluke than actually adaptive.

    ReplyDelete
  2. Maju, I plan to put up the quotes [that you mention] from the African Archaeology book edited by Stahl to back up Tishkoff's reference. It won't be for several weeks, however, as there is still plenty of material on the same topic in the Archaeology of Africa book (Shaw, Sinclair, Andah, and Okpoko, editors) that I haven't gotten to.

    Regarding E1b, I've put up earlier posts suggesting one early possible path of E1b into Europe during the LGM. That's probably enough from me on E1b, for now. (See the posts "Gazelle Hunters" and "Mediterranean Coastline During the LGM.")

    Regarding the dates that Tishkoff is mentioning, she is referring specifically to cattle domestication. The earlier dates that I believe you might be referring to are for sheep and goats. Zeder's 2008 open access paper "Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion and impact" has these domestication dates BP: sheep 11,000; goats 11,000; pigs 10,500; cattle 10,000(Upper Euphrates Valley). However, she states that morphologically altered domestic cattle are not found in Central Anatolia until after 8,500 BP. So there is a fairly long window for the Fertile Crescent cattle domestication event.

    Why not local evolution in Africa? The alleles for lactose persistence are different in most Africans from Middle Easterners and Europeans. There's plenty of evidence that the cattle are also different. The people living in Southern Egypt and Nubia certainly had plenty of opportunity to be around aurochs. They were adept hunters. From the rock art, they clearly hap many methods for rounding up and securing ungulates, including giraffes, if these Karkur Tahl pictures are correct. Frankly, I haven't posted some of these, as I find the images of trapping giraffes to be a little disheartening.

    I prefer to take the view of A. Muzzolini on this topic. Populations under demographic and climatic pressure simply refine what they already know. Domestication is a little over-rated. Hunters across the globe probably had been testing the idea for ten's of thousands of years until population pressure and climate forced the issue.

    There's some evidence that there were at least three different cattle domestication events in Africa. I'm not there yet. What I've discovered as I investigate this topic is that there is a huge amount of evidence for cattle domestication in Africa that is simply being ignored or is treated with great skepticism.

    I'm not sure of what you mean by your last paragraph. Not to be glib or anything, but I do think that Tishkoff et al make the case fairly strongly that lactase persistance in African pastoral groups is under very strong selection. This is perhaps due to the lack of water in the Sudan, Kenya and Tanzania and the fact that milk is an important source of water for these pastoralists.

    By the way, nice paper on Magdalenian mtDNA H. Thanks for putting it up. Much to digest there. It's a great summary paper and a great read. Very exhaustive methodology by the authors, as well.

    ReplyDelete
    Replies
    1. Just a quick search (I don't keep exhaustive record on the matter) led me to this abstract, which says 10,500 years ago in the Near East. Wikipedia, who lead me there, says that in the Turkish-Iraqi border area, that is: Kurdistan. Kurdistan was also where goats and maybe sheep were first domesticated - wheat and other cereals instead may have been domesticated first in Palestine instead.

      C. 9000 years ago Neolithic had arrived to Greece and Pakistan with all the animals and plants, so it makes sense that it also arrived to Egypt about the same time and with a very similar cultural and biological baggage.

      But I see undocumented claims for other areas, including Africa and India (zebuine cattle I presume), so I guess that the matter is at least somewhat controversial.

      "Domestication is a little over-rated. Hunters across the globe probably had been testing the idea for ten's of thousands of years until population pressure and climate forced the issue".

      I like the idea. However that doesn't mean that there was not a rather specific order of events in the Neolithic Revolution as such, meaning that there were centers of Neolithic Revolution and a periphery towards these innovations (often the whole package or most of it) spread towards. Said that, Neolithic was probably at first not much more efficient than foraging, so I agree that it's somewhat overrated in several senses.

      "... that there is a huge amount of evidence for cattle domestication in Africa that is simply being ignored or is treated with great skepticism".

      Logically I'll treat it with skepticism until I see the evidence because I've grown accustomed to the other claim, that of domestication in Kurdistan or SE Anatolia. More so when the dates claimed appear to be too late, more consistent with being a destination of cultural diffusion than the origin of that new bio-technology.

      "Not to be glib or anything, but I do think that Tishkoff et al make the case fairly strongly that lactase persistance in African pastoral groups is under very strong selection".

      45% of prevalence at the most is not "very strong" selection. 100% of prevalence is. But on the other hand 100% of prevalence may also be a mere random founder effect unless you can demonstrate that people lacking the allele die almost systematically without leaving offspring. That's strong selective pressure: have it or die.

      I think that there must be some adaptive value to lactose persistance but I doubt it's half of half of half as dramatic as some claim. I do not see the case clear at all: not in Africa (where there is a clear clinality from Sandawe to Afroasiatic but still lots can't normally digest milk - and they do not die off and have not died off in so many millennia) and not in Europe, where the alleged logic behind the high apportions of lactase persistence doesn't seem to hold scrutiny: apologists claim cows then we know people milked mostly goats and cows were used mostly for work and meat, goats are everywhere including where people is mostly lactose intolerant... and Neolithic peoples with both cows and goats were lactose intolerant... it just doesn't add up: it must have been a fluke, the allele was there the same R1b or Rh- are: founder effects and/or drift. In other words: a fluke.

      Never mind that alleles and phenotype do not add up either in many cases. For example Sudanese are almost 90% able to drink milk but the alleles only explain 45%. Even more radical is the case with Italians, most of which drink milk normally even if only 12% have the allele. Instead Tajiks are mostly lactose intolerant even if by genes they should be largely able to drink milk. There seems to be elements that are not genetic, as in so many other things (or unknown alleles).

      Delete
    2. "By the way, nice paper on Magdalenian mtDNA H. Thanks for putting it up. Much to digest there. It's a great summary paper and a great read. Very exhaustive methodology by the authors, as well".

      It's a most important paper because it should shut up those who have been claiming that H is hyper-recent in Europe and must have expanded only in the Neolithic.

      The paper was not just on H anyhow... for instance, Magdalenian/Epipaleolithic "Basques" appear to have been mostly U, although the sample is very small, and to have got at least some continuity into Bronze age (the same U haplotype was spotted in Magdalenian and Bronze Age in the same area, what should not be a fluke).

      Regardless, there may have been some expansion of H and other lineages which is already apparent in the Neolithic, which has mtDNA pools roughly modern.

      Delete
    3. "But I see undocumented claims for other areas, including Africa and India (zebuine cattle I presume), so I guess that the matter is at least somewhat controversial."

      Maju, I'll comment more on selection and lactase persistence later this evening. Regarding separate domestication events from that in the Upper Euphrates basin, I cannot say definitively that the domestication events there and in Egypt were independent. However, it does appear that the domestication of the Zebu was an independent event:
      http://mbe.oxfordjournals.org/content/27/1/1.full.pdf+html

      This paper does add to the body of evidence that cattle domestication wasn't a one off event.

      Regarding the paper on the Magdelenian in Northern Spain, I'm still reading and will comment on your blog when I have had a chance to digest it (which will be in a week or so!)

      Delete
    4. I think that the advantage of lactase persistence depends on several factors:

      (1) How available is clean drinking water?

      (2) What is the pathogenic load in the the available water? Would milk be a cleaner source of water than the available drinking water? "I think that there must be some adaptive value to lactose persistance but I doubt it's half as dramatic as some claim."

      (3) Is there an abundant, readily available year round source of protein (fish, meat), or are there parts of the year where fish and meat access are scarce.

      (4) If there has been a domestication of grains, are those grains available year round?

      (5) Was the demographic growth of the population steady, with limited family size, or where there population bursts with large families.

      I don't think you need a "have it our die" scenario for there to be strong selective pressure for lactase persistence in African populations. The lack of water&the sometimes lack of meat, fish and grains would probably be enough to drive selection for lactase persistence in Africa.

      These variables are clearly stacked differently in other parts of the world. In temperate zones with abundant year round supplies of fish and clean water, there probably is little selective advantage for lactase persistence (for example).

      Delete
    5. Points 1 and 2 don't matter because milk does not quench thirst (you need more water to digest it that it has AFAIK). Also boiling water, often in infusions, is an old remedy against water contamination.

      Point 4 is also not very important because the Neolithic package is mostly just one and grains (and dry legumes) are well preserved through the year normally provided some precautions. Fresh milk may not be available through the year instead (at least not with sheep).

      Point 3 sounds well but proteins are overrated. We only need 10% (or 20% according to some) of protein in our diet and it's readily available in grain+legumes combo, as any vegetarian knows well. High protein content in childhood may help to grow faster or taller but that's about it: you do not need them so much (and children have not major problems digesting milk anyhow, so there's no need for any genetic change).

      I do not understand point 5. Demographics are a function of the economy rather than vice-versa: if there are abundant resources the population grows and if there is lack it can't grow and may even collapse (epidemics are also easier and more virulent if people is undernourished).

      "I don't think you need a "have it our die" scenario for there to be strong selective pressure for lactase persistence in African populations. The (...) sometimes lack of meat, fish and grains would probably be enough to drive selection for lactase persistence in Africa".

      That can be a mild pulling force but it's only as good as any other factor. Sure milk is a great foodstuff but there are others. Why would the Sandawe have any lactase persistance at all if they are foragers? Because they just have it.

      Probably some day researchers will realize that lactase persistance is the norm and that it is lactose intolerance what needs an explanation (if anything): why would people lose the ability to digest a sugar? What benefit can it bring? Apparently none, unless their were suckling from their mothers (or other women) for way too long. Then it may have been healthy for women to have children who lost their ability to digest milk at some point in life - but were they ever subject to any such pressure? I doubt it but who knows?

      Delete
    6. From the above paper:

      "We classified individuals as having lactase persistence, lactase intermediate persistence (LIP) or lactase non-persistence (LNP) by examining the maximum rise in blood glucose levels after administration of 50 g of lactose using a lactose tolerance test (LTT)21 in 470 individuals from 43 ethnic groups originating from Tanzania, Kenya and Sudan."

      Your comment:

      "Probably some day researchers will realize that lactase persistance is the norm and that it is lactose intolerance what needs an explanation"

      Are you saying that the test for blood glucose response to lactose is invalid?

      Delete
    7. Not at all.

      Although measuring malabsorption of lactose (which the blood sugar test does) is not the same as lactose intolerance senso stricto. I imagine that you can not absorb lactose and still tolerate milk and absorb other nutrients from it like proteins, fat, vitamins or the most valuable milk nutrient probably: calcium (most foods have excess of phosphorus in the Ca-P balance). As long as drinking milk does not cause you harm (and many lactose malabsorbers do not suffer any symptoms unless they drink a lot of milk or maybe even at all) lack of lactase should not be any major problem (you don't want the sugar as much as the proteins, fat and very specially the calcium from the milk).

      I was anyhow just ranting about how odd it is that people lose the ability to digest an excellent foodstuff which they have the ability to digest as children in all cases. What's the evolutionary point? But I'm just so used to absolutely everybody being able to drink milk that is like "uh, what a useless loss of function - why does it happen in evolutionary terms?"

      Delete
    8. PS- By "Not at all" I meant not to this question of you: "Are you saying that the test for blood glucose response to lactose is invalid?" I do not mean it.

      However. As you ask, I have began to wonder how valid it is to infer intolerance (meaning practical impossibility to drink milk and use the other nutrients as opposed to merely being unable to exploit the sugar, a less important matter), as explained in the second paragraph of the previous comment.

      I figured it was a bit confusing.

      Delete
    9. OK. I'm sure there are a lot of adults who can't metabolize lactose, but in any case are asymptomatic.

      [Happy May Day]

      Delete
  3. I'd like to share a few observations on possible Cattle Domestication scenarios.

    First, as someone who grew up on a dairy farm in Ireland, domesticated cattle are very strong in general, and domestic bulls are dangerous - my grandfather was killed by one. It's inconceivable that people would be able to corral and domesticate Aurochsen - who were up to 2 feet taller at the shoulder - they would simply be too strong to contain.

    So, IMO, what would need to have happened is to a large extent a self-domestication.

    First, I think goats were domesticated, as they are relatively small and easy to manage. They were then removed from their mountainous natural environment and brought down to the plains. Here they had the effect of devouring shrubs and saplings, and causing deforestation, which would lead over time to forest clearances and open pasture. This would attract cattle herds. Obviously, only the tamer cattle would be comfortable in the surrounds of humans. If dangerous animals roamed too near, they would surely have been killed.

    Secondly, I saw an interesting documentary recently on Alaska, and it mentioned that so many young elk are killed on state highways each year, and people wondered why this was so. After they studied it a bit, they found that elk females about to give birth, had a preference for sites near highways, as bears were afraid to go there, as they might be shot by hunters. So the elk were giving birth to calves only feet from the highways to avoid predators. Now surely this would also have happened around human settlements, as Aurochsen would surely have been prey to wolf packs and maybe bears too.

    Thoughts??

    ReplyDelete
    Replies
    1. I've been thinking about the idea of "self domestication" as well. I've heard theories about dogs along the same lines. With dogs, I think they figured out that there was a ready supply of scrap food near humans. With cattle, they're not scavengers, so there's no obvious advantage from a scrap food perspective. With cows, perhaps for some reason, they found some advantage to establishing a proximity with humans. It might have been for some kind of protection, as you point out.

      I've never lived on a farm, but my grandfather and father were very interested in cattle. I got taken to a lot of agricultural fairs as a kid. It's true that the bulls are really something. Their fierce! However, the cows and calves can be surprisingly friendly. In general, I think farm animals are under appreciated for their affection and intelligence. That doesn't mean they can't be dangerous, but I do think that these animals, left to their own devices, are trying to work out their relationship with us, just as we work out a relationship with them.

      That's a very interesting observation about the elk in Alaska. Deer, obviously, also like to inhabit the grasslands that we create for them. I've also seen young wild Moose in Algonquin National Park stand for hours observing canoeists, even allowing people to gradually approach them within a few feet.

      Yes, I do think that they're must have been a long process of relationship development between cattle and humans before anyone actually got around to milking a cow.

      Thanks for the comment.

      Delete

Comments have temporarily been turned off. Because I currently have a heavy workload, I do not feel that I can do an acceptable job as moderator. Thanks for your understanding.

Note: Only a member of this blog may post a comment.