Traces of selection

A couple of interesting articles just came out in MBE on how natural selection has affected human populations that ran into problems with trace elements, either too much or too little.  One talked about adaptation to selenium shortages (which I’ve mentioned): this is  a problem in parts of  China, among other places.  It seems that there has been a shift in the frequencies of variants of several genes involved in selenium metabolism – polygenic selection .  The other paper discussed adaptation  to high arsenic levels among people in the northern Argentinian Andes: this involved a partial selective sweep on a variant of a single gene  (AS3MT) that appears to be the major gene for arsenic metabolism.

Probably there have been adaptive changes in response to iodine shortages, which are fairly widespread.  In principle,  shortage or oversupply could be a problem for any essential trace element; but it looks as if, in most cases, the trace element is fairly abundant in the environment (compared to the amount we need) while humans can tolerate a fair amount more than the minimum.  Selenium is something of an exception: shortages and toxicity both occur.

Vitamin shortages and surpluses we know something about.  I’m sure that most of my readers have learned their lesson and no longer gobble polar bear liver.  It looks as if you can suffer from an ergothioneine shortage from a wheat diet, and a more-active form of the ergothioneine transporter has undergone a partial sweep in southern Europe (EEF). Interesting that dietary scientists aren’t sure what problems are caused by ergothioneine shortages: but the existence of a specific ergothioneine transporter, and that partial sweep, sh0w it does indeed do something useful.  That’s a a useful approach to showing that something is useful or essential in humans, easier than putting a platitude of sophomores on a  special diet and seeing if their hair falls out  or they develop ED – show that there is specific molecular machinery for  importing it.

I think there’s a fair chance that some populations – I’m thinking of maize and Amerindians – have adapted to  poor amino acid quality: having too many of some essential amino acids and too few of others (like lysine): like Scrabble with more ‘Q’s than ‘U’s.

There might be adaptation to a cassava diet: cyanide tolerance.  In South America, of course, not Africa.

There are lot of examples in which any sensible person (of which there are  about five) knows that some between-population trait difference almost certainly has  a genetic cause (because we always see it in every sample of that pop, in different environments) but we don’t know the genetic details, or have only a limited knowledge.  For example, some populations have a lot more trouble handling alcohol than others – which, pace Robin Hanson , is genetic.  We know something about the basis of this among East Asians, but I don’t think we know the genetic architecture in other populations.

What  other factors that haven’t been considered  at  may have selected for various things in humans ?  Please  say something that we haven’t heard a million times before.

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76 Responses to Traces of selection

  1. Derek says:

    Perhaps an adaptation to high lithium levels leads to psychological problems when the water source changes (due to migration or technology) to a lower lithium level.

  2. Sam says:

    “There might be adaptation to a cassava diet: cyanide tolerance. In South America, of course, not Africa.”

    I have question related to sodium. In many parts of Africa, salt (sodium chloride) was not easily available. We know that many blacks are quite sensitive to modern levels of salt intake so much so that it’s highly correlated with hypertension. Is it correct to assume that sub-Saharan African may have adapted to low-sodium diets?

    • gcochran9 says:

      Ancestral humans, living in Africa, had a working version of the CYP3A5 gene. As you go farther north, you see higher and higher frequencies of a low-activity allele, CYP3A51/3. Probably holding on hard to salt was less valuable in cooler climes and had some kind of disadvantage.

  3. I don’t understand the reference to Robin Hanson, or what hich means :-/

  4. MawBTS says:

    Competitive bodybuilders must “prep” for a show, which means dieting down to 5-6 percent body fat and flushing subcutaneous water from the body. The idea is to give the muscles a sharp, defined look.

    These people typically have obsessive-compulsiveness and low intelligence, which leads to unhealthy prep strategies (for example, the widely mocked “fish and a rice cake” guy.) Steroids aren’t actually that dangerous if you know what you’re doing. What’s really dangerous is rapid crash diets, paired with dubious “gym bro” wisdom about the correct way to cut weight.

    I remember someone talking about their experience dieting, and how one day he cut himself shaving…and the blood wouldn’t clot. It just kept squirting out with each pulse of his heart, like he had haemophilia. The guy went to a doctor, and he was extremely deficient in some micronutrient due to his diet. My memory says it was potassium, but I’m not sure. Potassium doesn’t seem to have much to do with blood clotting platelets.

    I wonder if the guy was white or black. Certainly it could be worth studying athletes of various ethnicities, to see how they respond to high physical stress on a very restricted diet.

  5. ckp says:

    Has variation in groundwater fluoride concentration led to anything evolutionarily interesting?

    • melendwyr says:

      Since humans simply ignore fluoride, no. It’s not a nutrient.

      • Sean says:

        Not a nutrient but good for you because it’s bad for you and by challenging your metabolism it amps up your system, Hormesis. That may be the main positive effect of taking supplements. And pollution. Mountain peoples get a natural pollution through an excess minerals dissolved in their water and they often live long lives

        Maybe the elaborate Chinese irrigation system concentrated or removed selenium to a massive extent.

        Refined rice lacks a hell of a lot of vitamins and the once fashionable macrobiotic diet (gradually eliminating everything but plain rice) was notorious for causing deficiency diseases.

        The dopamine receptor for being socially influenced is associated with alcoholism. Peter Frost says rice farming selected for co-operation.

      • peppermint says:

        this is false. People who live in areas with lots of fluoride get fluoridated teeth. That’s why everyone puts fluorine in their water, and now doesn’t but puts it in their toothpaste. To what degree does whatever process builds teeth recognize and use fluorine? One of the symptoms of excessive fluorine is growing stained teeth.

        • melendwyr says:

          Nothing you’ve said supports your contention of falsehood.

          Our bodies do not seek out fluoride ions, as they do with iodine. It’s not a part of the process of forming teeth.

        • Anthony says:

          Fluoride, sufficient doses, causes fluorosis of the teeth, which causes staining, and brittleness. Lower doses make the teeth a little more resistant to caries (tooth decay). Without looking it up, I think the fluoride causes some of the calcium carbonate of the tooth to become calcium fluorite(?), which in small quantities may strengthen the mineral structure of the tooth, while in larger quantities, won’t fit right, and degrades the structure. It probably fights off tooth decay by being toxic to whichever bacteria is trying to eat the calcium carbonate of your teeth.

  6. szopeno says:

    I don’t know whether it was said a million times ago. Definetely I have said that few times in many different forums: dad vs cad thing – I would expect northern population would have higher proportion of males with “dad” strategy.

    Sex differences could be different in different human populations – e.g. in northern populations there could be a host of “feminine traits” which in other populations would be neutral, or which could go in other direction (e.g. the female aggressiveness, mate preferences, leadership, desire for children etc). I

  7. stalin says:

    There might be adaptation to a cassava diet: cyanide tolerance. In South America, of course, not Africa.
    Since this is an “of course” I must be stupid. But why?

  8. Bultare says:

    I think the Y-chromosomes(and maybe other genes related to male fertility, to a lesser extent) of highly patriarchal(especially polygamist) cultures should on average have a higher load of bad mutations than those from less patriarchal cultures where biological selection is a bigger factor than cultural. House of Saud could carry a mutation that decreases sperm quality by 20% and it wouldn’t have much of an effect to the spread of their Y-chromosome. Of course they probably don’t but there’s got to be at least some bad Y-chromosomes out there that are multiplying in frequency for cultural reasons.

  9. Greying Wanderer says:

    In not finding a neat chart of deuterium levels in groundwater by rock type the list of other things found too high (or maybe too low in some cases) in groundwater included: iron, manganese, chlorine, flouride and the arsenic already mentioned.

    http://en.wikipedia.org/wiki/Manganese#Manganese_in_drinking_water

  10. Tom says:

    What are your thoughts on fluoride? Should it be avoided? It’s only been in the water supply in significant amounts for a couple generations.

  11. AnonymousForGoodReason says:

    Here’s the opposite of what you asked for, a disproof of a hypothesized selection effect:

    It turns out that the women imagined to be biologically AIDS resistant have likely just been coasting on the tail of the luck distribution, and were eventually proven to be HIV susceptible.
    http://news.bbc.co.uk/2/hi/health/619316.stm

  12. melendwyr says:

    I’ve been wondering about selection for ‘vulnerability’ to helpful microbial populations and multicellular symbiotes. Infants which had an easier time picking up valuable gut flora from their parents might had an advantage.

    Also, we know about Toxoplasmosis, which probably doesn’t have nice effects, but what about dogs? Given how long dogs and humans have been associated, I’d be surprised if we hadn’t adapted to the microfauna of canines – and those adaptations might even be necessary.

    Are there any surviving human populations that have no associations with dogs whatsoever?

    • As an Rh negative pregnant woman, with a 50% chance of carrying an Rh positive fetus, I am very curious about why the hell the Rh negative blood type spread over Europe.

      Some geneticists have hypothesized that the rhesus factor conferred some protection against Toxoplasma gondii, which was especially prevalent in Europe. http://genetics.thetech.org/ask-a-geneticist/rh-did-not-come-neanderthals

      Perhaps the advantage came only with being heterozygous, and if you ended up, like me, homozygous for Rh, you had more of your share of stillborns and mentally retarded children. Since the 60’s Rh negative women are given the RhoGAM shot, which prevents Rh sensitization, so you don’t produce antibodies that attack your next Rh positive fetus’s blood.

      I have often wished Cochran or Harpending would address the Rh negative blood type.

    • Yudi says:

      Recently, I saw a woman on a swing in a park, holding her dog in her lap the whole time. I was a bit baffled. Of course, we all know about the WEIRD phenomenon and
      how some young people see their pets as surrogate children, but what made this possible in the first place? It is clear that early dogs were selected for their ability to like the company of humans. If dogs were as useful in hunting and protection as their ubiquity in human groups suggests, humans who really, really loathed the sight of them would have been at a selective disadvantage. Thus, humanity would have become more dog-loving over time, just as dogs became more human-loving.

  13. dearieme says:

    In spite of being partly of German descent, Englishmen have a genetic deficiency that precludes their pronouncing the consonant “ch”, as in ‘loch’.

    • melendwyr says:

      Dr. Cochran should have been more specific: intelligent hypotheses that haven’t been heard before.

    • reiner Tor says:

      Makes sense. Similarly, Germans cannot pronounce the sound(s) ‘th’, whether in ‘there’, ‘thing’ or ‘bathe’, which must also be due to differential selection. Or Melendwyr having a genetic deficiency that makes him think these suggestions are silly.

  14. AnonymousForGoodReason says:

    As for the highly differentiated rates of schizophrenia in different parts of the world:

    I still don’t have a good sense of why warmer climes select against schizophrenia so weakly.

    • chrisdavies09 says:

      That is not the ‘schizophrenia rate’. It is disability-adjusted life year for schizophrenia.
      “The disability-adjusted life year (DALY) is a measure of overall disease burden, expressed as the number of years lost due to ill-health, disability or early death. It was developed in the 1990s as a way of comparing the overall health and life expectancy of different countries.”

      • AnonymousForGoodReason says:

        But why does it differ so strongly? The discussion of the degree of heritability of schizophrenia mirrors that of IQ.
        http://en.wikipedia.org/wiki/Schizophrenia#Genetic

        I find it unlikely that the current distribution could have occurred by chance, particularly as it does not seem to follow IQ, so much as it follows “proximity to equator”, like eyeball size and skin color, leaving high-IQ, high-future-time-orientation people like the southern Chinese comparable to equatorial neighbors in Mexico..

  15. Tore says:

    The people of Ramsar seem to tolerate very high background radiation pretty well. Also the birds of Chernybyl. Nuclear accidents can be good for the enviroment, since non-ramsarian people have to stay away, while the most of the wildlife can adapt quiker because of shorter generation lenght and flourish in the free zone.

    • ursiform says:

      If wildlife can survive in an environment that humans have abandoned, wildlife will move in. There will likely be adaptation over time, but it’s not required for the initial populating of the area.

  16. Flinders Petrie says:

    The curative properties attributed to mare’s milk and koumiss for diseases such as
    chronic ulcer and tuberculosis may be due to the high concentration of polyunsaturated fatty acids – especially linoleic acid – when compared to cow and human milk. The same goes for horse meat.

    That would have surely offered some benefits to the Botai, until their descendants spread west and switched to cow.

  17. Greying Wanderer says:

    Fluoride

    http://en.wikipedia.org/wiki/Fluoride_toxicity

    “Fluoride’s suppressive effect on the thyroid is more severe when iodine is deficient”

    so there’s possibly indirect effects of shortage / abundance in combination with other shortage / abundances

    known problems in areas of naturally high fluoride in groundwater

    http://www.bgs.ac.uk/research/groundwater/health/fluoride.html

    places with naturally high levels in groundwater

    • Greying Wanderer says:

      Argentina is interesting there because if there were adaptations to excessive fluoride the Amerindians on that plain may have them/it but not the Euro descended population.

      • Greying Wanderer says:

        Argentina has naturally occurring fluoridated water and also adds fluoride in some areas like Buenos Aires – so maybe too much?

        or

        China thing (p. 100)

        http://www.who.int/water_sanitation_health/publications/fluoride_drinking_water_full.pdf

        “It has been demonstrated that people living in high fluoride drinking-water
        regions (>4 mg l–1) and consuming a nutrient deficient diet have the highest incidence
        of dental (and skeletal) fluorosis”

        Or high fluoride bad but only if combined with some other deficiency?

        • Anthony says:

          Depends if Buenos Aires drinks groundwater, or pipes in mountain water.

          • Greying Wanderer says:

            Yeah I couldn’t find the details. I was thinking if their food came from the countryside and the countryside had high natural fluoride and then BA added fluoride to their drinking water on top of that then there might be too much

            or

            the amount in either case was magnifying the effect of some other shortage e.g. iodine.

  18. jrm says:

    23andme gives data on warfarin sensitivity, but it is really based on differences in vitamin K recycling. Some K2 is made in the gut and some can be made by specific species of bacteria on food before consumption. Refrigeration may contribute to K2 deficiency and/or traditional use of cooking pots may provide a source of K2.

  19. George says:

    Could Intelligence, now a maladaptation (?), be responsible for the decrease in fertility? A PhD might be evolutionarily as expensive as were the Irish elk’s antlers.

  20. I keep reading vague references to mediterranean countries becoming darker in complexion since classical times without any actual proof. It makes sense that african alleles that protect against equator region diseases would move north with the northward movement of devastating diseases like malaria falciparum and in doing so would carry alongside them other africanized traits but damned if the whole subject isn’t in the “Voldemortean” zone of those subjects that can’t be honestly addressed. One of these days it would be nice if “Voltmortean” earned a place into wikipedia with maybe some hat tip to Cochran for spreading it. It’s a damn good word that deserves a place in our silly world where certain subject matters belong in the “he who can’t be named” category.

    • peppermint says:

      the reason tropical diseases are called tropical is that civilized people don’t get them, they drain the swamp instead. Civilized people die of tuberculosis (a.k.a. consumption), cholera, typhus, and bubonic plague.

    • idontrecall says:

      “damned if the whole subject isn’t in the “Voldemortean” zone of those subjects that can’t be honestly addressed”

      Yes, the PC police will hunt you down for recycling 19th-20th century Nordicism and contemporary WN-iana. Poor you.

      Here’s a discussion on the issue: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC547919/. See also Robert Sallares – The Ecology of the Ancient Greek World. Evaluate on your own.

    • AnonymousForGoodReason says:

      Does the rapid increase in African genetics in cold, Western countries in the past centuries have anything to do skin color or malaria resistance? Of course not.

  21. RCB says:

    Dog whispering.

  22. Tequoia says:

    Well, really trying to make this concise and at least with this call for open responses thinking not to be burned for off-topicness. This topic has obviously not been overlooked so much as there is a lot of published garbage, likely wrong. That would be on the simple human consumption of caffeine. In particular if anyone knows of any experimental studies that aren’t 50 years old or have even N=100 subjects (we’d like thousands…) it’d be nice to hear, if not go for impromptu metanalysis. I have made some effort looking myself over time and am avoiding unnecessary, non-spontaneous background knowledge, so please consider that this request is not idle but is frustrating; the research community has some shoddy standards.

    It is plausible that subset(s) of some ethnic groups, all in the obvious sensible contexts here, have uniquely positive responses to caffeine consumption and metabolization due to genetic heritage. I’d bet against that claim still, but that’s because of a more important part of the broader picture; failure to establish and explore this is still an unacceptable black eye, given how relevant true medical knowledge ought to be to society here.

    Of course mass, popular perception can be and is completely wrong in every way, that is not the issue we’re after. It’s the literature shows both that there are still many questions considered open and and currently is lacking in cross-disciplinary understanding. (particularly psychometrics and genetics)

    Utlimately, there’s underwhelming, little evidence against the statement that caffeine consumption has no cognitive benefits and probably not any positive effects whatsoever, in normal circumstances and for the adult human population. It appears shocking amount of research has only been done under unreasonably extreme conditions (eg military testing) and with strong selection bias, let alone the baseline of just terrible statistical analysis pervasive in social science and even medical publications. Messing with people’s sleep schedules (to no benefit) and subjective experiences in a psychoactive sense are established. But those too are still tremendously understudied in the sense of genetics or for important medical distinctions like sex. For anything performance releated, there are the known but still understudied facets of placebo effects, and alleviation of withdrawal symptoms is likely a common enough occurence. Altogether it’s that the null hypothesis hasn’t been decisively shown false and every publication bias under the sun has clearly built up over the decades

    What is desperately needed, with a range of a few thousand otherwise healthy adult test subjects but no terrible cost, is controlled blinded experiments in normal everyday conditions with groupings like mere sugary beverages, “sportsade” beverages including sugar and electrolytes, vs. caffeinated versions. A battery of basic relevant psychometric tests, for reaction, alertness, throw in Kahneman-esque stuff if desired as an investigator’s pet issue, is all that’s needed. Of course larger sample sizes and proper controls have been needed since forever for other studies too. Any non-null results that then exist might beg for full GWAS exploration or similar follow-up.

    There is finally the double issue that individual knuckleheads if not what the majority of the literature in the field have problems with psychometric measures themselves, such that at the current point in time they unreasonably complicate the situation. Assuming, say, human reaction time has no prior expected correlations with g, sex, or race and arbitrarily going with weird corrections or selection for that guarantees some wrong confounds in the research methodology. Still, if someone could run a proper experiment, or collectively people could find enough prior work for novel metanalysis, with a sufficient sample of subjects that’s useful regardless.

  23. j says:

    Re the dad vs cad thing, their respective frequency tends to oscillate in a population. That is, the frequency of the respective genes is what oscillate. There are many such “pairs” that must also oscillate, for example, left and right handedness (lefties have an advantage in face-to-face encounters when they are few of them). High and low IQ frequencies must oscillate in the same way, only that it doesnt. Or maybe it does.

    Traces of human selection toward goat/sheep milk/meat could be noticeable in all Mediterranean islands. Much before the mutant Polyphemus, there was no other domestic ruminant found on the islands.

  24. Hipster says:

    I wonder about (and this has probably been answered already) our adaptations to different diets generally since the Neolithic revolution.
    Paleo Dieters suppose that we shouldn’t eat grains, but obviously Europeans have had a much longer time to evolve to digest wheat than they have Tomatoes or Turkey.
    What sorts of food-specific adaptations are there really in different populations? Is there any evidence that an “ancestral” diet, is beneficial? Should Europeans swear off Squash and Tomatoes? Should Native Americans never eat Apples? Or is that basically all bunk and we can eat whatever.

    • Greying Wanderer says:

      “but obviously Europeans have had a much longer time to evolve to digest wheat”

      Some have had more time than others though.

      http://en.wikipedia.org/wiki/Coeliac_disease

      “Globally coeliac disease affects between 1 in 100 and 1 in 170 people;[5] rates do however vary between different regions of the world from as few as 1 in 300 to as many as 1 in 40”

      I think it’s partly that you’re more likely to have allergies to non-ancestral foods because they have had less time to be selected out. So if you feel unhealthy on a standard modern diet then by gradually removing non-ancestral foods one at a time you might find something you have an allergy to. I can see how the paleo diet could work on that basis (on individuals it works for) because instead of removing non-ancestral foods one by one you do it all at once.

      • Hipster says:

        Also just removing processed junk works wonders, it seems like most truly healthy diets just rely on “real food” instead of stuff sold in packages with cartoons on them. Whether you’re eating Corn, Beef, Carrots, Wheat, whatever, it’s better than Cheetos, Coca Cola, or Frosted Flakes.

        • Hipster says:

          But my specific question remains. Do Europeans have any problems with American crops?Do Native Americans have any problems with European crops? Should Africans give up Manioc? Should Bolivians give up rice?

          • Greying Wanderer says:

            I think the general case is people should give up foods they are allergic to. On that basis it seems to me giving up all non-ancestral foods is probably overkill but would probably work.

            (nb the list of non-ancestral foods would vary)

  25. Tore says:

    These kids swimming joyfully in Yamuna probably have an interesting immune defence. A friend of mine asked a local when he was there about this. The answer came quik: They’re not normal:

    • Tore says:

      Finishing off with a little copy+paste
      From Human Physiological Adaptations to the Arctic Climate JUHANI LEPPALUOTO’ and JUHANI HASSI’ http://arctic.journalhosting.ucalgary.ca/arctic/index.php/arctic/article/view/1530/1509
      “The central Australian aborigines demonstrated a hypometabolic and hypothermic
      response to the standardized cold test, which was evidently due to their continuous exposure to cool nights in their natural habitat. The aborigines also had lower body heat conductivity values than the white controls and lower fat percentage
      as well (Hammel, 1964). The low heat conductivity was thus based on the effective constriction of skin blood vessels in cold. This hypometabolic and insulative type of adaptation has some advantages, since the lowering of the metabolic rate observed in the aborigines decreases the energy expenditure by 20% during the night, which may be important in a land where food is not abundant (Hammel, 1964).”

      I think they also have thick fat insulation around the vital organs of the chest and abdomen to protect them during the cold nights.

  26. rob says:

    Myopia. It must come with some positives, maybe IQ or personality traits. Agriculture or division of labor opened niches for nearsighted people that didn’t exist in other types of societies.

  27. The fourth doorman of the apocalypse says:

    Selection for tolerance of parasitic viruses?

    http://onlinelibrary.wiley.com/doi/10.1111/mec.12307/full

  28. z_kerwin@yahoo.com says:

    Any thoughts on why APOe4 which I understand to be the ancestral allele persists in populations despite being maladaptive to the modern Western diet?

    Curious as an E4/E3 myself

  29. Yudi says:

    Why do Europeans and East Asians have long, straight hair? Is long hair just due to EDAR in the case of East Asians, or do other genes contribute to it? If long hair is just a cold adaptation, why do Middle Easterners have it? Sexual selection? Is it tied to a gene that confers some other advantage?

  30. Alan Rogers says:

    How many sophomores does it take to make a “platitude”?

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