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From bioRxiv:

Reconstruction of nine thousand years of agriculture-based diet and impact on human genetic diversity in Asia

Download PDF here

Srilakshmi M Raj, Allison Pei, View ORCID ProfileMatthieu Foll, Florencia Schlamp, Laurent Excoffier, Dorian Q Fuller, Toomas Kivisild, Andrew G. Clark

This article is a preprint and has not been peer-reviewed

Abstract
Domestication of crops and animals during the Holocene epoch played a critical role in shaping human culture, diet and genetic variation. This domestication process took placeacross a span of time and space, especially in Asia. We hypothesize that domestication of plants and animals around the world must have influenced the human genome differentially among human populations to a far greater degree than has been appreciated previously. The range of domesticated foods that were available in different regions can be expected to have created regionally distinct nutrient intake profiles and deficiencies. To capture this complexity, we used archaeobotanical evidence to construct two models of dietary nutrient composition over a 9000 year time span in Asia: one based on Larson et al. (2014) and measured through composition of 8 nutrients, and another taking into account a wider range of crops, cooking and lifestyle variation, and the dietary variables glycemic index and carbohydrate content. We hypothesize that the subtle dietary shifts through time and space have also influenced current human genetic variation among Asians. We used statistical methods BayeScEnv, BayeScan and Baypass, to examine the impact of our reconstructed long-term dietary habits on genome-wide genetic variation in 29 current-day Asian populations (Figure S1, Figure 1, Figure 2). Our results show that genetic variation in diet-related pathways is correlated with dietary differences among Asian populations. SNPs in five genes, GHR, LAMA1, SEMA3A, CAST and TCF7L2, involved in the gene ontologies ‘salivary gland morphogenesis’ and ‘negative regulation of type B pancreatic cell apoptotic process’ suggest that metabolism may have been primary targets of selection driven by dietary shifts. These shifts may have influenced biological pathways in ways that have a lasting impact on health. We present a case that archaeobotanical evidence can provide valuable insight for understanding how historical human niche construction might have influenced modern human genetic variation.

From the full paper:

Our primary dietary model (see Methods) infers that the Southwest Asian populations (mostly sampled from present-day Pakistan) had a greater increase in carbohydrates, lipids and protein content due to domestication events from 9000 years ago. In contrast, South Asian populations showed the latest and at least these three major dietary changes in their diets, as domestication started later here. The greatest nutrient increases in all populations due to diet changes were carbohydrates, followed by protein, then lipids. Separated into segments of 3000 years, consumption of all three components from the domesticated diet increased over time, following known increased adoption of domestication practices throughout Asia (Figure 2a, Tables S1-8).

The Fertile Crescent in the Middle East was the site of much early innovation in agriculture a long time ago, such as growing wheat. Farming rapidly spread outward from there in multiple directions, such as eastward to the Indus River valley in modern Pakistan. But then, apparently, there was a long pause before Middle Eastern wheat could be raised further east in the Indian subcontinent. The problem was that in the Middle East, it mostly rains in the winter, but in South Asia the monsoon dumps rain in the summer, so it took a long time for grain-breeders to flip the seasons.

This is why civilization has less ancient roots in India than in the middle east (treating the Indus as the eastern boundary of the Middle East; interestingly, that’s where Alexander the Great wept because he had no more worlds to conquer, despite the vast South Asian peninsula still in front of him).

Or maybe I’ve got this all wrong …

As for the rest of the paper, I don’t pretend to understand it, but it might be relevant to questions of what kind of diet is best for you individually. For example, in the later 20th Century, federally-funded nutrition experts were much impressed by the fact that the Japanese in Japan lived a long time eating a diet that was relatively low in fat, low in animal protein, high in soy, and high in carbohydrates (like rice), and thus strongly recommended it to white Americans, who just kept getting fatter and then dying younger.

But the Japanese evolved over a long time to eat that kind of diet. Did your ancestors?

Our study complements a growing body of literature showing that the more predictable and static external environmental factors such as elevation, climate and disease affect human evolution, by showing that dietary factors also drove genetic adaptations [28–31]. We have provided data that suggests regional adaptations to Neolithic diets which varied in nutrient profiles. Humans have shaped their own food environment over millennia, through a broadening range of food processing techniques and through domestication and the construction of agricultural systems [32–34]. These changes have left signatures on the genomes of different populations, and may have powerful implications for disparities in disease etiology as well as aging and life expectancy among historical and contemporary human populations[35].

 
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  1. Or maybe I’ve got this all wrong …

    Or maybe not.

    Did your ancestors?

    No. Give me a bacon cheeseburger and leave me alone.

  2. We used statistical methods BayeScEnv, BayeScan and Baypass…

    What? Not BayeWatch?

    • LOL: jim jones
    • Replies: @Mr McKenna
    Baywatch? Funny you should mention! Fat girls from coast to coast are busy re-tweeting this Atlantic story today. "A New Study says It's not your fault!!"

    Why It Was Easier to Be Skinny in the 1980s

    A new study finds that people today who eat and exercise the same amount as people 20 years ago are still fatter.

    https://www.theatlantic.com/health/archive/2015/09/why-it-was-easier-to-be-skinny-in-the-1980s/407974/

     

    PS: As everyone here knows, you can eat "the same amount" and exercise "the same amount" but eat different things, and just sit on your @$$ more, but whatevs.
  3. Race based diets?

    Promoted by a NAM = mildly acceptable, maybe even revolutionary. Promoted by a stale pale male = literally Nazis.

    Fun world….

  4. Anonymous[375] • Disclaimer says:

    As far as longevity goes, calories are the most important factor. Caloric restriction is really the only thing that’s been shown to lengthen lifespans.

    Traditional Japanese consumed few calories and worked outside all day. Modern Americans live in an environment of caloric surplus and stay indoors and lead sedentary lifestyles.

    Low carb diets “work” when they do because they’re basically hacks to trick yourself into consuming fewer calories. It’s the same with fasting, intermittent fasting, etc. If you eat 5,000 calories of cheese every day, you will gain weight even if you’re consuming zero carbs.

    • Replies: @Colin Wright
    'As far as longevity goes, calories are the most important factor. Caloric restriction is really the only thing that’s been shown to lengthen lifespans...'

    Except that it hasn't. The studies were flawed.
    , @Redneck farmer
    Someone once described those experiments this way: "The rats with the longest life spans were given all the vitamins and minerals they needed to be healthy. And just enough calories to barely get out of the way of their own excrement."
    , @anonymous coward

    If you eat 5,000 calories of cheese every day, you will gain weight even if you’re consuming zero carbs.
     
    5000 calories of cheese is something like 1.3 kilograms. I'm pretty sure you'd get sick before finishing all of it if you tried to eat that much.
  5. I had an ancient history class in college where the prof said that Alexander wept because he had been talking to Buddhists who said that there were an infinite number of worlds.

    • LOL: Digital Samizdat
  6. @Reg Cæsar

    We used statistical methods BayeScEnv, BayeScan and Baypass...
     
    What? Not BayeWatch?



    https://cdn-04.independent.ie/incoming/article35646440.ece/48072/AUTOCROP/w620/baywatch%20babes.jpg

    Baywatch? Funny you should mention! Fat girls from coast to coast are busy re-tweeting this Atlantic story today. “A New Study says It’s not your fault!!”

    Why It Was Easier to Be Skinny in the 1980s

    A new study finds that people today who eat and exercise the same amount as people 20 years ago are still fatter.

    https://www.theatlantic.com/health/archive/2015/09/why-it-was-easier-to-be-skinny-in-the-1980s/407974/

    PS: As everyone here knows, you can eat “the same amount” and exercise “the same amount” but eat different things, and just sit on your @$$ more, but whatevs.

  7. Shout out to the farmers of Ethiopia, who, living on a high altitude plateau suitable for grain agriculture, domesticated one of the local grasses into the teff grain that they still use to make injera bread. (The oil seed noog, the false banana, and several varieties of yam were also first cultivated there as well.) The highlands of Ethiopia are really interesting in that they’re ecologically a lot more like Southern Europe and the Near East than they are like the rest of Sub-Saharan Africa. It’s the only place in SSA with wolves, for example. It also has grain agriculture, early state formation, and the kinds of monumental architecture (castles and rock-cut churches) that a lot of people on this website don’t think don’t think exist in Sub-Saharan Africa.

    • Replies: @PiltdownMan
    Ethiopia and Eritrea really deserve their own geographic classification, rather than being lumped into Sub-Saharan Africa, because, well, they are not in the Sahara. The Amhara and many other peoples of Ethiopia are a type that's distinctly different in appearance from other SSAs, their culture is Coptic Christianand goes back to early Christianity, and the land, at average elevations of 8,000 feet, is very different from most of the rest of the continent.
    , @Anonymous
    You just don't want them roaming around DC....
    , @MEH 0910
    Spend a Day With the World’s Only Grass-Eating Monkeys | National Geographic
    https://www.youtube.com/watch?v=hFHcXxaqMhg

    Geladas, one of the flagship species of Africa’s alpine grasslands, are found only in the Ethiopian Highlands. They are the smallest vestige of a genus that millions of years ago stretched from South Africa to Spain and into India. Once among the most prominent primates—one species was the size of a gorilla—they were likely driven to extinction by climate changes, competition with more adaptable baboons, and our ancestors, who butchered them. Today all that remains of Theropithecus are geladas, which offer valuable, if imperfect, insight into the world inhabited by our predecessors. There is no other animal like them. Geladas’ most recognizable features are crimson patches of hairless skin on their chests. In females, this region changes color, and tiny sacs around its edge fill with fluid, often indicating that they are ready to mate. The pink on dominant males darkens to red. Other primates signal sexual readiness with their rumps, but these monkeys spend most of the day scooting on their rears, gorging. Most primates climb trees to eat fruit and leaves. Geladas use opposable thumbs to pluck grass blades and herbs. Like zebras, they mince food with their molars.
     
    How Geladas Evolved to Become the Only True Grazing Primate
    https://www.youtube.com/watch?v=EH4UU7k_fdc

    These Ethiopian Geladas Produce a Very Human-like Sound
    https://www.youtube.com/watch?v=JbdQumeqo50

    The call of the Geladas is known as a wobble, and it's unlike anything else in the natural world. It's a complex hybrid of mouth movements and vocalization, reminiscent of human speech.
     
    Are Gelada Cries the Closest Thing We Have to Human Speech?
    https://www.youtube.com/watch?v=lBiwsEIcxMI
  8. @Earl Lemongrab
    Shout out to the farmers of Ethiopia, who, living on a high altitude plateau suitable for grain agriculture, domesticated one of the local grasses into the teff grain that they still use to make injera bread. (The oil seed noog, the false banana, and several varieties of yam were also first cultivated there as well.) The highlands of Ethiopia are really interesting in that they're ecologically a lot more like Southern Europe and the Near East than they are like the rest of Sub-Saharan Africa. It's the only place in SSA with wolves, for example. It also has grain agriculture, early state formation, and the kinds of monumental architecture (castles and rock-cut churches) that a lot of people on this website don't think don't think exist in Sub-Saharan Africa.

    Ethiopia and Eritrea really deserve their own geographic classification, rather than being lumped into Sub-Saharan Africa, because, well, they are not in the Sahara. The Amhara and many other peoples of Ethiopia are a type that’s distinctly different in appearance from other SSAs, their culture is Coptic Christianand goes back to early Christianity, and the land, at average elevations of 8,000 feet, is very different from most of the rest of the continent.

    • Replies: @Mr McKenna
    Agreed: they're more "East of Sahara" than "South of Saraha". Unfortunately they've still multiplied until now there are over 100 million of them, and their country's biggest export is Ethiopians.
    , @dearieme
    Ethiopia and Eritrea really deserve their own geographic classification

    The classic is to refer to them as The Horn of Africa. But you're right, perhaps something that specifically says that the land lies east of the Sahara or east of the Nile would be useful.
  9. The lead researcher in that paper must be really into rice culture. She is standing in the midst of a rice field in the image that fills her home page.

    https://srimraj.weebly.com/

  10. @Anonymous
    As far as longevity goes, calories are the most important factor. Caloric restriction is really the only thing that's been shown to lengthen lifespans.

    Traditional Japanese consumed few calories and worked outside all day. Modern Americans live in an environment of caloric surplus and stay indoors and lead sedentary lifestyles.

    Low carb diets "work" when they do because they're basically hacks to trick yourself into consuming fewer calories. It's the same with fasting, intermittent fasting, etc. If you eat 5,000 calories of cheese every day, you will gain weight even if you're consuming zero carbs.

    ‘As far as longevity goes, calories are the most important factor. Caloric restriction is really the only thing that’s been shown to lengthen lifespans…’

    Except that it hasn’t. The studies were flawed.

  11. It does seem entirely possible that Northern Europeans, in particular, are more susceptible to ballooning up on high-carb diets.

    Shorter growing seasons probably led to a diet heavy in fat and protein from meat and milk. By contrast, the Mediterranean diet had a lot more grain and carbs.

    Roman historians like Tacitus commented on how the Germanic tribes cooked with lard instead of olive oil. And how they also tended to be several inches taller (presumably from a higher-protein diet).

    But if you take a lard-eating barbarian and give him an unlimited supply of high-fructose corn syrup to eat . . . well, the results aren’t pretty.

  12. @PiltdownMan
    Ethiopia and Eritrea really deserve their own geographic classification, rather than being lumped into Sub-Saharan Africa, because, well, they are not in the Sahara. The Amhara and many other peoples of Ethiopia are a type that's distinctly different in appearance from other SSAs, their culture is Coptic Christianand goes back to early Christianity, and the land, at average elevations of 8,000 feet, is very different from most of the rest of the continent.

    Agreed: they’re more “East of Sahara” than “South of Saraha”. Unfortunately they’ve still multiplied until now there are over 100 million of them, and their country’s biggest export is Ethiopians.

  13. @Anonymous
    As far as longevity goes, calories are the most important factor. Caloric restriction is really the only thing that's been shown to lengthen lifespans.

    Traditional Japanese consumed few calories and worked outside all day. Modern Americans live in an environment of caloric surplus and stay indoors and lead sedentary lifestyles.

    Low carb diets "work" when they do because they're basically hacks to trick yourself into consuming fewer calories. It's the same with fasting, intermittent fasting, etc. If you eat 5,000 calories of cheese every day, you will gain weight even if you're consuming zero carbs.

    Someone once described those experiments this way: “The rats with the longest life spans were given all the vitamins and minerals they needed to be healthy. And just enough calories to barely get out of the way of their own excrement.”

  14. We need to increase funding for increasing individual life expectancy; too much money is sitting in the Social Security and Medicare trust funds!

  15. Anon[243] • Disclaimer says:

    I read an interesting bit about why celiac disease has hit people of European descent so hard.
    Before 500 years ago, wheat bread with given a rise with the type of bacteria you use to cure milk products as the leavening agent, namely various types of lactic acid bacteria. This had the effect of destroying gluten and other dangerous lectins in bread, but only if given a very long rise. It creates a sourdough. With the development of commercial baking, yeast-raising took over, and it leaves gluten intact. You can’t make the old type of sourdough today because they still use yeast in it, and the rise of our commercial bread is too short to wipe out the gluten.

  16. @Anonymous
    As far as longevity goes, calories are the most important factor. Caloric restriction is really the only thing that's been shown to lengthen lifespans.

    Traditional Japanese consumed few calories and worked outside all day. Modern Americans live in an environment of caloric surplus and stay indoors and lead sedentary lifestyles.

    Low carb diets "work" when they do because they're basically hacks to trick yourself into consuming fewer calories. It's the same with fasting, intermittent fasting, etc. If you eat 5,000 calories of cheese every day, you will gain weight even if you're consuming zero carbs.

    If you eat 5,000 calories of cheese every day, you will gain weight even if you’re consuming zero carbs.

    5000 calories of cheese is something like 1.3 kilograms. I’m pretty sure you’d get sick before finishing all of it if you tried to eat that much.

  17. @PiltdownMan
    Ethiopia and Eritrea really deserve their own geographic classification, rather than being lumped into Sub-Saharan Africa, because, well, they are not in the Sahara. The Amhara and many other peoples of Ethiopia are a type that's distinctly different in appearance from other SSAs, their culture is Coptic Christianand goes back to early Christianity, and the land, at average elevations of 8,000 feet, is very different from most of the rest of the continent.

    Ethiopia and Eritrea really deserve their own geographic classification

    The classic is to refer to them as The Horn of Africa. But you’re right, perhaps something that specifically says that the land lies east of the Sahara or east of the Nile would be useful.

  18. But the Japanese evolved over a long time to eat that kind of diet. Did your ancestors?

    Probably not. I’ve probably evolved to eat plenty of fish, hazelnuts, butter, cheese, bacon, lamb, and oats. Doesn’t stop me enjoying hummus and olives though. I’d probably enjoy beef more if only lamb weren’t so superior.

  19. Speaking of Diversity… Poor Dariusz Grzesista didn’t know what hit him. First, his English is poor. Then, he’s a tad naïve about Twitter mobs. And finally, he thinks Diversity means something to do with fairness. When almost anyone can see it’s really war on whiteness.

    Now, he’s ruined. A parable, perhaps.

    https://www.rt.com/op-ed/467471-sjw-php-conference-tech-programming/

  20. @Earl Lemongrab
    Shout out to the farmers of Ethiopia, who, living on a high altitude plateau suitable for grain agriculture, domesticated one of the local grasses into the teff grain that they still use to make injera bread. (The oil seed noog, the false banana, and several varieties of yam were also first cultivated there as well.) The highlands of Ethiopia are really interesting in that they're ecologically a lot more like Southern Europe and the Near East than they are like the rest of Sub-Saharan Africa. It's the only place in SSA with wolves, for example. It also has grain agriculture, early state formation, and the kinds of monumental architecture (castles and rock-cut churches) that a lot of people on this website don't think don't think exist in Sub-Saharan Africa.

    You just don’t want them roaming around DC….

  21. @Earl Lemongrab
    Shout out to the farmers of Ethiopia, who, living on a high altitude plateau suitable for grain agriculture, domesticated one of the local grasses into the teff grain that they still use to make injera bread. (The oil seed noog, the false banana, and several varieties of yam were also first cultivated there as well.) The highlands of Ethiopia are really interesting in that they're ecologically a lot more like Southern Europe and the Near East than they are like the rest of Sub-Saharan Africa. It's the only place in SSA with wolves, for example. It also has grain agriculture, early state formation, and the kinds of monumental architecture (castles and rock-cut churches) that a lot of people on this website don't think don't think exist in Sub-Saharan Africa.

    Spend a Day With the World’s Only Grass-Eating Monkeys | National Geographic

    Geladas, one of the flagship species of Africa’s alpine grasslands, are found only in the Ethiopian Highlands. They are the smallest vestige of a genus that millions of years ago stretched from South Africa to Spain and into India. Once among the most prominent primates—one species was the size of a gorilla—they were likely driven to extinction by climate changes, competition with more adaptable baboons, and our ancestors, who butchered them. Today all that remains of Theropithecus are geladas, which offer valuable, if imperfect, insight into the world inhabited by our predecessors. There is no other animal like them. Geladas’ most recognizable features are crimson patches of hairless skin on their chests. In females, this region changes color, and tiny sacs around its edge fill with fluid, often indicating that they are ready to mate. The pink on dominant males darkens to red. Other primates signal sexual readiness with their rumps, but these monkeys spend most of the day scooting on their rears, gorging. Most primates climb trees to eat fruit and leaves. Geladas use opposable thumbs to pluck grass blades and herbs. Like zebras, they mince food with their molars.

    How Geladas Evolved to Become the Only True Grazing Primate

    These Ethiopian Geladas Produce a Very Human-like Sound

    The call of the Geladas is known as a wobble, and it’s unlike anything else in the natural world. It’s a complex hybrid of mouth movements and vocalization, reminiscent of human speech.

    Are Gelada Cries the Closest Thing We Have to Human Speech?

  22. But then, apparently, there was a long pause before Middle Eastern wheat could be raised further east in the Indian subcontinent. The problem was that in the Middle East, it mostly rains in the winter, but in South Asia the monsoon dumps rain in the summer, so it took a long time for grain-breeders to flip the seasons.

    This is also the story southern Africa, much more recently. The Bantu expansion relied on summer-rain crops, and this stopped them at the line where the climate changes to winter rain, around 200 miles east of Cape Town. So various pre-Bantu, Khoisan-speaking, people survived there.

  23. Yeah, the Japanese might live long, but never develop completely, and are weaker as a result, similar to China. The Mongols, on the other hand…

    Reminds me of that one story where a Chinese and a Mongolian army were camping close by. The Chinese were weirded out by how flexible the Mongols were simply due to a better quality diet, not having to sit down to eat gruel every goddamn day

  24. This may be a wee bit OT, but has anyone else noticed how today’s wealthier, high-status, far-eastern Asians just LOVE highly processed wheat- and corn-based snacks, breads and treats? It always surprises that the same kind of baked and crazily processed snack stuff that is in the USA marketed to illegal day laborers from Guatemala or Honduras is considered high class in Taiwan, the Chinese mainland and Japan.

    Weird. I feel guilty eating Cheetos, Doritos, or shitty and sugary donuts at a local dive.

    But visit, for example, a popular Asian dessert place in L.A., and there are lines out the door for stuff that I would never eat.

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