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Thread: Can Ancient Dna predict stature?

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    Can Ancient Dna predict stature?

    See:
    Predicting skeletal stature using ancient DNA

    Samantha L Cox, Hannah Moots, Jay T Stock, Andrej Shbat, Bárbara D Bitarello, Wolfgang Haak, Eva Rosenstock, Christopher B Ruff, Iain Mathieson
    https://www.biorxiv.org/content/10.1...03.31.437877v1


    ​The bottom line? Yes, but not all that well.


    Abstract

    Objectives Ancient DNA provides an opportunity to separate the genetic and environmental bases of complex traits by allowing direct estimation of genetic values in ancient individuals. Here, we test whether genetic scores for height in ancient individuals are predictive of their actual height, as inferred from skeletal remains. We estimate the contributions of genetic and environmental variables to observed phenotypic variation as a first step towards quantifying individual sources of morphological variation.

    Materials and Methods We collected stature estimates and femur lengths from West Eurasian skeletal remains with published genome-wide ancient DNA data (n=167, dating from 33,000-850 BP). We also recorded genetic sex, genetic ancestry, date and paleoclimate data for each individual, and δ13C and δ15N stable isotope values where available (n=67).

    Results A polygenic score (PRS) for height predicts 6.8% of the variance in femur length in our data (n=117, SD=0.0068%, p<0.001), controlling for sex, ancestry, and date. This is consistent with the predictive power of height PRS in present-day populations and the low coverage of ancient samples. Comparatively, sex explains about 15% of the variance in femur length in our sample. Environmental effects also likely play a role in variation, independent of genetics, though with considerable uncertainty (longitude: R2=0.0317, SD=0.009, p=0.019).

    Discussion Polygenic scores explain a small but significant proportion of the variance in height in ancient individuals, though not enough to make useful predictions of individual phenotypes. However, environmental variables also contribute to phenotypic outcomes and understanding their interaction with direct genetic predictions will provide a framework with which to model how plasticity and genetic changes ultimately combine to drive adaptation and evolution.


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    1 members found this post helpful.
    I think we may say yes and no.
    The genes play a big role, but food, activity, and other environmental factors are at play too, it has been already discussed.
    The factors which encrease stature are not always good things at every level. The today occidental well developped countries people are proportionally less broad shouldered, more weakly boned, and sexual differences seem to me a bit weakened too. Nevertheless I have not a detailed study about all that.

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    Quote Originally Posted by MOESAN View Post
    I think we may say yes and no.
    The genes play a big role, but food, activity, and other environmental factors are at play too, it has been already discussed.
    The factors which encrease stature are not always good things at every level. The today occidental well developped countries people are proportionally less broad shouldered, more weakly boned, and sexual differences seem to me a bit weakened too. Nevertheless I have not a detailed study about all that.
    To the extent this is true, it's probably due to genetic factors. Non-genetic limits on growth (aka stunting) result in both shorter stature and a weaker bone structure. East Africans and certain other Indian Ocean peoples have naturally very long, narrow bodies. I have not noticed this to be the case for Europeans. Northern Europeans especially seem quite broad-shouldered, across the range of height. In fact during the admittedly limited occasions I've been there I found this striking. Spaniards on the other hand seem to have smaller frames, probably due to long legs and small torsos, though in the outskirts of Madrid I did see people who were quite robust and muscular.

    Today northern Europeans, and probably southerners as well, in their vast majority grow to be as tall as their genes allow them to be, as their diets are rich in protein and calcium. Maybe Eastern Europe is still somewhat stunted. If it is in fact true that some of the developed countries are less robust, perhaps this is the result of Neolithic admixture?

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    Previous work found a relationship between latitude and height in Europe which we do not observe in our sample. Cox et al. (2019) suggested that the observed latitudinal trend might be genetically driven by post-Neolithic Steppe migrations; however, even if we remove the ancestry term from our model, latitude is still not significant. However, our sample is biased towards Northern European collections for which we found more published metrics on DNA sampled individuals. Lack of a substantial Southern European sample might explain why we do not see a relationship.


    Longitude has also previously been shown to correlate with stature in the European pre-Bronze Age periods (Ruff, 2018; Cox et al., 2019), as have climate variables (Ruff, 2018). We do replicate this observation. However, this is partly driven by the relatively tall individuals from the Danube Gorges region of Southeastern Europe (12 individuals in our sample). It has been well documented that the populations of this region do not follow the same height decreases that affect the rest of the continent through history.
    This study concludes that it is not currently practical to use genetic data to predict individual phenotypes for height. However, there are two ancient population groups which are strongly associated with height. Mathieson et al. (2015) suggested that the modern South-North gradient in height across Europe is due to both increased steppe ancestry in northern populations, and selection for decreased height in Early Neolithic migrants to southern Europe. Yamnaya pastoralists from the Caspian steppe consumed dairy products and they were tall and healthy with little caries. Their advanced lifestyle could have contributed to their increased height. 12 tall individuals from the Danube Gorges region of Southeastern Europe are also included in this study. The abundance of protein-rich resources in this region may be a factor, contributing to the long-lasting existence of the population over several millennia. The environment of the Danube Gorges is ideal for fishing large species of migratory sturgeon and other river fish.
    Давайте вместе снова сделаем мир великий!

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    I dont think so..

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    Quote Originally Posted by MOESAN View Post
    I think we may say yes and no.
    The genes play a big role, but food, activity, and other environmental factors are at play too, it has been already discussed.
    The factors which encrease stature are not always good things at every level. The today occidental well developped countries people are proportionally less broad shouldered, more weakly boned, and sexual differences seem to me a bit weakened too. Nevertheless I have not a detailed study about all that.

    The general nutrition we have is excellent, we just have problems with individual diets and our general way of life, especially the high levels of sugar, fat and artificial ingredients, but even more so lack of an active lifestyle with lots of physical exercise is a problem. Those people which reduce the unhealthy aspects and train on a healthy, non-excessive level, are surely more healthy and better in shape in every thinkable way than any of their ancestors would have been. So its not our environment as such became worse, surely not, if looking at the past, but the individual lifestyles differ a lot and some of these are very negative.
    Like if you compare Korean people, even those without having done any beauty jobs, the South Koreans are as a rule more healthy and attractive looking, except when they are overweight. But the lack of food and nutrients in the North is very clearly not favourable for the development, and decreases height at the same time. So a high intake of food, expecially proteins, as long as it is a generally good & balanced diet, combined with exercise, is good for the development.

    Don't forget that among the tallest people in the past were foragers with an excellent, protein-rich nutrition, some of the strongest people encountered, among which were the Ancient North Eurasians. The diet of the poor peasants and workers in the factories was a negative deviation, oftentimes with a lack of animal proteins and fresh fruits and vegetables, sometimes even fresh air and clean water. So basically, if being in the same genetic range, stature can be used as an information for how well off and healthy a population was. This is evident in the 19th century, as it is Neolithic times. The LBK people for example had in some of their settlements a decrease of stature and clear signs of malnutrition, disease and inbreeding shortly before their collapse. Same for some Maya settlements and so on.

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    Quote Originally Posted by American View Post
    To the extent this is true, it's probably due to genetic factors. Non-genetic limits on growth (aka stunting) result in both shorter stature and a weaker bone structure. East Africans and certain other Indian Ocean peoples have naturally very long, narrow bodies. I have not noticed this to be the case for Europeans. Northern Europeans especially seem quite broad-shouldered, across the range of height. In fact during the admittedly limited occasions I've been there I found this striking. Spaniards on the other hand seem to have smaller frames, probably due to long legs and small torsos, though in the outskirts of Madrid I did see people who were quite robust and muscular.

    Today northern Europeans, and probably southerners as well, in their vast majority grow to be as tall as their genes allow them to be, as their diets are rich in protein and calcium. Maybe Eastern Europe is still somewhat stunted. If it is in fact true that some of the developed countries are less robust, perhaps this is the result of Neolithic admixture?
    Your are not on hte same path as me.
    My last phrase concerned diachronic evolution, not geography or genetic background.
    Have you ever compared in same countries with roughly same ancestry the evolution of proportions: body internal ones and head compared to body?
    Diet is not all: too less rich or unbalanced diet very often leads to same results: too rich one is not so systematically expressed in bones, because metabolism can regulate easier excess than lack.
    one big cause of modern phenotypic evolution (and ignored too often) is the lack of physical activity and the oxygenation linked to it and the effet on ossification;
    more: a long legged body is NOT AT ALL linked to narrow shoulders; we know all athletic types with long leggs, not the type of eastern Africans; and the Kenyan/Ethioian marathon riders are not long legged!!! 'makroskele' # 'longiligne' or 'filiforme': all these vague descriptions of "robust" and "gracile" are abusing readers; genetic heredity and /selectionevolution(S) produced quantities of diverse forms of skeletons, which cannot be resumed so naively and so erroneously. Even Coon when he wrote some descriptions like "lateral" bodies (Turks, Armenians by instance) put someones to believe "lateral" = "broad shoulders"; it isn't the case for most of Turks.

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    The majority of my ancient ancestors are Anatolian_N, and I am 6 foot 2 inches tall, 215 pounds. I don't think it has much to do with the American diet, since my maternal grand parents were tall and hardy people.

    It is no wonder a good number of my relatives are police officers.

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    I add some other possible cause for stature increase: less local endogamy?

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    a good thing to do to compare: look at the football (soccer) players national teams since the 1950's to our days (but today, "team" has no more value, only "stars" are of worth, it's true so it's hard to have teams pictures). Look at the proportion of the head compared to body, and "robisticity".

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    Quote Originally Posted by MOESAN View Post
    a good thing to do to compare: look at the football (soccer) players national teams since the 1950's to our days (but today, "team" has no more value, only "stars" are of worth, it's true so it's hard to have teams pictures). Look at the proportion of the head compared to body, and "robisticity".
    Maybe football teams are not representative for a comparison, since the selection is much more serious today, more towards athletic stature as it used to be. Haircuts could also be misleading.

    But people living in the same areas with the same genetics for the last few centuries are much higher in average than they were 100 years ago. So definitely diet, abundance of food and easier life play a role in stature and growth. I've read somewhere (if I would remember I would quote) that the old Romans had a meat scarcity for a while and ate almost only barley for a longer period. Which made them shorter within a relatively short time. It seems that it doesn't take long for a significant variation in size. I don't see a long term correlation between genes and stature expectations. Genetic drift is something else.

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    Quote Originally Posted by don_joe View Post
    Maybe football teams are not representative for a comparison, since the selection is much more serious today, more towards athletic stature as it used to be. Haircuts could also be misleading.

    But people living in the same areas with the same genetics for the last few centuries are much higher in average than they were 100 years ago. So definitely diet, abundance of food and easier life play a role in stature and growth. I've read somewhere (if I would remember I would quote) that the old Romans had a meat scarcity for a while and ate almost only barley for a longer period. Which made them shorter within a relatively short time. It seems that it doesn't take long for a significant variation in size. I don't see a long term correlation between genes and stature expectations. Genetic drift is something else.
    Agree partly; concerning the "bias" in my football comparisons, i saw the same in normal pop and in rugby where selection for statures is at play too and since long ago.
    concerning genes, there IS correlation, but it is'nt so easy to see because genes are not the only factors, it's evident. But at a long scale of time, the genetic correlation is confirmed; it's enough seeing the 2 last centuries states for diverses regions and countries.

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    I forgot: some new elements in food can produce bad effects for size regulation; too hig stature can be a problem for skeleton and health in general;
    often enough the very big people had anomalies in their body: a supplementary vertebra, a third kidney and so on...

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    A survey of the 1920's on the living skeletons proportions in Sweden; some results:
    Sweden as a whole was a rather homogenous country (surely a bit more immigrants in big towns, in despite there ere not too much recent immigrants there, then).
    North a bit shorter in proportions than other great regions in for legs, and longer for arms; often a link between proportions of arms length and shoulder breadth > span -
    Differences between socio-occupational groups as big than the regional differences, bigger if we exclude the 4 bigger towns of Swede.
    from the proportionally broader shouldered to shorter shouldered:
    1- peasants, countrymen / 2- workmen, commerce employees / 3- public services /
    the shorter legged, shorter shouldered (and span): 4 bigger towns of Swede, spite thay are not shorter in absolute stature than the others; it's true they were abit more dolichocephalic than the national mean.
    It seems confirmed in other countries (places) and times that countrymen are a bit shorter but longer spanned and broader shouldered than cities men, at least since the 20th century; and proportional legs length is not at all linked to allover stature, in a same region! (confirmed in Brittany of the1950's). Not that proportions of types would not be at play, but even in rather homogenous regions, the tendancy is to higher stature in towns, but not longer legs.
    As towns produce higher statures without external inputs we could say this stature increase (vertical) is not as a whole followed by lateral increase and supposed robusticity.

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    Quote Originally Posted by MOESAN View Post
    Your are not on hte same path as me.
    My last phrase concerned diachronic evolution, not geography or genetic background.
    Have you ever compared in same countries with roughly same ancestry the evolution of proportions: body internal ones and head compared to body?
    Diet is not all: too less rich or unbalanced diet very often leads to same results: too rich one is not so systematically expressed in bones, because metabolism can regulate easier excess than lack.
    one big cause of modern phenotypic evolution (and ignored too often) is the lack of physical activity and the oxygenation linked to it and the effet on ossification;
    more: a long legged body is NOT AT ALL linked to narrow shoulders; we know all athletic types with long leggs, not the type of eastern Africans; and the Kenyan/Ethioian marathon riders are not long legged!!! 'makroskele' # 'longiligne' or 'filiforme': all these vague descriptions of "robust" and "gracile" are abusing readers; genetic heredity and /selectionevolution(S) produced quantities of diverse forms of skeletons, which cannot be resumed so naively and so erroneously. Even Coon when he wrote some descriptions like "lateral" bodies (Turks, Armenians by instance) put someones to believe "lateral" = "broad shoulders"; it isn't the case for most of Turks.
    Have you ever compared in same countries with roughly same ancestry the evolution of proportions: body internal ones and head compared to body?
    Not sure what you mean here. Are you talking about head shape and body shape independently of one-another?

    Diet is not all: too less rich or unbalanced diet very often leads to same results: too rich one is not so systematically expressed in bones, because metabolism can regulate easier excess than lack.
    one big cause of modern phenotypic evolution (and ignored too often) is the lack of physical activity and the oxygenation linked to it and the effet on ossification;
    I agree if you're talking about soft-tissue things like obesity that can result from a "too rich" diet, as is common in the US and Polynesia. Lack of physical activity definitely results in less prominent cortical bones (studies of people with Ehlers-Danlos have confirmed this), but I have no idea what it does to actual skeletal shape as a whole.

    more: a long legged body is NOT AT ALL linked to narrow shoulders; we know all athletic types with long leggs, not the type of eastern Africans; and the Kenyan/Ethioian marathon riders are not long legged!!! 'makroskele' # 'longiligne' or 'filiforme': all these vague descriptions of "robust" and "gracile" are abusing readers; genetic heredity and /selectionevolution(S) produced quantities of diverse forms of skeletons, which cannot be resumed so naively and so erroneously. Even Coon when he wrote some descriptions like "lateral" bodies (Turks, Armenians by instance) put someones to believe "lateral" = "broad shoulders"; it isn't the case for most of Turks.
    [/QUOTE]

    Here I have to disagree. It definitely is. Kenyan and Ethiopian runners do have long legs for their height, they're just not strikingly tall. They're not like Nilotic peoples or Somalis, but their legs are long for their height. Relative sitting height is lowest around the Indian Ocean, as is relative shoulder and hip width. These are highest in Arctic populations and to a lesser extent Northern Europeans, Koreans, and Japanese. A shorter torso and longer legs definitely correlates with narrower shoulders and hips in proportion to stature. Coon is quite clear about Southern Europeans having a lower relative sitting height and narrower frames (especially in the shoulders). Same for peninsular Arabs, Tuaregs, East Africans, etc. Australian aborigines are kind of at the extreme of the long, narrow body shape, even though they aren't exceptionally tall, they have the lowest relative sitting height. As such they also have very narrow frames.

    Perhaps northern Euros have the widest shoulders in proportion to trunk length, which is probably an WHG/ANE trait.

    As far as your issue with the terms, I don't even know some of them. I have read Coon (at least Races of Europe) but am not into the really obscure race-science stuff so prevalent on the internet, so I have no idea about "makroskele", "longiligne", or "filiforme".

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    @American; me in vertical, you in italics letters

    Have you ever compared in same countries with roughly same ancestry the evolution of proportions: body internal ones and head compared to body?
    Not sure what you mean here. Are you talking about head shape and body shape independently of one-another?
    I meant : internal proportions fo body, and global head size compared to allover body size ; (in fact I think lateral sizes of head are comparatively decreasing (more the breadth), spite head height tends to increase a bit, in USA at least) ; surely internal proportions of head change too, but it is a bit complicated.



    I agree if you're talking about soft-tissue things like obesity that can result from a "too rich" diet, as is common in the US and Polynesia. Lack of physical activity definitely results in less prominent cortical bones (studies of people with Ehlers-Danlos have confirmed this), but I have no idea what it does to actual skeletal shape as a whole.
    I ‘ll try to make me understand : « metaboslism an regulate easier excess than lack » means for me that a very healthy person’s body can eliminate some of the excess of food elements but it cannot « create » the needed elements it doesn’t absorb. It’s true it depends on kinds of metabolism : someones, even without too much physical activity, eliminates more easily excess than others which tends to accumulate and accumulate as by « fear of lacking » (some theories about hunters gatherers heredity are born not too long ago…). Metabolism is a complicated matter I don’t know enough about it to say more, but I was not speaking of fet parts of body, only of skeleton. ATW, it ‘s not only a matter of food quantity but of food quality ; lack of food can lead to lack of stature growing, but too much food doesn’t lead necessary to more stature growing.




    Here I have to disagree. It definitely is. Kenyan and Ethiopian runners do have long legs for their height, they're just not strikingly tall. They're not like Nilotic peoples or Somalis, but their legs are long for their height. Relative sitting height is lowest around the Indian Ocean, as is relative shoulder and hip width. These are highest in Arctic populations and to a lesser extent Northern Europeans, Koreans, and Japanese. A shorter torso and longer legs definitely correlates with narrower shoulders and hips in proportion to stature. Coon is quite clear about Southern Europeans having a lower relative sitting height and narrower frames (especially in the shoulders). Same for peninsular Arabs, Tuaregs, East Africans, etc. Australian aborigines are kind of at the extreme of the long, narrow body shape, even though they aren't exceptionally tall, they have the lowest relative sitting height. As such they also have very narrow frames.
    Perhaps northern Euros have the widest shoulders in proportion to trunk length, which is probably an WHG/ANE trait.


    As far as your issue with the terms, I don't even know some of them. I have read Coon (at least Races of Europe) but am not into the really obscure race-science stuff so prevalent on the internet, so I have no idea about "makroskele", "longiligne", or "filiforme".



    Europe is a very small land for North American. Europe is full of local variations even concerning Humans. Northern and Southern Europe show big differences on short distances for some traits, in the same country. We cannot put in the same bag Touaregs, Andalusians and Campania Italians, no more Western Balkans people and Eastern Balkans ones, or all Northern Europe people ; Irish people seems rather comparatively short legged, British people almost the same (less Welsh people, I guess), but Frisians are rather long legged as the typical ‘nordic’ pop of Central Norway, spite N-W Norwegians are rather moderately legged ; high statured ex-Yugoslavian people are moderately long legged ; in Iraq, Nasiriya Liwa folk wre long legged when Al Sawaad ones were short legged, and I could speak of regions of Spain and Portugal too.. (general terms, because in every population the extremes types are very far at the individual level, but here and there dominates some type over the other). And I affirm that a lot of sturdy people are not as bread shouldered as believed, what doesn’t contradict they are vey solidly built for bones and muscles. I red too often stereotypes and generalisations as BI « North-Africans are long legged », or: « short trunk = narrow trunk ».

    It’s true that in some measure, some mechanisms link skeleton proportions when there is increase in size within a body morphology type (a link between increase in stature for a type and a slight increase of relative legs length, but the differences between types (and their genetic making) comes to destroy this too simplistic way to link traits. Concerning Kenyans and generally East-African natives I wait for precise data (I had someones but I cannot put ma hand on them for now). I gave some European relative trunk length in some thread here, long time ago, easy for me to find again. But I 've not for extra-Europe ones which I misplaced.





    Longiligne (french) : slender
    filiforme (french) : lanky, spindly (for me : high or long, and narrow)
    macroskèle (french < greek) : long legged compared to trunk length

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