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Thread: Phenotype doesn't necessarily correlate with specific levels of ancestry

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    4 members found this post helpful.

    Phenotype doesn't necessarily correlate with specific levels of ancestry



    Opinion piece by Khan on a new paper:
    https://www.gnxp.com/WordPress/2019/...ply-admixture/

    The paper:
    https://www.biorxiv.org/content/10.1101/773663v2

    "Source populations for an admixed population can possess distinct patterns of genotype and phenotype at the beginning of the admixture process. Such differences are sometimes taken to serve as markers of ancestry---that is, phenotypes that are initially associated with the ancestral background in one source population are taken to reflect ancestry in that population. Examples exist, however, in which genotypes or phenotypes initially associated with ancestry in one source population have decoupled from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. We develop a mechanistic model for describing the joint dynamics of admixture levels and phenotype distributions in an admixed population. The approach includes a quantitative-genetic model that relates a phenotype to underlying loci that affect its trait value. We consider three forms of mating. First, individuals might assort in a manner that is independent of the overall genetic admixture level. Second, individuals might assort by a quantitative phenotype that is initially correlated with the genetic admixture level. Third, individuals might assort by the genetic admixture level itself. Under the model, we explore the relationship between genetic admixture level and phenotype over time, studying the effect on this relationship of the genetic architecture of the phenotype. We find that the decoupling of genetic ancestry and phenotype can occur surprisingly quickly, especially if the phenotype is driven by a small number of loci. We also find that positive assortative mating attenuates the process of dissociation in relation to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype. The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might be a reliable proxy for ancestry for only a short time, especially if the trait is determined by relatively few loci. The results are potentially relevant in admixed human populations, in which phenotypes that have a perceived correlation with ancestry might have social significance as ancestry markers, despite declining correlations with ancestry over time."

    I've sort of had a gut feeling about this for a long time. My brother is more "southern" than I am genetically, but looks more "Central European". You can have siblings, as in the case of my husband and his sister, who are basically the same in terms of "components", yet he is very "Med" looking and she is blonde, blue eyed and fair skinned.

    For these to happen, the phenotypic traits would have had to have "decoupled" from the original ancestry.

    People haven't wanted to believe it, however, perhaps partly because that would call into question the use of such "appearance" traits to determine ancestry or proportions of ancestry, let us say.

    Of course, the more isolated a population the more such a correlation might exist, which is why physical anthropology might "work" in Finland, but not in Italy.


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    2 members found this post helpful.
    There is a lot of phenotypic diversity between me and my siblings. My brother is the most Mediterranean, phenotypically. But is the most northern, genetically.

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    This is very common in Brazil. We are a very mixed people. My youngest sister was Mediterranean like Sophia Loren (unfortunately she died of rectal cancer shortly after her 40th birthday - she was pregnant with a girl and did not want to interrupt her pregnancy - the girl is beautiful child and is my goddaughter).
    My older brother is handsome as Sean Connery (ie totally Mediterranean), my younger brother looks like Thor and I stayed in halfway (I think that I am a kind of mix of my older brother and my youngest brother).
    Please, don't laugh at my comparisons with the celebrities - of course that I wouldn't compare my brothers with ugly people, LOL. Good thing there is my younger brother, because my son looks a lot like him. If he did not exist I might think that my son would have been changed in the maternity ward. LOL.
    I think I'm the only genetics buff in the family. No one is interested in the tests, not even my son.

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    Phenotype is basically what came out from gambling with genes, you get traits that had only a 5% chance.

    I wouldn't say they correlate or don't, because Northerners were never 100% blonde with blue eyes, so Med features don't make you less Northern. Phenotype is still an indicator of what admixture you have though.

    I remember many years ago people were "fighting" racist claims with the example of a fair haired and eyed Albanian who had one of the most Southern European results.

    Plus what we call Northern or Southern nowadays is based on the location of people in the last hundreds of years. You could similarly say that before the Northerners were dark and the Central Asians were light, and the Southerns got lighter skin and eyes than Northerners from the migrating farmers from Levant and Anatolia.

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    is this even a surprise? it has always been clear that phenotype doesn't correspond to 100% of your genotype. a reason why racial categories in the US for example are too overrated and almost useless.

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    We are totally a mixed family. My father and younger sister are very light brown/dark blond with blue gray eyes. Mother and other two siblings dark/black hair and dark brown eyes. My cousins on my mother's side are "ginge", reddish blonde hair with light green eyes. My aunt on my father's side dark wavy hair, brown eyes. My half uncle dark hair, dark eyes, totally stick up straight hair. My eye color according to GEDMatch is gray. My actual color is chocolate brown. I must have some gray recessive genes from my father.
    Last edited by bigsnake49; 03-10-19 at 01:48.

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    Quote Originally Posted by Duarte View Post
    This is very common in Brazil. We are a very mixed people. My youngest sister was Mediterranean like Sophia Loren (unfortunately she died of rectal cancer shortly after her 40th birthday - she was pregnant with a girl and did not want to interrupt her pregnancy - the girl is beautiful child and is my goddaughter).
    My older brother is handsome as Sean Connery (ie totally Mediterranean), my younger brother looks like Thor and I stayed in halfway (I think that I am a kind of mix of my older brother and my youngest brother).
    Please, don't laugh at my comparisons with the celebrities - of course that I wouldn't compare my brothers with ugly people, LOL. Good thing there is my younger brother, because my son looks a lot like him. If he did not exist I might think that my son would have been changed in the maternity ward. LOL.
    I think I'm the only genetics buff in the family. No one is interested in the tests, not even my son.
    it is not to challenge the most of your post but to precise my thought about "types": Sean Connery as nothing of a 'mediter'! He is only dark haired, rather dark eyed and maybe "dark-white" skinned (uneasy to say for an actor). If I had to work on his skeleton, never shall I say he is 'mediter' in type.
    We very often confuse global geographical appartenance to true types. there are the geographically Mediterraneans (ihabitants), distinct for a part from the 'mediter' types.

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    Quote Originally Posted by MOESAN View Post
    it is not to challenge the most of your post but to precise my thought about "types": Sean Connery as nothing of a 'mediter'! He is only dark haired, rather dark eyed and maybe "dark-white" skinned (uneasy to say for an actor). If I had to work on his skeleton, never shall I say he is 'mediter' in type.
    We very often confuse global geographical appartenance to true types. there are the geographically Mediterraneans (ihabitants), distinct for a part from the 'mediter' types.
    Dear MOESAN.
    So what would the skeleton of a Mediterranean type look like, to you? A miniature Nordic, as I’ve heard some people saying for around? It wouldn't nice for my older brother and his one meter and eighty six centimeters of hight and, not to be modest, he was so successful with women that, even, he bothered me a lot, when we were young. I, for example, know that many Laplander have blue-eyes, have blond hair and very fair skin, but the shape of the face, chin type, and other features such as ossature and height, typical of people of Asian origin. I made no anthropometric measurements to know if my skeleton or the my brothers' skeleton is Nordic, Alpine, Dinaric, Mediterranean, Mongol, Negroid, etc. I believe you are seeking pseudo-scientific rigor that is not the purpose of this topic. I just wanted to highlight the phenotypic diversity that exists in my first-degree family by focusing only on the most obvious characteristics such as skin, eye and hair color.
    Regards.


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    Quote Originally Posted by Duarte View Post
    Dear MOESAN.
    So what would the skeleton of a Mediterranean type look like, to you? A miniature Nordic, as I’ve heard some people saying for around? It wouldn't nice for my older brother and his one meter and eighty six centimeters of hight and, not to be modest, he was so successful with women that, even, he bothered me a lot, when we were young. I, for example, know that many Laplander have blue-eyes, have blond hair and very fair skin, but the shape of the face, chin type, and other features such as ossature and height, typical of people of Asian origin. I made no anthropometric measurements to know if my skeleton or the my brothers' skeleton is Nordic, Alpine, Dinaric, Mediterranean, Mongol, Negroid, etc. I believe you are seeking pseudo-scientific rigor that is not the purpose of this topic. I just wanted to highlight the phenotypic diversity that exists in my first-degree family by focusing only on the most obvious characteristics such as skin, eye and hair color.
    Regards.


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    I agree with you in the sense that it's extremely hard or even impossible to draw the line between specific subraces but I think you misunderstood Moesan's point.

    Sean Connery might not be Nordic but he's not Med either, rather an old Celto-Germanic type centered around the Alps and spread around IMO. Of course I'm not saying his type originated with the linguistic group of Celts or Germanics but for the purpose of simplification I'm referring to this group.

    But it can get even more complicated if we see some pictures when he was very young and looking quite British too, so yes in his case he's definitely genetically and phenotypically Northern and not Southern so not a good example to debunk this study.

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    Quote Originally Posted by Duarte View Post
    Dear MOESAN.
    So what would the skeleton of a Mediterranean type look like, to you? A miniature Nordic, as I’ve heard some people saying for around? It wouldn't nice for my older brother and his one meter and eighty six centimeters of hight and, not to be modest, he was so successful with women that, even, he bothered me a lot, when we were young. I, for example, know that many Laplander have blue-eyes, have blond hair and very fair skin, but the shape of the face, chin type, and other features such as ossature and height, typical of people of Asian origin. I made no anthropometric measurements to know if my skeleton or the my brothers' skeleton is Nordic, Alpine, Dinaric, Mediterranean, Mongol, Negroid, etc. I believe you are seeking pseudo-scientific rigor that is not the purpose of this topic. I just wanted to highlight the phenotypic diversity that exists in my first-degree family by focusing only on the most obvious characteristics such as skin, eye and hair color.
    Regards.


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    I'm sad you consider what I wrote as a try to 'pseudo-scientific' rigor. I think I took more reserve in my post than you do here. (I'm taking just now some pills to overcome a nervous breakdown, I'm fragile, you know).
    Types making are a try to approach what could have been phenotypical features sets supposed or hoped as genetically inherited and statistically very overrepresented in some ancient rather homogenous pops, so a tool when analysing modern or less ancient pops to guess proportions in admixtures. It's an approach, not always with success, and even if seriously based, without any value at an individual level concerning the total autosomes DNA making, but it can help and it did really. So, I was not trying to debunk what you said on other points no more than I was doing concerning Angela points. It was just this 'mediterranean' label on Sean Connery, I read so often.
    Some traits are surely useful, I think. Eastern English people are lighter pigmented than Irish people, spite being globaly less 'north' (it' to say, less mesolithic in some way. some features like pigmentation could help to separate the differences respective frequencies between sorts of mesolithic and sorts of neolithic heritage among modern pops. Some of the "EEF" inheritage among Anglo-Saxons are more on the N/N-E Europe side (GAC?) than it is among Celts (Cardial?), I suppose. It could be interesting too, to focalize on the "EEF" inheritages among Italian pops of North compared to South, too...
    I was joking just above. No offense, no psychologic shock!

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    Quote Originally Posted by MOESAN View Post
    I'm sad you consider what I wrote as a try to 'pseudo-scientific' rigor. I think I took more reserve in my post than you do here. (I'm taking just now some pills to overcome a nervous breakdown, I'm fragile, you know).
    Types making are a try to approach what could have been phenotypical features sets supposed or hoped as genetically inherited and statistically very overrepresented in some ancient rather homogenous pops, so a tool when analysing modern or less ancient pops to guess proportions in admixtures. It's an approach, not always with success, and even if seriously based, without any value at an individual level concerning the total autosomes DNA making, but it can help and it did really. So, I was not trying to debunk what you said on other points no more than I was doing concerning Angela points. It was just this 'mediterranean' label on Sean Connery, I read so often.
    Some traits are surely useful, I think. Eastern English people are lighter pigmented than Irish people, spite being globaly less 'north' (it' to say, less mesolithic in some way. some features like pigmentation could help to separate the differences respective frequencies between sorts of mesolithic and sorts of neolithic heritage among modern pops. Some of the "EEF" inheritage among Anglo-Saxons are more on the N/N-E Europe side (GAC?) than it is among Celts (Cardial?), I suppose. It could be interesting too, to focalize on the "EEF" inheritages among Italian pops of North compared to South, too...
    I was joking just above. No offense, no psychologic shock!
    Hello MOESAN,
    I know you are a civilized person. I did not mean to offend anyone, much less you, who are one of the most lucid and respected figures in this forum. I am very averse to racial classifications and even more averse to theories of physical anthropology, which gained notoriety from author publications from the mid-nineteenth to the mid-twentieth century, declining after WW2. If I said something that offended you or made you overly sensitive, I apologize. You are one of the great ones I admire in Eupedia. Hugs

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    @Duarte:
    I'm blushing, you're too kind! LOL

    Phylosophy: Races are AND are not, for men as for animals, but for animals more isolation and selection pressure gets close to the "race" pseudo invatiant paradygm. Humans have "racial" differences if they are not of different races; it's only the % of differences within pops which is very lower than among animals, by the fact of bigger pops (so less drift and brutal selections) and constant re-admixtures. Constant opposition of raciation and "dis-raciation" (this last going very faster than the first one in an open world!).
    That said, typology is NOT racism, and the value classification between "races" (inequality) and the abuses it allows to someones is not an obliged consequence of it. Yet, for me, true inequality (if it exists) is not an excuse for abuses and crimes. But you can suppress the "racial" question", the ones who need to be on the "right and good side" will find some other distinction to impose themselves over others (cultural achievement, work merit and so on... Sorry for my poor french English).
    More seriously:
    Types in my meaning are kind of modelizations to try to measure differences of heritages between pops, whatever the depth of these differences. They are stereotypes, but useful stereotypes sometimes. The typology (individuals), compared to global metrics (pop means), has helped to show modifications in southern France in the Baumes (natural caves), at the Neolithic/Eneolithic-Chalco transitions, and more useful, return close to previous situations after, so not a environment mediated modification/evlution on an unique direction. It has helped to see a move of eastern France pops through parisian bassin into Eastern Brittany at Iron Age, or the differences between Danubian farmers and Cardial farmers in France and their meeting around the Parisian Basin at Mid-Last Neolithic (in SOM cultu, with another type, very archaic, surely more autochtonous). So a finer approach than have made ancient auDNA surveys sometimes (but some finer surveys on auDNA has showed these differences too). Helped to see a slight 'corded' so surely a North Europe input in Brittany in the Rich Tumuli period there, linked to Wessex culture (last Chalco).
    At Neolithic too, in Catalunya, typology has shown an input of 'danubian' types linked to cultural traits from N-Italy.
    The ancient physical anthropology had seen the differences between Anglo-Saxons in ancient England Settlements, and the conquered Celts and more precisely the sex mediated desiquilibrium in these precise settlements. + ...
    I stop here, I'm becoming boring. Boa Sera.

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    Quote Originally Posted by MOESAN View Post
    @Duarte:
    I'm blushing, you're too kind! LOL

    Phylosophy: Races are AND are not, for men as for animals, but for animals more isolation and selection pressure gets close to the "race" pseudo invatiant paradygm. Humans have "racial" differences if they are not of different races; it's only the % of differences within pops which is very lower than among animals, by the fact of bigger pops (so less drift and brutal selections) and constant re-admixtures. Constant opposition of raciation and "dis-raciation" (this last going very faster than the first one in an open world!).
    That said, typology is NOT racism, and the value classification between "races" (inequality) and the abuses it allows to someones is not an obliged consequence of it. Yet, for me, true inequality (if it exists) is not an excuse for abuses and crimes. But you can suppress the "racial" question", the ones who need to be on the "right and good side" will find some other distinction to impose themselves over others (cultural achievement, work merit and so on... Sorry for my poor french English).
    More seriously:
    Types in my meaning are kind of modelizations to try to measure differences of heritages between pops, whatever the depth of these differences. They are stereotypes, but useful stereotypes sometimes. The typology (individuals), compared to global metrics (pop means), has helped to show modifications in southern France in the Baumes (natural caves), at the Neolithic/Eneolithic-Chalco transitions, and more useful, return close to previous situations after, so not a environment mediated modification/evlution on an unique direction. It has helped to see a move of eastern France pops through parisian bassin into Eastern Brittany at Iron Age, or the differences between Danubian farmers and Cardial farmers in France and their meeting around the Parisian Basin at Mid-Last Neolithic (in SOM cultu, with another type, very archaic, surely more autochtonous). So a finer approach than have made ancient auDNA surveys sometimes (but some finer surveys on auDNA has showed these differences too). Helped to see a slight 'corded' so surely a North Europe input in Brittany in the Rich Tumuli period there, linked to Wessex culture (last Chalco).
    At Neolithic too, in Catalunya, typology has shown an input of 'danubian' types linked to cultural traits from N-Italy.
    The ancient physical anthropology had seen the differences between Anglo-Saxons in ancient England Settlements, and the conquered Celts and more precisely the sex mediated desiquilibrium in these precise settlements. + ...
    I stop here, I'm becoming boring. Boa Sera.
    Bonjour MOESAN,
    Thanks for the deference. You are not being boring, but just didactic, as a scientist must be.
    Bonsoir :)




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