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Thread: Does this data from human 1000 make sense?

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    Does this data from human 1000 make sense?

    I used to imagine that the number of homozygous people for lactose tolerance would be similar in Iberia and Tuscany. Some data in the 1000 human genomes are strange. According to human 1000 genomes, there are more homozygous people for lactose tolerance in Colombia than in Tuscany ( ? )

    lactose tolerante.jpg

    CLM: Medellin, Colombia.
    GBR: British
    IBS: Iberian
    TSI: Tuscany

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    The researched allele was: rs4988235

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    Quote Originally Posted by Ack View Post
    I used to imagine that the number of homozygous people for lactose tolerance would be similar in Iberia and Tuscany. Some data in the 1000 human genomes are strange. According to human 1000 genomes, there are more homozygous people for lactose tolerance in Colombia than in Tuscany ( ? )

    lactose tolerante.jpg

    CLM: Medellin, Colombia.
    GBR: British
    IBS: Iberian
    TSI: Tuscany
    Quote Originally Posted by Ack View Post
    The researched allele was: rs4988235
    I can't give you a precise answer, because I don't know the theme in discuss. I just can display my genotype refering to gene MCM6:

    rsid chromosome position genotype
    rs4988235 2 136608646 AG
    rs182549 2 136616754 CT

    Cheers.

    PS: This is my genetic diagnonis for lactose tolerance: People with your genotype are more likely to be lactose tolerant and digest milk.

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    1 members found this post helpful.
    Quote Originally Posted by Duarte View Post
    I can't give you a precise answer, because I don't know the theme in discuss. I just can display my genotype refering to gene MCM6:

    rsid chromosome position genotype
    rs4988235 2 136608646 AG
    rs182549 2 136616754 CT

    Cheers.

    PS: This is my genetic diagnonis for lactose tolerance: People with your genotype are more likely to be lactose tolerant and digest milk.
    Cool, I'm homozygous for tolerance. No surprise since I love cheeses, yogurts and dairy products in general.






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    Quote Originally Posted by Ack View Post
    Cool, I'm homozygous for tolerance. No surprise since I love cheeses, yogurts and dairy products in general.






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    It is true. Every day I eat cheese, drink yogurt and drink milk

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    1 members found this post helpful.
    Quote Originally Posted by Duarte View Post
    I can't give you a precise answer, because I don't know the theme in discuss. I just can display my genotype refering to gene MCM6:

    rsid chromosome position genotype
    rs4988235 2 136608646 AG
    rs182549 2 136616754 CT

    Cheers.

    PS: This is my genetic diagnonis for lactose tolerance: People with your genotype are more likely to be lactose tolerant and digest milk.
    I'm also not an expert on the subject, but I found it very strange that tolerance in Tuscany is so low, it doesn't make sense to me.






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    Quote Originally Posted by Ack View Post
    I used to imagine that the number of homozygous people for lactose tolerance would be similar in Iberia and Tuscany. Some data in the 1000 human genomes are strange. According to human 1000 genomes, there are more homozygous people for lactose tolerance in Colombia than in Tuscany ( ? )

    lactose tolerante.jpg

    CLM: Medellin, Colombia.
    GBR: British
    IBS: Iberian
    TSI: Tuscany
    Well, it's not too different from TSI in SNPedia's graph:

    https://www.snpedia.com/index.php/Rs4988235

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    Quote Originally Posted by Regio X View Post
    Well, it's not too different from TSI in SNPedia's graph:
    https://www.snpedia.com/index.php/Rs4988235
    what could explain that? For some reason the allele was not very selected in TSI?






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    Italian_North 0.00 3.18 5.03 0.00 0.20 0.00 0.00 29.03 0.00 0.00 0.00 27.88 0.00 0.74 0.00 4.22 4.16 0.00 0.00 0.00 0.00 0.00 25.56
    Colombian 21.63 1.47 2.57 0.17 0.59 0.08 0.11 13.93 0.09 0.68 0.18 32.98 0.14 0.35 1.51 2.59 3.95 0.14 0.18 0.17 3.98 0.13 12.39

    In MDLP-K23b Colombians have more EEF than North Italy.

    According to the Wikipedia article, Columbia received both Basque and German migrants.

    https://en.wikipedia.org/wiki/Immigration_to_Colombia

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    Quote Originally Posted by Ack View Post
    what could explain that? For some reason the allele was not very selected in TSI?






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    Truth is that I don't know. Perhaps it was not selected as in other parts of Europe, for some reason. Dairy products may have no lactose, btw, such aged cheeses. Possibly Tuscans consumed few milk and more of this kind of dairy? Or dairy was not important in their diet? No idea. Would be also possible that later movements from South (reaching also North Italy) contributed somehow to "brake" the increase of frequency? Finally, who are the TSI exactly? Considering there're regional variations in Italy, would be possible that Tuscany has spots with substantially higher and lower frequencies of tolerance?

    Or something else?

    Probably Angela and Pax can help you more with all of this.

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    TSI are from one village northwest of Florence, so it's not a representative sample of Tuscans for that trait perhaps.

    Actually, that looks extremely low for everyone, unless it's because those are just the homozygous numbers. Perhaps it's because even being heterozygous makes you lactose tolerant.



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    Quote Originally Posted by Angela View Post
    TSI are from one village northwest of Florence, so it's not a representative sample of Tuscans for that trait perhaps.
    Actually, that looks extremely low for everyone, unless it's because those are just the homozygous numbers. Perhaps it's because even being heterozygous makes you lactose tolerant.
    My guess is that it's based on phenotype. If so, it should include heterozygous.

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    Quote Originally Posted by Angela View Post
    TSI are from one village northwest of Florence, so it's not a representative sample of Tuscans for that trait perhaps.

    Actually, that looks extremely low for everyone, unless it's because those are just the homozygous numbers. Perhaps it's because even being heterozygous makes you lactose tolerant.

    I was unable to check human 1000 genomes for the specific origin of any of the population samples - I hated that. How do you get information about the geographical origin of the samples? I would love to know too. Even adding the TSI heterozygotes is far behind all other samples - which makes very little sense to me. The regional methodology of human 1000 is terrible. And what is the source of this chart that you posted? It makes a lot more sense to me.






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    Quote Originally Posted by Ack View Post
    I was unable to check human 1000 genomes for the specific origin of any of the population samples - I hated that. How do you get information about the geographical origin of the samples? I would love to know too. Even adding the TSI heterozygotes is far behind all other samples - which makes very little sense to me. The regional methodology of human 1000 is terrible. And what is the source of this chart that you posted? It makes a lot more sense to me.
    I forgot I had this:

    https://topseudoscience.wordpress.co...nomes-samples/

    (...)
    "The Tuscan sample from Italy was collected in a single small town, hence is biased towards rural people of a specific town. Similarly, the British sample is rural, although scattered around a wider area."
    (...)
    "TSI (Toscani in Italia): These cell lines and DNA samples were prepared from blood samples collected in a small town near Florence in the Tuscany region of Italy. All of the samples are from unrelated individuals who identified themselves as having at least three out of four Tuscan grandparents."
    (...)

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    Quote Originally Posted by Regio X View Post
    I forgot I had this:
    https://topseudoscience.wordpress.co...nomes-samples/
    (...)
    "The Tuscan sample from Italy was collected in a single small town, hence is biased towards rural people of a specific town. Similarly, the British sample is rural, although scattered around a wider area."
    (...)
    "TSI (Toscani in Italia): These cell lines and DNA samples were prepared from blood samples collected in a small town near Florence in the Tuscany region of Italy. All of the samples are from unrelated individuals who identified themselves as having at least three out of four Tuscan grandparents."
    (...)
    Thanks for the link, it helped a lot. Is there any reason to believe that people in rural areas are more or less tolerant to lactase? I do not know this type of association, but I do not know many things. On the other hand, if the samples were from large cities with a large number of migrants from other regions, the results could be even more uncertain - due to the 'great' regional variation within Italy. In fact: samples in TSI could cover larger areas.






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    Quote Originally Posted by Ack View Post
    Thanks for the link, it helped a lot. Is there any reason to believe that people in rural areas are more or less tolerant to lactase? I do not know this type of association, but I do not know many things. On the other hand, if the samples were from large cities with a large number of migrants from other regions, the results could be even more uncertain - due to the 'great' regional variation within Italy. In fact: samples in TSI could cover larger areas.
    I don't think being rural is an issue. I think the issue here is that all samples come from the same little location, at the same time there may be relevant regional variations in Italy, be it regarding overall autosomal, be it concerning phenotypes in general (the phenotype in discussion is LP, but it could be, say, eye color, or whatever). Whether tolerance in Tuscany does vary substantially or not, I really don't know. Neither I'm sure drifts such local founder effects could explain it. Probably not. Perhaps the village just falls in a sort of gradient. The map posted by Angela seems to support a SE-NW cline in that area, higher in the former and lower in the latter. If so, the average for Tuscany as a whole could be slightly higher than that one based on TSI. It would be still somewhat low though. Just a guess.

    Btw, my father, my mother-in-law and myself are tolerant (all heterozygous). My mother and my wife are not.
    Last edited by Regio X; 21-05-20 at 01:11.

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    @Ack
    This may interest you. I was reading parts of this "paper" regarding Trentino (shared in another thread), little by little, and the following called my atention. It's about LP from Neolithic to BA in this Italian region.
    (Regarding the study itself, there're some interesting infos in there, but I also identified some "inconsistencies". Well, that's another story. I still have to read more of it anyway.)

    LP in Neo-BA
    "Originally thought to have spread during the Neolithic, more recent studies have shown that the derived allele may still have been rare at the start of the Bronze Age, and gradually spread with the Steppe-driven expansions. Its apparent absence in South Tyrol-Trentino, therefore, is unsurprising. However, the selective pressure may also have been lower in this region. The archaeological evidence documents a variety of available foodstuffs, and the persistence of hunting as an additional subsistence strategy until well into the Bronze Age, although proportion of wild animals amongst the faunal remains gradually dwindles. The region is a fertile one, combining a Mediterranean climate in the valley with extensive pasture grounds on the adjacent plateaux. The general availability of various food sources may therefore have reduced the specific selective advantage in this region, with the allele spreading to its extant frequencies gradually over time."

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    1 members found this post helpful.
    ^^over time and with subsequent migrations.

    When you live in fertile lands with a Mediterranean climate, surviving is easier. That's why the Neolithic began with the Natufians. There's a great video explaining how the Levant was a paradise for early men.

    You can fish from the sea as well as rivers, forage for edible plants and berries almost year long, including the wonderful chestnut trees and hazelnut trees, hunt wild game, i.e. boar, rabbit, birds, and some pigs to take you through the winter and a cow or two or goats and sheep. There's pasture for those animals almost year round. In my own Lunigiana valley, much of which has the Mediterranean climate of Liguria, you can grow crops three seasons a year. The olive tree was also a great boon once the Greeks and Romans introduced it. As for dairy products, hard cheeses cause few problems, and you don't need to be able to drink the milk of the animals to survive.

    Of course, despite the beautiful climate, most of Liguria is mountainous with poor soil, but, as I said, a Mediterranean climate and decent soil is a winning combination. I don't think the selective pressure would be as strong.

    One other thing occurs to me as a possibility for the timing of the beginning of the sweep. Lactating all year long is not something that these domesticated animals did naturally. The cows, for example, lactated when the young were born, as do humans. It took a long time to get these animals to provide the calorie rich milk year round.

    Another point which I think needs to be remembered is that

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    Quote Originally Posted by Angela View Post
    ^^over time and with subsequent migrations.

    When you live in fertile lands with a Mediterranean climate, surviving is easier. That's why the Neolithic began with the Natufians. There's a great video explaining how the Levant was a paradise for early men.

    You can fish from the sea as well as rivers, forage for edible plants and berries almost year long, including the wonderful chestnut trees and hazelnut trees, hunt wild game, i.e. boar, rabbit, birds, and some pigs to take you through the winter and a cow or two or goats and sheep. There's pasture for those animals almost year round. In my own Lunigiana valley, much of which has the Mediterranean climate of Liguria, you can grow crops three seasons a year. The olive tree was also a great boon once the Greeks and Romans introduced it. As for dairy products, hard cheeses cause few problems, and you don't need to be able to drink the milk of the animals to survive.

    Of course, despite the beautiful climate, most of Liguria is mountainous with poor soil, but, as I said, a Mediterranean climate and decent soil is a winning combination. I don't think the selective pressure would be as strong.

    One other thing occurs to me as a possibility for the timing of the beginning of the sweep. Lactating all year long is not something that these domesticated animals did naturally. The cows, for example, lactated when the young were born, as do humans. It took a long time to get these animals to provide the calorie rich milk year round.

    Another point which I think needs to be remembered is that
    The explanation makes sense. I was doubtful because steppe ancestry is relatively high in Tuscany, so I expected a higher level of lactose tolerance. But if we consider everything that has been said, it probably makes sense to have less permanence / selection for alleles of tolerance.

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    Quote Originally Posted by Ack View Post
    The explanation makes sense. I was doubtful because steppe ancestry is relatively high in Tuscany, so I expected a higher level of lactose tolerance. But if we consider everything that has been said, it probably makes sense to have less permanence / selection for alleles of tolerance.
    Steppe admixed people may have spread it, but lactase tolerance did not develop on the steppe. They were lactose intolerant. It developed in farmer communities in central to eastern Europe.

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