Comments on: Structure within Houston Gujaratis resolved? http://sepiamutiny.com/blog/2011/04/29/structure_with/ All that flavorful brownness in one savory packet Sat, 30 Nov 2013 11:11:28 +0000 hourly 1 http://wordpress.org/?v=3.2.1 By: boston_mahesh http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283581 boston_mahesh Mon, 02 May 2011 05:03:59 +0000 http://sepiamutiny.com?p=6522#comment-283581 <p>We are pre-supposing the point of origins of various immigrant groups into the Deshlands by measuring how similar or how frequent certain haplotypes/SNP/etc. show up amongst the Baltic-Caucaus Belt and India. I would think that a great experiment could be done the following way(s): 1. If we wanted to see how similar the various peoples of S.Asia are to a "polar node", then we should see what haplotype/SNP/etc. this polar node has an extreme amount of (i.e. they express a STR many times about 95% of the time, whereas the rest of the world expresses it much less. Or conversely, they express it 2% and the rest of the world expresses it higher).</p> <p>For example: Suppose that you set up the experiment to detect how closely Desis cluster with Georgians, you would want to test for a gene expression that the Georgians have a <b>lot</b> or a <b>dirth</b> of. OTOH, if they only expressed something at an intermediate level, say 50%, than this is much less useful by itself. The neighbors of the Georgians may express it more or less than 50% but further out, they may express it at 50% as well. So it's useless unstable information.</p> <ol> <li><p>Why not have one of the nodes at Tajikistan, which was the original homeland of the Aryans before they migrated to Desh and Iranian plateau? The Tajiks weren't supplanted by the Turks either, but by other Iranian groups (i.e. Sogdians, etc.).</p></li> <li><p>Has anything been elucidated about the Greek/Persian immigration into Afghanistan/Pakistan in ~300BC?</p></li> <li><p>Why not have a "polar node" from the people who now live at the Harappa/Indus Valley area, and compare how the vicinal areas have this gene set and at what frequency? Another words, this would measure the equally-likely supposition that Harappans migrated OUTSIDE to even Afghanistan/Turkmenistan/etc. This actually makes sense, since this area was prepopulated early on and had a big population. They were very likely to migrate outwards.</p></li> </ol> <p>Thanks for all of your amazing insights and contributions here, Razib. I love your articles.</p> We are pre-supposing the point of origins of various immigrant groups into the Deshlands by measuring how similar or how frequent certain haplotypes/SNP/etc. show up amongst the Baltic-Caucaus Belt and India. I would think that a great experiment could be done the following way(s): 1. If we wanted to see how similar the various peoples of S.Asia are to a “polar node”, then we should see what haplotype/SNP/etc. this polar node has an extreme amount of (i.e. they express a STR many times about 95% of the time, whereas the rest of the world expresses it much less. Or conversely, they express it 2% and the rest of the world expresses it higher).

For example: Suppose that you set up the experiment to detect how closely Desis cluster with Georgians, you would want to test for a gene expression that the Georgians have a lot or a dirth of. OTOH, if they only expressed something at an intermediate level, say 50%, than this is much less useful by itself. The neighbors of the Georgians may express it more or less than 50% but further out, they may express it at 50% as well. So it’s useless unstable information.

  1. Why not have one of the nodes at Tajikistan, which was the original homeland of the Aryans before they migrated to Desh and Iranian plateau? The Tajiks weren’t supplanted by the Turks either, but by other Iranian groups (i.e. Sogdians, etc.).

  2. Has anything been elucidated about the Greek/Persian immigration into Afghanistan/Pakistan in ~300BC?

  3. Why not have a “polar node” from the people who now live at the Harappa/Indus Valley area, and compare how the vicinal areas have this gene set and at what frequency? Another words, this would measure the equally-likely supposition that Harappans migrated OUTSIDE to even Afghanistan/Turkmenistan/etc. This actually makes sense, since this area was prepopulated early on and had a big population. They were very likely to migrate outwards.

Thanks for all of your amazing insights and contributions here, Razib. I love your articles.

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By: Razib Khan http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283561 Razib Khan Sun, 01 May 2011 23:58:38 +0000 http://sepiamutiny.com?p=6522#comment-283561 <p>blood groups are subject to natural selection, so i don't think we should rely on them much today. O seems ancestral, with A & B probably arising due to some selective pressure more recently.</p> <p>here's a map of B if ppl are curious:</p> <p>http://johndenugent.com/images/map-of-b-blood-in-the-world.gif</p> blood groups are subject to natural selection, so i don’t think we should rely on them much today. O seems ancestral, with A & B probably arising due to some selective pressure more recently.

here’s a map of B if ppl are curious:

http://johndenugent.com/images/map-of-b-blood-in-the-world.gif

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By: my_dog_jagat http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283559 my_dog_jagat Sun, 01 May 2011 23:50:45 +0000 http://sepiamutiny.com?p=6522#comment-283559 <p>I recall the B blood group being linked to S.Asia (including Afghan/Tajik populations). A map of the B blood group shows these regions being highlighted at 15% of the population (deep South India is not one of these regions--it tends to run in some brahmin families, most other people are O). This I think would be due to the Aryan contribution to the S.Asian gene pool. In Western Europe the B is not present at these levels. I've not really seen any discussion on this but maybe you could comment further.</p> I recall the B blood group being linked to S.Asia (including Afghan/Tajik populations). A map of the B blood group shows these regions being highlighted at 15% of the population (deep South India is not one of these regions–it tends to run in some brahmin families, most other people are O). This I think would be due to the Aryan contribution to the S.Asian gene pool. In Western Europe the B is not present at these levels. I’ve not really seen any discussion on this but maybe you could comment further.

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By: Razib Khan http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283555 Razib Khan Sun, 01 May 2011 23:20:04 +0000 http://sepiamutiny.com?p=6522#comment-283555 <p><i>Also, what is the centroidal European gene set? Is it someone from the geographic/population center of Europe in SE France/Lithuania? Or is it from the eskaru who may have been descendants if the original cromagnons? Or from someone just west of the Urals in Kazakhstan?</i></p> <p>the "european" in south asians is clearly affiliated with eastern europeans. i'm not going to get into the details, but it is pretty obvious if you run ADMIXTURE yourself. it's a band from the baltic down to the caucasus and sweep to northwest india and a little beyond.</p> <p><i>We could have even framed the poles as a Tamil Dalit Node, a Tibetan Node, a Portuguese Node (to detect admixtures amongst Konkani Brahmins and Goan Christians), a Tajik/Sogdian/Pamiri Node to detect Scythians, or even a Persian Node to detect Greeks (since Alexandrea troops were mostly Iranians when he came to Pakistan).</i></p> <p>some populations really are more "types" than others. a tamil dalit and portuguese node makes sense. the others don't. those groups are simply always linear combinations of other groups in all the runs i've seen.</p> Also, what is the centroidal European gene set? Is it someone from the geographic/population center of Europe in SE France/Lithuania? Or is it from the eskaru who may have been descendants if the original cromagnons? Or from someone just west of the Urals in Kazakhstan?

the “european” in south asians is clearly affiliated with eastern europeans. i’m not going to get into the details, but it is pretty obvious if you run ADMIXTURE yourself. it’s a band from the baltic down to the caucasus and sweep to northwest india and a little beyond.

We could have even framed the poles as a Tamil Dalit Node, a Tibetan Node, a Portuguese Node (to detect admixtures amongst Konkani Brahmins and Goan Christians), a Tajik/Sogdian/Pamiri Node to detect Scythians, or even a Persian Node to detect Greeks (since Alexandrea troops were mostly Iranians when he came to Pakistan).

some populations really are more “types” than others. a tamil dalit and portuguese node makes sense. the others don’t. those groups are simply always linear combinations of other groups in all the runs i’ve seen.

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By: Boston_mahesh http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283554 Boston_mahesh Sun, 01 May 2011 23:15:20 +0000 http://sepiamutiny.com?p=6522#comment-283554 <p>Also, what is the centroidal European gene set? Is it someone from the geographic/population center of Europe in SE France/Lithuania? Or is it from the eskaru who may have been descendants if the original cromagnons? Or from someone just west of the Urals in Kazakhstan?</p> <p>Now that I think about it, there are many "poles" which to reference data sets.</p> <p>We could have even framed the poles as a Tamil Dalit Node, a Tibetan Node, a Portuguese Node (to detect admixtures amongst Konkani Brahmins and Goan Christians), a Tajik/Sogdian/Pamiri Node to detect Scythians, or even a Persian Node to detect Greeks (since Alexandrea troops were mostly Iranians when he came to Pakistan).</p> <p>All this being said, I'm very surprised at how homogenous Desi are when it comes to the "Indian" gene an it seems to cut off sharply when you go outside the pashtun/baluchi area in a non-cline manner.</p> Also, what is the centroidal European gene set? Is it someone from the geographic/population center of Europe in SE France/Lithuania? Or is it from the eskaru who may have been descendants if the original cromagnons? Or from someone just west of the Urals in Kazakhstan?

Now that I think about it, there are many “poles” which to reference data sets.

We could have even framed the poles as a Tamil Dalit Node, a Tibetan Node, a Portuguese Node (to detect admixtures amongst Konkani Brahmins and Goan Christians), a Tajik/Sogdian/Pamiri Node to detect Scythians, or even a Persian Node to detect Greeks (since Alexandrea troops were mostly Iranians when he came to Pakistan).

All this being said, I’m very surprised at how homogenous Desi are when it comes to the “Indian” gene an it seems to cut off sharply when you go outside the pashtun/baluchi area in a non-cline manner.

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By: Razib Khan http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283552 Razib Khan Sun, 01 May 2011 23:03:28 +0000 http://sepiamutiny.com?p=6522#comment-283552 <p><i>India was peopled LONG ago: about 60,000 years ago. To put this into perspective, the following were colonized at </i></p> <p>there's no guarantee that the first settlers made much of an impact and weren't replaced. i think this has happened in europe, and, in much of east africa.</p> <p><i>This doesn't make sense, and it's like saying that apes have a lot of human genes (not the semantically more lucid "humans have a lot of ape genes."). The research's narrative should attempt to elucidate how much Proto-Indian genes remains in C Asia and S Asia and SE Asia.</i></p> <p>there is a non-trivial probability that all of non-africa was settled from the fringes of south asia. but the ASI lineage which is oldest in india, even if it is descended from the first settlers, obviously has changed since the last common ancestor with other lineages.</p> <p>fwiw, i bet ASI is basal to all east eurasian, oceanian, and amerindian lineages. it might be basal to west eurasian ones though. there is mounting evidence that anatomically modern humans left africa closer to ~100,000 years ago, but that there was a "pause" or interregnum somewhere in southwest asia before a second expansion event.</p> India was peopled LONG ago: about 60,000 years ago. To put this into perspective, the following were colonized at

there’s no guarantee that the first settlers made much of an impact and weren’t replaced. i think this has happened in europe, and, in much of east africa.

This doesn’t make sense, and it’s like saying that apes have a lot of human genes (not the semantically more lucid “humans have a lot of ape genes.”). The research’s narrative should attempt to elucidate how much Proto-Indian genes remains in C Asia and S Asia and SE Asia.

there is a non-trivial probability that all of non-africa was settled from the fringes of south asia. but the ASI lineage which is oldest in india, even if it is descended from the first settlers, obviously has changed since the last common ancestor with other lineages.

fwiw, i bet ASI is basal to all east eurasian, oceanian, and amerindian lineages. it might be basal to west eurasian ones though. there is mounting evidence that anatomically modern humans left africa closer to ~100,000 years ago, but that there was a “pause” or interregnum somewhere in southwest asia before a second expansion event.

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By: Boston_mahesh http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283551 Boston_mahesh Sun, 01 May 2011 22:25:50 +0000 http://sepiamutiny.com?p=6522#comment-283551 <p>India was peopled LONG ago: about 60,000 years ago. To put this into perspective, the following were colonized at - N. America - 25KYA Europe - 40KYA Australia - also 60KYA. Humans emigrated from Africa around 60 KYA as well.</p> <p>Anyways, the narrative here seems to patronize the indigenous genotypes here. This doesn't make sense, and it's like saying that apes have a lot of human genes (not the semantically more lucid "humans have a lot of ape genes."). The research's narrative should attempt to elucidate how much Proto-Indian genes remains in C Asia and S Asia and SE Asia.</p> India was peopled LONG ago: about 60,000 years ago. To put this into perspective, the following were colonized at - N. America – 25KYA Europe – 40KYA Australia – also 60KYA. Humans emigrated from Africa around 60 KYA as well.

Anyways, the narrative here seems to patronize the indigenous genotypes here. This doesn’t make sense, and it’s like saying that apes have a lot of human genes (not the semantically more lucid “humans have a lot of ape genes.”). The research’s narrative should attempt to elucidate how much Proto-Indian genes remains in C Asia and S Asia and SE Asia.

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By: Razib Khan http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283550 Razib Khan Sun, 01 May 2011 22:08:21 +0000 http://sepiamutiny.com?p=6522#comment-283550 <p><i> I am wondering if the S.Asian in this case is ANI (not ASI).</i></p> <p>yes.</p> <p><i>Also the (single) Rajasthani brahmin with E.Asian--is it a Scythian or Mongol contribution or just migrations from within other parts of N.Indai. There have been a lot of those as I've said before. Can you clarify what E.Asian is (something shared with peoples of SE Asia, the Han etc...)?</i></p> <p>these results won't allow clarification. but it's not that hard. generally it is as you expect, ppl from nw south asia are more 'turk', those from east south asia more 'southeast asian.'</p> I am wondering if the S.Asian in this case is ANI (not ASI).

yes.

Also the (single) Rajasthani brahmin with E.Asian–is it a Scythian or Mongol contribution or just migrations from within other parts of N.Indai. There have been a lot of those as I’ve said before. Can you clarify what E.Asian is (something shared with peoples of SE Asia, the Han etc…)?

these results won’t allow clarification. but it’s not that hard. generally it is as you expect, ppl from nw south asia are more ‘turk’, those from east south asia more ‘southeast asian.’

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By: Razib Khan http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283549 Razib Khan Sun, 01 May 2011 21:56:20 +0000 http://sepiamutiny.com?p=6522#comment-283549 <p><i>Apologies for the confusion but is there any resolution or clarity on Gujarati B?</i></p> <p>so zack calls "gujarati b" "gujarati a." so it is resolved. probably patels.</p> Apologies for the confusion but is there any resolution or clarity on Gujarati B?

so zack calls “gujarati b” “gujarati a.” so it is resolved. probably patels.

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By: Zachary Latif http://sepiamutiny.com/blog/2011/04/29/structure_with/comment-page-1/#comment-283548 Zachary Latif Sun, 01 May 2011 20:51:55 +0000 http://sepiamutiny.com?p=6522#comment-283548 <p>I imagine that the Indo-Aryans were more of a "settling" population than the Scythian who were a tribal/ruling elite hence the disproportionate genetic impact.</p> <p>Impressive that the n.w south asia (indus) has seen an admixure of other "continental" influences like African & N.E Asian so is Bengal in that matter; they were really the "borderlands".</p> <p>Apologies for the confusion but is there any resolution or clarity on Gujarati B?</p> I imagine that the Indo-Aryans were more of a “settling” population than the Scythian who were a tribal/ruling elite hence the disproportionate genetic impact.

Impressive that the n.w south asia (indus) has seen an admixure of other “continental” influences like African & N.E Asian so is Bengal in that matter; they were really the “borderlands”.

Apologies for the confusion but is there any resolution or clarity on Gujarati B?

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