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Author Topic: Adaptation is ancient: the story of the Duffy gene
BrandonP
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This is from GNXP.

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quote:
Anyone with a passing familiar with human population genetics will know of the Duffy system, and the fact that there is a huge difference between Sub-Saharan Africans and other populations on this locus. Specifically, the classical Duffy allele exhibits a nearly disjoint distribution from Africa to non-Africa. It was naturally one of the illustrations in The Genetics of Human Populations, a classic textbook from the 1960s.
Interesting that while most SSA populations today have the FY*O allele, it's not nearly so ubiquitous in the Khoisan of southernmost Africa.

quote:
From their sequence data analysis the different alleles have been segregating for a long time in the collective human population, and powerful sweeps fixed FY*O in both the ancestors of the Bantu and Pygmies before they diverged from each other. In contrast the Khoisan samples suggest that FY*O introgressed into their population from newcomers, while variants of FY*A are ancestral.
Any thoughts on this?
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Swenet
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Kinda puts a damper on certain ideas floating around here. And that's putting it politely.
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BrandonP
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It stands out to me that the Central African "Pygmy" populations have the same predominance of FY*O as the other equatorial African populations (most of which speak Niger-Congo languages IIRC) rather than the allele combo seen in the Khoisan or in the OOA populations. But aren't these "Pymgy" populations even further removed from OOA than Niger-Congo or Nilo-Saharan Africans?

 -

Because that would suggest to me that while the fixation of FY*O in equatorial Africans would postdate their divergence from the Khoisan, it would still predate OOA (assuming OOA came after the divergence between Pygmies and the other Africans). But then how did the other alleles reappear in OOA populations? [Confused]

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Elmaestro
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Interesting, though the distribution follows my purported model for recent sweeping/purifying selection in equatorial Africa, the researchers are adamant that the FY*O sweep happened before the Biaka/Mbuti split... Despite Mota being heterogeneous negative.
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DD'eDeN
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(Haven't seen the GNXP info yet.)

As ALWAYS I distrust anything said or written about Pygmy genetics, and almost all re. KhoiSan, if is authored by tall-Agro-Industrial people.

"Heightism" is rife among academia, often by ignorant tall people who have no concept of people living in rainforest in an egalitarian fashion.

Note: Pygmies traditionally lived along crystal brooks but far enough to avoid mosquitoes and the rare crocodile (both of which lived near slow or murky or deeper water), malaria affected them much less than Bantu & Sudanic farmers who lived in clearings and along shaded peripheries of rainforests where mosquitoes are rife. So probably these farming people had strong selection against malaria, while Pygmies and KhoiSan may have had weaker but longer selection against malaria.
- - -
Duffy gene makes protein, linked to vivax malaria, linked to brain function.

--------------------
xyambuatlaya

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xyyman
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"In CONTRAST the Khoisan samples suggest that FY*O introgressed into their population from newcomers, while variants of FY*A are ancestral."

Blue=khoisan=East Asian=known to have highest Native American ancestry in Africa=has all 3 colors

FY*B, what does the study state about FY*B. Tic! Toc!

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xyyman
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huh?


quote:
Originally posted by Elmaestro:
Interesting, though the distribution follows my purported model for recent sweeping/purifying selection in equatorial Africa, the researchers are adamant that the FY*O sweep happened before the Biaka/Mbuti split... Despite Mota being heterogeneous negative.


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Elmaestro
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They opted to come to the conclusion that sweeping selection happened before the mbuti split in Africans... But their only/oldest African specimen is FY*A/FYB heterozygous...

I should have put a *however* before "...the researchers.." In my first post. I disagree with an early sweep.

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the lioness,
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 -

http://eurogenes.blogspot.com/2017/03/southern-european-blues.html

lolz

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xyyman
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When a person who has the power to delete stuff only delete SOME stuff you know that you are on the right track. He is "selectively" deleting information that poses a threat to him. Davidski is fighting a losing battle and he knows it. Also. Notice he do NOT have a rebuttal and cannot debunk what I post. So like a bully who get beaten at his own game he takes up his toys and go home. When they start calling you names instead of a factual come back. You know they are either too uneducated to debunk what you stated or they are too stupid to know what is going on.
Name calling won't do it. Many have already called for my ban. But banning me is not going to solve his problems. It is too late. Look at the counter argument he is getting from other posters.

And the more I read his stuff the more I am convinced he is a total retard. He is stubbornly holding on to R1b-M269 originated from the Steppes of Asia when there is more than enough evidence now that is NOT the case.

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xyyman
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Hey! If I am banned I will spend more time on ES and ESR plus I can get more exercise in on evening. Wink.

I am a glass half full guy........Capitalist to the bone. "How do I profit from this"?. Not necessarily monetarily of course.

--------------------
Without data you are just another person with an opinion - Deming

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the lioness,
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quote:
Originally posted by xyyman:
When a person who has the power to delete stuff only delete SOME stuff you know that you are on the right track. He is "selectively" deleting information that poses a threat to him. Davidski is fighting a losing battle and he knows it. Also. Notice he do NOT have a rebuttal and cannot debunk what I post. So like a bully who get beaten at his own game he takes up his toys and go home. When they start calling you names instead of a factual come back. You know they are either too uneducated to debunk what you stated or they are too stupid to know what is going on.
Name calling won't do it. Many have already called for my ban. But banning me is not going to solve his problems. It is too late. Look at the counter argument he is getting from other posters.

And the more I read his stuff the more I am convinced he is a total retard. He is stubbornly holding on to R1b-M269 originated from the Steppes of Asia when there is more than enough evidence now that is NOT the case.

I still see a lot of your posts up there on Eurogenes, not deleted

So what are you saying now? You say modern Europeans are not from the Steppes, that they are depigmented Africans.

So now you are saying these R1b-M269 Steppe people are African as well?

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Doug M
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quote:
Originally posted by Nodnarb:
This is from GNXP.

 -
quote:
Anyone with a passing familiar with human population genetics will know of the Duffy system, and the fact that there is a huge difference between Sub-Saharan Africans and other populations on this locus. Specifically, the classical Duffy allele exhibits a nearly disjoint distribution from Africa to non-Africa. It was naturally one of the illustrations in The Genetics of Human Populations, a classic textbook from the 1960s.
Interesting that while most SSA populations today have the FY*O allele, it's not nearly so ubiquitous in the Khoisan of southernmost Africa.

quote:
From their sequence data analysis the different alleles have been segregating for a long time in the collective human population, and powerful sweeps fixed FY*O in both the ancestors of the Bantu and Pygmies before they diverged from each other. In contrast the Khoisan samples suggest that FY*O introgressed into their population from newcomers, while variants of FY*A are ancestral.
Any thoughts on this?

So? Change is ancient and predates the human species. Everything exists because of change.

Not sure what the point is, especially the OBSESSION with Africans South of the Sahara. Humans have been in Africa longer than any other place on the planet. And most evidence says that the first humans originated South of the Sahara.....

So what about Africans in other parts of Africa, not South of the Sahara? Notice there are no pie charts for populations in North Africa.

Anyway, the Duffy blood antigen only represents exposure to malaria. If they are saying that only SOME Africans, particularly those in tropical areas, have this form of blood antigen, then that is not particularly shocking. The question becomes when did this blood antigen arise among Africans and is it present in ALL African populations or only certain ones? IE, do East Africans have it? Do Saharans Have it? Do Nile Valley Africans have it? Etc. Yes it does help identify whether any population had prolonged exposure to malaria or had a relationship to populations that had such exposure but that isn't anything special. There are many traits and characteristics at the biological level that vary across ANY population including Africans.

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Elmaestro
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Doug, read the damn paper man...

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006560

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Doug M
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quote:
Originally posted by Elmaestro:
Doug, read the damn paper man...

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006560

I think you missed the point or maybe I missed your point.

Are you claiming that this Blood Pathogen defines "African" ancestry? Come on. This is ridiculous.
Africans are diverse. They adapted to many different conditions before leaving Africa. There are many different patterns of diversity at all biological levels among AFRICAN populations over history.

Why do you keep harping on dividing Africa into "Sub Saharan" vs the rest of Africa?

Or to be more technical, maybe some of the Africans who participated in OOA did not have this antigen. So? They were still African. I don't understand this focus on dividing up Africans.

Again, my point being it only serves to dilute and mask the fact that all OOA populations are African by any definition. As there were no humans anywhere else. This blood antigen doesn't change that.

And most folks familiar with any kind of biology realize that adaptation is part of biology of any species not just human. So the implication of this study is that this is some 'surprising' finding as if everything about the evolution of humans isn't based on that concept....

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xyyman
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It light of what Doug just said there. "everyone is an African". Lioness let me rephrase. Modern Europeans are a subset of RECENT migrated depigmented Africans. Better?

--------------------
Without data you are just another person with an opinion - Deming

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Elmaestro
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Doug, did you read the paper?

Your comments come off as vague and dismissive. You're complicating something that's actually not that serious and relatively simple.

Genetically, SSA is categorized by a lack of shared OOA/non-African drift, and Neanderthal DNA... It's just a term... It doesn't matter what you feel about about the word or how you personally use it for that matter.

Now I've posted a whole 6 sentences prior to this post. None of them has me at a position where I'm dividing Africa. I'm addressing the DATA and that solely, save the politics. The authors think they've cornered the time at which populations in Africa underwent sweeping selection. They put it before the mbuti split.... I pointed out that MOTA is FY*A/FY*B --> basically the complete opposite of the proposed African genotype due to an early sweep.

...Mota is technically more African than Yorubans.

These researchers might not even have knowledge on demographic history, cultural practices, anthropology, etc. which is why people like us should read the damn paper and apply the findings to what we know, offer various perspectives and talk about what we'd like to see in relation to these studies. Stop making everything so damn political.

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Doug M
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quote:
Originally posted by Elmaestro:
Doug, did you read the paper?

Your comments come off as vague and dismissive. You're complicating something that's actually not that serious and relatively simple.

Genetically, SSA is categorized by a lack of shared OOA/non-African drift, and Neanderthal DNA... It's just a term... It doesn't matter what you feel about about the word or how you personally use it for that matter.

Now I've posted a whole 6 sentences prior to this post. None of them has me at a position where I'm dividing Africa. I'm addressing the DATA and that solely, save the politics. The authors think they've cornered the time at which populations in Africa underwent sweeping selection. They put it before the mbuti split.... I pointed out that MOTA is FY*A/FY*B --> basically the complete opposite of the proposed African genotype due to an early sweep.

...Mota is technically more African than Yorubans.

These researchers might not even have knowledge on demographic history, cultural practices, anthropology, etc. which is why people like us should read the damn paper and apply the findings to what we know, offer various perspectives and talk about what we'd like to see in relation to these studies. Stop making everything so damn political.

Just to be clear I am just restating why I believe that "SSA" is a very broad term and not useful for understanding African diversity. The presence of this blood pathigen doesn't change that, in fact the way it is presented in this paper reinforces the problems with such generalizations. It is helpful for understanding the spread of certain BLOOD traits within African populations but it doesn't make populations South of the Sahara any more or any less African than populations anywhere else in Africa. Because of course it should be obvious that all Africans were not affected by this adaptation/exposure to Malaria. That is the whole reason I reject such broad characterizations like "SSA" in the first place.

Interestingly enough this kind of work ties into some of the concerns raised in this video:
https://www.youtube.com/watch?v=tx2j_nMubX4

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^ Lol at this pan-Africanist political loon. Doug rejects dividing North Africans from Sub-Saharan Africans since the latter is too broad, but he has no problem with combining SSA with North Africa into a broader territory (the whole of Africa). [Roll Eyes]

There is no pan-"African" continental race/cluster. Doug is no different than Stormfront nazis' who propose there is a European race/cluster.

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the lioness,
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quote:
Originally posted by Cass/:
^ Lol at this pan-Africanist political loon. Doug rejects dividing North Africans from Sub-Saharan Africans since the latter is too broad, but he has no problem with combining SSA with North Africa into a broader territory (the whole of Africa). [Roll Eyes]

There is no pan-"African" continental race/cluster. Doug is no different than Stormfront nazis' who propose there is a European race/cluster.

 -

Mitochondrial group L is common to Sub-Saharan Africans including Khosians and some North African groups

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quote:
I don't understand this focus on dividing up Africans.
Because you're a pan-Africanist. Bio-anthropologists don't though cling to your silly political ideology, i.e. they divide populations in Africa as they please depending if it provides useful for analysis. The latter though upsets you (e.g. if North Africa is split from Sub-Saharan Africa) because it conflicts with your racialist agenda to lump all Africans together as part of continental unit, grouping or bloc.
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the lioness,
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quote:
Originally posted by Cass/:
[QB]
quote:
I don't understand this focus on dividing up Africans.
Because you're a pan-Africanist. Bio-anthropologists don't though cling to your silly political ideology,
It's not a silly political ideology. It's an attempt to unify on some level to resist exploitation of Africa by foreigners, recall the slave trade and "The Scramble for Africa"
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Haplogroup L doesn't have high frequency in North Africa, only Sub-Saharan Africa. But there's nothing wrong with an analyst making an operational SSA unit/cluster for this very high trait frequency in Sub-Saharan African populations since it is useful. This SSA division though upsets Doug's pan-African politics. [Roll Eyes]
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the lioness,
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quote:
Originally posted by Cass/:
Haplogroup L doesn't have high frequency in North Africa, only Sub-Saharan Africa. But there's nothing wrong with an analyst making an operational SSA unit/cluster for this very high trait frequency in Sub-Saharan African populations since it is useful. This SSA division though upsets Doug's pan-African politics. [Roll Eyes]

Y DNA Haplogroup E is common all over Africa, except with Khosians but Khosians are linked by these E carriers maternally by L and they are well under 1% of the African population
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quote:
Originally posted by the lioness,:
quote:
Originally posted by Cass/:
[QB]
quote:
I don't understand this focus on dividing up Africans.
Because you're a pan-Africanist. Bio-anthropologists don't though cling to your silly political ideology,
It's not a silly political ideology. It's an attempt to unify on some level to resist exploitation of Africa by foreigners, recall the slave trade and "The Scramble for Africa"
Kabyle Berber women-

 -

Zulu women-

 -

lol. So do you really think these people are closely related to the extent you can pool them into a single ("[pan-]African") group? [Roll Eyes] This "pan-African" ideology is the most stupid thing ever.

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sudanese
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Cass


 -

The most predominant [E1b1b] sub-clade in the Maghreb is E-M81 -- a clade derived from the Northeast African E-M35. This clade has a frequency of 100% in certain regions of the Maghreb and is observed at a frequency of 89% for the Tuareg, so what exactly makes you think that the modern Kabyle Berbers are representative of the ancient Maghreb? The Tuaregs have a common origin with the Beja of Sudan, and it's well established that the Berber language originates in Northeast Africa.

The Tuaregs actually look like Northeast Africans, and I really do think that the Tuareg Berbers of the Fezzan in Libya are physically representative of the earliest populations of the Maghreb. Other Berbers that resemble Northeast Africans include the Zenata, Masmuda, the Sanhaja and the Siwa. There are also non-Berbers of North Africa like the Toubou.

Libyan and Tunisian Berbers:

 -

 -

 -

 -

 -

 -

And Toubou

 -

The paternal E-M81 clade of the Maghreb [derived from East African E-M35] makes it impossible for you to genetically extricated these people from the rest of the continent, so your pathetic attempts are a complete fail.

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Swenet
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quote:
Originally posted by the lioness,:
Mitochondrial group L is common to Sub-Saharan Africans including Khosians and some North African groups

Your underlying intention with this statement is just wrong. The fact that most African lineages are grouped under "L" is a nominal thing, just like Lazaridis et al's "non-African" label is a nominal thing. It has nothing to do with phylogenetic facts on the ground. Hence, L3 is phylogenetically many times closer to M and N than L1 is to either. mtDNA-wise it's impossible to juxtapose Africans, as a continent, against Eurasians, just like it's impossible to juxtapose Africans, as a continent, against Lazaridis "non-African" construct.

I don't know why this is so hard for people to understand in 2017.

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xyyman
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The problem with you is you don't understand or have a handle on science. You depend too much on "pictures" ie images, to formulate ideas.

If you had a healthy understanding of genetics you would understand the pan-African nature of PN2- yDNA Haplogroup E.


The odd thing is what you visualize as "African" in that tiny brain of yours is not what it is. The fascinating thing is E1b1b-Amazig is OLDER than many SSA, E1b1a subclades. That also goes for R1b-M269 dated at only 6000years old. That means YOUR Western European male line is was conceive ONLY about 6000years ago.

quote:
Originally posted by Cass/:
Haplogroup L doesn't have high frequency in North Africa, only Sub-Saharan Africa. But there's nothing wrong with an analyst making an operational SSA unit/cluster for this very high trait frequency in Sub-Saharan African populations since it is useful. This SSA division though upsets Doug's pan-African politics. :rolleyes:


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Thereal
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That's not it,he's one of those people who try to find an unnecessary difference were the context doesn't call for one and he probably has a color issue on his insistence on what constitute an African.
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Swenet
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Filling in the blanks of the map in the OP

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The global distribution of the Duffy blood group
http://www.nature.com/articles/ncomms1265

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Ish Geber
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quote:
Originally posted by sudaniya:
Cass


 -

The most predominant [E1b1b] sub-clade in the Maghreb is E-M81 -- a clade derived from the Northeast African E-M35. This clade has a frequency of 100% in certain regions of the Maghreb and is observed at a frequency of 89% for the Tuareg, so what exactly makes you think that the modern Kabyle Berbers are representative of the ancient Maghreb? The Tuaregs have a common origin with the Beja of Sudan, and it's well established that the Berber language originates in Northeast Africa.

The Tuaregs actually look like Northeast Africans, and I really do think that the Tuareg Berbers of the Fezzan in Libya are physically representative of the earliest populations of the Maghreb. Other Berbers that resemble Northeast Africans include the Zenata, Masmuda, the Sanhaja and the Siwa. There are also non-Berbers of North Africa like the Toubou.

Libyan and Tunisian Berbers:

 -

 -

 -

 -

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And Toubou

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The paternal E-M81 clade of the Maghreb [derived from East African E-M35] makes it impossible for you to genetically extricated these people from the rest of the continent, so your pathetic attempts are a complete fail.

This post surely slapped the teeth out of Cass has mouth.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010  |  IP: Logged | Report this post to a Moderator
Askia_The_Great
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Sahelian women are very beautiful.^^^
Posts: 1891 | From: NY | Registered: Sep 2014  |  IP: Logged | Report this post to a Moderator
   

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