Talk:Genetic history of Europe/Archive 2

Archive 1

Archive 2

Archive 3

Archive 4

Archive 5

Edit War by Wapondaponda

Wapondaponda's attemps to make this article an afrocentrist panflet, as well as in Sub-Saharan DNA admixture in Europe were he has already broke 3RR, have produce an edit war. This can not continue as it is! The Ogre (talk) 15:41, 2 June 2009 (UTC)

I've asked for a 3rd opinion. The Ogre (talk) 15:57, 2 June 2009 (UTC)

It seems 3O doesn't aplly due to the number of editors being more than 2... The Ogre (talk) 16:11, 2 June 2009 (UTC)

As you and Causteau are the ones doing the deleting here, and Wapondaponda's section is cited and he has tried to explain it on the talkpage, can you both please explain what you are objecting to.--Andrew Lancaster (talk) 18:58, 3 June 2009 (UTC)

I started working Wapondaponda's disputed section in isolation. In isolation it now looks better in my opinion. But here comes the question: why do we now have this section about a geographical origin for migrations within the chronological section? Later in the article nearly everything which is said here is said again, here, here and here. So there is now redundancy, and the logical structure of the article is up the creek. I have suggested before that we could consider restructuring the whole article in terms of immigration routes, but this has not happened, and I admit it would not be simple. So we need to stick to the chronological pattern for now or else we are going to have enormous redundancy. We can have small skeletal sections on immigration routes like we already did, but they should not cover all detail twice. So my proposal is that we should use whatever we like out of this section and put it into the appropriate other sections which already exist.--Andrew Lancaster (talk) 10:51, 5 June 2009 (UTC)

Concerning smaller aspects of the edit war:

1. I looked up the Malyarchuk ref just by clicking the link and I see that the abstract specifically mentions M1 being African, just not West African. So just deleting it from the description of Malyarchuk said seems wrong.
2. I don't agree with Wapondaponda's constant deleting of the word apparent. This field is often misunderstood as being more certain than it is.
3. Can everyone who has done reverts please check to make sure you have not reverted things like spelling corrections? In general, reverts are not a good way to work.--Andrew Lancaster (talk) 11:02, 5 June 2009 (UTC)

Yes the structure is the biggest obstacle to this article. I think in the long term Cavalli-Sforza's PCs will be the most appropriate way to structure the article. Wapondaponda (talk) 06:24, 6 June 2009 (UTC)

The section on African admixture breaches WP:UNDUE. The 6 % of Iberians who carry 'direct' African lineages hardly warrant an entire section in the G.H.o.E article, certainly nothing which cannot be accomodated in the postulated migrations section and/ or a seperate article on Spanish people. I am inclined to remove it soon, and if parties object, then it will have to come down to a vote Hxseek (talk) 22:30, 20 June 2009 (UTC)

Coffman quote

Is quoted [1] Unfortunately, misinformation about these haplogroups continues to pervade the public and media. Haplogroup E3b is often incorrectly described as “African,” leaving a misimpression regarding the origin and complex history of this haplogroup.

This statement is somewhat ambiguous and contradictory. On one hand the authors writes Although E3b arose in East Africa approximately 25,000 years ago and on the other the author states there is a missimpression regarding the origin. There is no standard method of describing haplogroups in relation to populations that harbor them. So in reality there are no African haplogroups, or European haplogroups or Asian haplogroups. There are haplogroups that are frequent in Africa, Asia, Europe, America or Australia but not elsewhere, and we may colloquially refer to them as African, Asian, European, American or Australian. This applies to all haplogroups not just e3b. We can also objectively refer to haplogroups by their most likely region of origin, in which case e3b is indeed "African". However this is complicated by the fact that haplogroups tend to move around and are continuously evolving. This obviously applies to e3b which is found in Africa, Asia and Europe. From a scientific perspective, the Coffman quote is not really useful because the author does not describe what is incorrect about describing e3b as "African". If the origin is the criteria for describing a haplogroup, it is legitimate to describe e3b as African. In short the author prefers not to consider e3b as african but this a personal opinion or choice in how to describe a haplogroup. It may contain some social commentary but it serves no value from a scientific perspective. Wapondaponda (talk) 22:03, 10 June 2009 (UTC)

I agree. There are two clear and extreme ways to interpret the idea of an African clade: that it is a clade that is today only present there, like A and B Y haplogroups, or else all haplogroups are African. However it may reasonably be said that E1b1b is somewhere in between, and it was in any case amongst the last to leave the room, as per the Underwood and Kivisild quote I keep reminding you of Wapondaponda. By the way you might want to see http://wiki.riteme.site/wiki/Talk:Haplogroup_E1b1b_(Y-DNA)/Archive_5#Ellen_Coffman-Levy_.282005.29 which I think confirms that Ellen was not looking for this type of confusion, but rather had specific misunderstandings in mind.--Andrew Lancaster (talk) 19:56, 12 June 2009 (UTC)

Protection

I protected the article for a week after looking at its recent history, but its been suggested to me that that was not necessary. If everyone agrees of course I'll lift the protection. Dougweller (talk) 04:24, 11 June 2009 (UTC)

It might be a good idea to ask interested editors to first propose what text they think would represent a reasonable compromise in the sections being reverted the most.--Andrew Lancaster (talk) 14:13, 13 June 2009 (UTC)

"Tat C"

When this page is unlocked can someone please update the terminology which refers to "tat C". I understand that this is a clade with what is now called Y haplogroup N: http://wiki.riteme.site/wiki/Haplogroup_N_(Y-DNA)#N-Tat.--Andrew Lancaster (talk) 14:11, 13 June 2009 (UTC)

Percentages

Please show percentages for your map and please don't exagerate the frequency of E3B in eastern Europe Wapondaponda Sincerely The Count of Monte Cristo (talk) 03:30, 21 June 2009 (UTC)

The source does not say that so you are saying something that a source says something when it does not right? If it does please tell me the page if I find it in the source I will delete it no more de The Count of Monte Cristo (talk) 03:37, 21 June 2009 (UTC) Wapondaponda

Sources

Why do so many people say things without sources in this article? Sincerely The Count of Monte Cristo (talk) 00:20, 22 June 2009 (UTC)

I will be parousing through and tidying the article hopefully in the coming week. Not every single thing needs to be sourced. Someone recently made some modifications, and perhaps left out citations. Feel free to outline particular comments which you belive need clarifying or are lacking sources. Hxseek (talk) 12:23, 22 June 2009 (UTC)

I think it is an important point that we should all have some common sense and patience about sourcing on these articles where there has recently been a lot of reverts and edit wars. I have also found it very difficult to line up all the citations again given the amount of things that have been deleted, re-inserted, etc. If anyone sees a missing citation please first post a in the text as a marker, and if you have some extra time try looking through old versions, or google, to find the missing information. Do not delete too hastily.--Andrew Lancaster (talk) 13:12, 22 June 2009 (UTC)

Well said Hxseek (talk) 00:45, 23 June 2009 (UTC)

Iberian refugium theory.

I added some sourced material from a scientific journal about the Iberian refugium theory if you delete it there may be content dispute. To HXSEEK from Sophian otherwise known as The Count of Monte Cristo (talk) 20:45, 25 June 2009 (UTC)

I deleted it - the abstract didn't mention the Iberian refugium theory, have you got a quote from the article that does? Dougweller (talk) 21:09, 25 June 2009 (UTC)

SOPHIAN, (1) please do not make polemic comments on talk pages (2) I have followed the link to try to find the justification for your edits and I do not see them in the abstract or pages accessible to non logged-in users. Please can you provide an exact quotation on which you are basing your edits? --BozMo talk 21:13, 25 June 2009 (UTC)

I've just tried to tidy up the new attempt by Sophian to create a properly sourced statement about R1b and refugia. This material was clearly cut and paste from somewhere and needs improvement, but I decided not to just delete it. Sophian, what are the tables being referred to? And how can readers understand the flow of discussion which suddenly mentions ht15 and ht35? Please do not expect that people will always take time this way if you paste material in such a sloppy way.--Andrew Lancaster (talk) 05:24, 26 June 2009 (UTC)

I think that whole section is an 'eye sore'. It should be worked into the migrations and/or summarized a bit. Why does it focus on an ad nauseum cataloguing of R1b frequencies ?

Moreover, it appears that Sophonian is being disruptive at times, although his R1a map is good. Yet he blatantly breached copy right of Dupanloup's map. He needs to be watched because he has a tendency of introducing some bizarre/ fringe/ unsourced/ deceptive theories. All this undermines his credibility

I am aware that some of my edits need eloboration of references. These will be done within the next 2 days

Hxseek (talk) 05:30, 26 June 2009 (UTC)

I agree that focusing upon 1 Y haplogroup is a bit weird. I also happen to know that what is being written about R1b and refugia does not match recent thinking, although so much of this progress has been done within the "amateur" genetic genealogy field, and the action has been so fast and furious, that we still await an article we can cite as a snapshot of more recent thinking. I believe Cruciani is presenting one. In summary R1b-M269 probably entered Europe after the Neolithic, from the Middle East. The phylogeny under R1b-M269 was unknown when the present sources were written, and changes everything. I know that for example Mike Hammer has acknowledged in public (but not in writing?) that all the old estimates of R1b being old enough to have been in a European refugia are now no longer tenable. This is of course also a problem over on the R1b article, so we could look there for inspiration, but I think it is also difficult there.--Andrew Lancaster (talk) 05:53, 26 June 2009 (UTC)

Really? Yes, in Anthropological Genetics, 'The Peopling of Europe", it states that R1b is much younger than origianally proposed. That throws the Basque being some special representatives of "Old Europe" theory right out the window ! (which i was always suspect of). Barbujani has always maintainted that, in general, we are overestimating the ages of haplogroups . Maybe we are Neolithic newcomers, afterall ! The problem is, I have not seen any recent articles on R1b Hxseek (talk) 06:21, 26 June 2009 (UTC)

Exactly. For example for Hammer's remark, I saw it on several twitters coming from the FT DNA conference in Texas this year. I really look forward to seeing what Cruciani has written but I fear it will be out of date before it gets into the public. It seems he'll be writing about the two major sub-clades we now know of, R1b-U106/S21 and R1b-L21, but the latest news is all the phylogenetic structure that has been discovered between these two clades, and M269, some of which sub-clades are apparently only found in Western Asia.--Andrew Lancaster (talk) 06:48, 26 June 2009 (UTC)

R1a1

I added mention of the fact that there is a sizable presence of R1a1 in Scandinavia, and a small presence in the British Isles. User SOPHIAN added the fact that there was also a sizable presence in Paris and attached a footnote, but I see nothing in the footnote which substantiates the statement. MarmadukePercy (talk) 19:40, 26 June 2009 (UTC) I am not trying to argue I am just trying to list all the parts of Western Europe that have decent frequencies of R1A. The frequency of R1A in Paris is 15.2% (Similar to Scandinavia) go to page 43 of my link to see this. Sincerely The Count of Monte Cristo (talk) 23:19, 26 June 2009 (UTC)

Sorry, but I cannot find any mention on page 43 of the link for R1a1 in Paris. MarmadukePercy (talk) 23:44, 26 June 2009 (UTC)

Look at the table at the very bottom of the page (Note:The word Paris is a Image in that article so you can not find it by using find and search) I don't know why they did it like that but oh well :) Sincerely The Count of Monte Cristo (talk) 23:56, 26 June 2009 (UTC)

Whilst that's all very interesting, I do not see why we have to include the frequency of R1a1 in Paris ? This is about the genetic history of Europe. Logic dictates that we should give a panoramic view into the overall genetic landscape of Europe, pointing out obvious patterns, not getting bogged down with frequencies of R1a1 in Paris, or how many Galicians sport sub-Saharan DNA ? Hxseek (talk) 02:18, 27 June 2009 (UTC)

I agree with Hxseek. Let's try to keep our eyes on the forest, and not the trees. MarmadukePercy (talk) 02:48, 27 June 2009 (UTC)

R1 origins

Well article (2001), page 5 re: M173: This finding, as well as geography, strongly suggests that the source of both of these migrations was an ancient Central Asian population.

'Putative' means 'possible', does it not. Secondly, this is the general concensus, although a fewer papers have proposed a southern Asian (ie Indian) origin. Thirdly, where abouts in Asia isn;t even the main point of the discussion in the article. It mainly is intended to highlight the difference between mtDNA which appears to mostly have appeared from the Near East, where as a far more significant proportion of Y Hgs seem to have arisen in more distant parts of Asia- whether it is 'central' asia or 'southern Asia' Hxseek (talk) 03:02, 27 June 2009 (UTC)

Are you saying that there is a consensus that R1 did not originate in the Near East?--Andrew Lancaster (talk) 09:19, 27 June 2009 (UTC)

I cannot recall any author placing it in the Near East Hxseek (talk) 15:34, 27 June 2009 (UTC)

Genetic drift, founder effect and population bottleneck

I'm fed up with those with various axes to grind (left, right, up, down, inside and out, rascist and politically correct) trying to draw massive conclusions from just a few pieces of selected data. A link to the articles on genetic drift, founder effect and population bottleneck - which are absolute musts for anybody interested in these sorts of studies - will help to at least stem some of this nonsense. Provocateur (talk) 00:53, 6 July 2009 (UTC)

Copyvio

I've just removed some copied from [2] - I've checked the history of the article and the removed bits only show up after the post to the blog. Dougweller (talk) 20:03, 11 July 2009 (UTC)

E3b-North African vs Middle Eastern vs Sub-Saharan African

This issue needs to be clarified. Firstly North African populations as we know them today are not representative of mesolithic North Africans. This is clearly illustrated in the study The Levant versus the Horn of Africa: Evidence for Bidirectional Corridors of Human Migrations. According to this study the majority of Y haplotypes in Egypt, about 59% are of Eurasian origin. 41% of the haplotypes are African of which 32% is E3b(XE3b*) and 9% is E(XE3b), E3b*, A and B. Modern Egyptians are thus an admixed population 59% Eurasian and 41% African based on the Y chromosome.

The Eurasian component having entered Egypt after the Neolithic revolution according to A Predominantly Neolithic Origin for Y-Chromosomal DNA Variation in North Africa. Prior the arrival of Eurasian haplotypes, the inhabitants of Egypt would have been allied with Nilotic populations to the south. It is these peoples who migrated into the middle east during the mesolithic carrying with them E-M78, which would later disperse into Europe. To summarize, African haplotypes entered Eurasia before Eurasian haplotypes entered Africa, and thus contemporary North Africans are not representative of the African migrants who carried E-M78 into Eurasia. In this case the presence of E-V13 in Europe should not be considered "North African admixture" in the sense that it does not represent contact between Eurasians and populations similar to contemporary North Africans. Rather it represents contact between Eurasians and mesolithic African population with Sub-Saharan affinities.

This is no longer an "Afrocentrist" position but is supported by multiple and independent lines of evidence. The three lines of evidence include the classical genetics, E3b itself and archaeological evidence.

Classical studies

"The classical genetics studies" by Cavalli-Sforza were published between 1991 and 1993 before the discovery of most Y-chromosomal haplotypes. Haplogroup DE for example, was discovered in 1994. This particular study was careful to use aboriginal peoples to minimize the effects of recent admixture. So for Africans, Zaire pygmies, Central African pygmies and Senegalese Mandenka were used. North Africans, East Africans and Horn Africans who are likely to have Eurasian admixture, were not sampled. Yet these studies were able to detect some form of pygmoid African admixture in the European population. So this admixture is clearly Sub-Saharan, not North African. Cavalli-Sforza states that the spread of farming from the middle east may have been responsible for this apparent African admixture. [3],[4],[5]. This admimxture has been detected accross several genetic measures. Cavalli-Sforza states:

"There is one important exception to the rule in Table 1, namely that in the first column of the matrix Europe shows a shorter distance from Africa than do all the other continents. The difference is statistically significant and is consistently found with all markers, ranging from “classical” ones based on gene products (blood groups and protein polymorphisms) to DNA markers such as restriction polymorphisms and microsatellites" [6].

Xavier Bolton (talk) 20:06, 28 June 2009 (UTC)

Identification of E3b

The identification of E3b, which was once thought to be of Near Eastern origin is now known to be of Sub-Saharan African origin.

See the edits I have recently made to the Sub Saharan genetic mixture article. The points you raise above are all linked to the question of "what is that article actually about?" Rather than fighting to delete the article I have inserted an introductory discussion mentioning the problems there are in having a clear definition. Clearly different people will be defining things different ways. For example is E1b1b considered to have left Africa to long ago in order to consider it worth mentioning as an African clade? There is no correct answer.--Andrew Lancaster (talk) 07:47, 29 June 2009 (UTC)

Archaeological evidence

Archaeological evidence-Regarding the African affinities of skeletal remains from Turkey, Ricaut et al state

"From the Mesolithic to the early Neolithic period different lines of evidence support an out-of-Africa Mesolithic migration to the Levant by northeastern African groups that had biological affinities with sub-Saharan populations. From a genetic point of view, several recent genetic studies have shown that Saharan genetic lineages affiliated with the Y-chromosome PN2 clade have spread through Egypt into the Near East, the Mediterranean area, and, for some lineages, as far north as Turkey , probably during several dispersal episodes since the Mesolithic. This finding is in agreement with morphological data that suggest that populations with sub-Saharan morphological elements were present in northeastern Africa, from the Paleolithic to at least the early Holocene, and diffused northward to the Levant and Anatolia beginning in the Mesolithic."Discrete Traits in a Byzantine Population and Eastern Mediterranean Population Movements

Another study of Natufian crania by Loring Brace also detected biological affinities with peoples of Sub-Saharan Africa. The Neolithic revolution is believed to have arisen from the Natufian culture in Israel. Agriculture is thought to have spread by demic diffusion from the middle east to Western and Northern Europe. Brace et al. state

"If the Late Pleistocene Natufian sample from Israel is the source from which that Neolithic spread was derived, then there was clearly a Sub-Saharan African element present of almost equal importance as the Late Prehistoric Eurasian element. The interbreeding of the incoming Neolithic people with the in situ foragers diluted the Sub-Saharan traces that may have come with the Neolithic spread so that no discoverable element of that remained. This picture of a mixture between the incoming farmers and the in situ foragers had originally been supported by the archaeological record alone, but this view is now reinforced by the analysis of the skeletal morphology of the people of those areas where prehistoric and recent remains can be metrically compared.The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form

Xavier Bolton (talk) 19:51, 28 June 2009 (UTC)

Nothing wrong with admixture

All human populations are the result of some form of genetic admixture. Being a single species, whenever human populations have come in contact, they have interbred. This is especially true for hunter gatherers as their populations were low, finding a mate was more of a challenge. Hunter gatherers couldn't afford to be too choosy and are more inclined to overlook language, ethnic or religious differences when looking for a mate. Strict endogamy is more of a recent phenomenon that is associated with post neolithic stratified societies. But even with strict endogamy, just a few exogamous liasons are sufficient to introduce new genes and over a sustained period alter the genetic profile of a population. This has been the case with Ashkenazi Jews who are now genetically similar to European populations.

So their is nothing wrong with Europeans having African admixture or Africans having European admixture. Its simply a natural phenomenon. Some people feel that having African admixture is a terrible thing that they are trying to de-Africanize what is clearly African DNA. This is unscientific and it shouldn't be tolerated. Xavier Bolton (talk) 19:52, 28 June 2009 (UTC)

Good points. We are still going through the article, and making revisions. So far , I am just up to the Neolithic section.

My issue with C-V's work is that he did not include Nth Africans and Western Asians in his genetic distance calculations, but only Europeans, far east Asians and sub-saharan Africans. Although he gave reasons as to why he did not, I think they would clarify the real genetic relationships between Europeans and the rest.

The origins of V-13 have still not been elucidated clearly. Eg Battaglia sees that it did originate in Nth Africa and had a swift early Holocene spread into Europe, and subsequently spread widely from the Balkans at a later period. However, we need to be careful with associating Y haplogroups with ethnicity/ race. Not only is this scientifially incorrect (Y-DNA does not carry 'racial traits'), but it might offend some people. It is nice that you such a positive outlook, but not everyone shares your opinions. Afterall, the NRY is a kind of genetic vestige. It tells nothing about the actual genetic composition of modern populations. Therfore, instead of labelling E3b as "African", one might better state that the mutation defining the said haplgroup first appeared in Africa, or whatever the case may be.

As for jews, they have clear 'Middle Eastern lineages'

Hxseek (talk) 03:10, 29 June 2009 (UTC)

I think Cavalli-Sforza has been clear in stating that North Africans are intermediate between Sub-Saharan Africans and Europe, though more similar to Europeans than Sub-Saharans. He estimates Ethiopians are 60% Sub-Saharan and 40% Eurasian.

This is true for North-Eastern Africans but obviously wrong for North-Western Africans. At least we should not consider "North Africans" as a whole. And concerning NorthWest Africa, we should distinguish, at least, Saharan Berbers and Mediterraneans Berbers . According to the most recent autosomal by Jun Z. Li 2009 Saharan Berbers (Mozabites) do have Sub-Saharan ancestry but only around 15-20% (http://1.bp.blogspot.com/_Ish7688voT0/R79MXyHURCI/AAAAAAAAAFg/8MeKImXcV34/s1600-h/structurescience.jpg), so it is very likely that Mediterranean Berbers would show very little sub-saharan ancestry in this kind of study. By the way this is strongly suggested by mtDna studies that found sub-saharan L hg at frequencies around 3%-15% in Mediterrean Berbers (less or same level found in South-Portugal) and up to 20-45% in Saharan Berbers. By the way I share my (portuguese) genetic profile with some mediterranean North-Africans (Morocco, Libya, Algeria and Egypt) at 23andme and I even show slightly more sub-saharan African dna (1%) than them (<1%) in the AncestryPainting--DosReis77 (talk) 08:52, 12 July 2009 (UTC)

I agree that we need to be careful when associating any haplogroup with race, especially since the y-chromosome has relatively few genes. It's major function seems to make a person male but little else. According to Adam's Curse by Bryan Sykes the Y-chromosome is shrinking because of lack of function. Unfortunately there is a tendency, especially in the blogosphere, to associate these haplogroups with issues of race or ethnic pride.

However, V-13 is a subclade of M78 which according to Battaglia et al may have dispersed from Wadi Howar in Sudan near the border with Egypt. M78 is subclade of E-m35 which originated in East Africa. So it clearly represents a migration of peoples from East Africa to Europe. What is most telling about the "Africanness" of E-V13 is that Cavalli-Sforza was able to detect Sub-Saharan admixture in Europeans using blood proteins. The blood proteins represent phenotype, which means African DNA is found not only in the y-chromosome but in other parts of the genome. It also means that African admixture is being expressed in the actual genes and is not simply part of junk DNA. This analysis was done primarily using the pygmies of Zaire and Central Africa.

Thus the Mesolithic North Africans from which E-v13 arose would have been similar to other African populations. The North Africans who lived at that time E-m78 came into being were not similar to modern North Africans who are the product of recent admixture between Eurasians and Africans. In Egypt the current Eurasian component is at least 60% NRY whereas in Tunisia the Eurasian component is 70% via mtdna[7]. So when E-M78 is described as being North African, there maybe a wrong impression about the people who lived there 12,000 years ago before the arrival of Eurasians during the Neolithic. Xavier Bolton (talk) 04:50, 29 June 2009 (UTC)

I think you are both wrong about Battaglia et al. They felt that E-V13 was likely to have originated somewhere in the area of their study, most likely in the Balkans itself. Personally I think they ignored some important information and they should have stuck to Cruciani et al's proposal that it was probably in the Levant, which I still consider the standard. Of course this lineage is said by both authors to go back to Egypt, and in fact arguing about where a mutation happened is often pointless. --Andrew Lancaster (talk) 06:20, 29 June 2009 (UTC)

I think you have to be careful about equating a Y lineage's movements with a migration. Better to look at autosomal DNA for this.--Andrew Lancaster (talk) 06:20, 29 June 2009 (UTC)

I think Xavier is not correct about Afrocentrism. Where science comes to a conclusion of African origins, like with E1b1b, then fine. But a strange form of Afrocentrism exists whereby the same African origins position is taken for unscientific reasons for all haplogroups that MIGHT have originated in Africa, even if scientific discussion is inconclusive or even tending away from this. Take for example Y haplogroup DE and mitochondrial haplogroup M. To look at Y lineages, please consider how there are discussions on the internet calling me a "white cultist" because of the fact that I said in my review article that E-M123 originated in the Middle East or Egypt, instead of saying Africa or Ethiopia. Then tell me there is no "Afrocentrism"?--Andrew Lancaster (talk) 06:20, 29 June 2009 (UTC)

Yes. My mistake. Battaglia argues V-13 arose somewhere in southern Balkans/ Anatolia Hxseek (talk) 06:45, 29 June 2009 (UTC)

There are extreme positions on the Afrocentrism side too, if they are unscientific then they should have no place on wikipedia. It was initially thought that E-M35 was of Near Eastern origin. In the same way that some scholars still refuse to consider Afro-asiatic as being of East African origin despite this being the most parsimonious solution. So there may be a tendency to over-compensate and be suspicious of any hypothesis that does not consider the African origins of shared haplogtypes. Xavier Bolton (talk) 07:09, 29 June 2009 (UTC)

Affirmative action has no place in science I'm afraid. Proper scientific debate and information should be nurtured, and then the truth will have a tendency to appear. People writing based on arguments they think others will make are a BIG PROBLEM. The worst POV editing I see is coming from two sides with good intentions. If everyone would take the moral high ground, we would all be better off for it, and any remaining POV pictures would look far less justified!--Andrew Lancaster (talk) 07:44, 29 June 2009 (UTC)

Do you have a published source for saying E-M35 was thought to have Near Eastern origins ever? I know that some casual ideas existed, but did anyone ever argue such a case anywhere? I think that when E-M35 was first distinguished, web masters just pasted in whatever people used to think about E and DE more generally? I have been asking around about this for quite a long time now. It seems to be like an "urban myth".--Andrew Lancaster (talk) 07:44, 29 June 2009 (UTC)

Concerning Afro-asiatic, I think that you have to distinguish the real authors on this subject from the general public. The main reason I think a minority propose a non African origin is to do with the paradigm that major modern languages were all spread by the first farmers. So for them it seems parsimonious. Most of these people are archaeologists, and therefore more influenced by clear archaeological evidence than linguistic knowledge. Basically there is only one major linguist who proposes a Near Eastern origin, Militarev, and he proposes it right on the border with Africa so to speak. This theory also is affected by another paradigm which has nothing to do with what worries all the POV pushers, and this is that Militarev is looking for ways to link languages into a super family.--Andrew Lancaster (talk) 07:44, 29 June 2009 (UTC)

Western Europeans are very different from Eastern Europeans

http://www.plosone.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pone.0005472.s003 Pair-wise Fst between Europeans: Sykes theory is not out of date infact he implys a expansion from Iberia during the neolithic which would be the perfect origin for R1B1B2 (Although it is always possible that R1B1B2 is of paleolithic origin since it is very diffecult to put a time estimate on a haplogroup) R1A and R1B are the 2 largest y-dna haplogroups in Europe so they deserve much attention and your version awards them little atterntion. The Count of Monte Cristo (talk) 17:37, 11 July 2009 (UTC)

R1b and R1a are already discussed in this article, as is the East-West cline in genetic variation. We should not explain everything two or three times in the same article. (And please remember that R1b is not the only haplogroup in Europe and the East-West differences are not the only differences in Europe.) What other explanations can you give for your edits? These ones do not explain your edits at all.--Andrew Lancaster (talk) 21:03, 11 July 2009 (UTC)

SOPHIAN, please explain your edits!

• Why does this article need a listing of dozens of R1b percentages, when this is not an R1b article?
• Why does this article need two maps showing R1a percentages?
• Why is R1a in Paris so important?
• Why does this article need to take a side in the argument about where R1b originated, and why are we giving undue weight to one old source?

And when you paste in your material, and then refuse to allow anyone to change it, can you please try to check to make sure that formatting, and flow of discussion, and spelling etc are all perfect?--Andrew Lancaster (talk) 07:09, 12 July 2009 (UTC)

Please everyone note that this article has had problems over time because of people inserting too much repetitive material, unduly focused on details

Can all editors of this article please consider that this article has had problems over its history coming from people casually adding material that interests them about details (and then sometimes going on to defend it with more effort than they put into the initial edit). This leads to:-

• Extra material being added without first checking to see whether it is already covered, and where and how it should fit into the structure article. This has led in turn to

• repetition,
• broken structure or flow of discussion,
• inconsistent nomenclature and use of terminology not defined in the article (meaning non expert readers will not understand it)

• Frequent problems with casual additions not being sourced or properly sourced, or "polished" enough to keep in various ways.
• Excessive and unbalanced detail being given to very specific subjects, such as R1a in Paris.

Please aim at a high quality Wikipedia. Any efforts you expend without taking the above into account may force other editors to delete your work. Do not assume that they will be able or willing to go and find sourcing, fix formatting, etc.--Andrew Lancaster (talk) 09:27, 12 July 2009 (UTC)

Indeed. This is one of those horrible articles in Wiki, where everyone cherry pics information for one purpose or the other. The only two serious books about genetic history in Europe that are out there are those of Stephen Oppenheimer and Bryan Sykes. They deal mainly with the British Isles, but also with Europe, especially Oppenheimer. To see the quality of the article, they are not even mentioned here. This article is of those that give Wiki a bad name. Kun. —Preceding unsigned comment added by 80.30.190.254 (talk) 09:37, 12 July 2009 (UTC)

I do not believe these two sources are what is called for at all! They are out of date and unscientifically written. Please review the talkpage history on this subject.--Andrew Lancaster (talk) 10:14, 12 July 2009 (UTC)

Sub-Saharan DNA admixture

The article Sub-Saharan DNA admixture in Europe was recently deleted. This article was patrolled primarily by Small Victory. Recently Causteau, SOPHIAN and The Ogre were the primary editors to the article. The deletion of the article Sub-Saharan DNA admixture in Europe means that the community rejected the content of the article. The community has rejected the approach that editors to the article were using. Therefore, users should not transfer the same content onto this article. This time, we have administrative recourse, it is no longer a content dispute. If the same content is transferred into this article we can request administrative intervention based on the findings of Wikipedia:Articles for deletion/Sub-Saharan DNA admixture in Europe (2nd nomination). Likewise, I will delete the content that has been transferred from the deleted article. Wapondaponda (talk) 13:17, 19 July 2009 (UTC)

I agree that any use of this material needs to be very carefully agreed to by editors. I really think nothing in that article can be salvaged in a neutral form.

But I also want to point out once more that this article is currently broken up in one specific way, which is not the only possible way. All material added to this article should be inserted in a way which sticks to the current structure or otherwise we'll have big redundancy problems.--Andrew Lancaster (talk) 13:26, 19 July 2009 (UTC)

It's funny that the person who, just the other day, accused me (falsely) of trying to suppress evidence of Sub-Saharan admixture in Europe is now himself suppressing said evidence as I'm trying to incorporate it into the article (as was originally proposed). Of course, these genetic lineages are present in Europe and must be mentioned in this article that's called "Genetic history of Europe", just like their Central/East Asian counterparts in that same section. You're not seriously going to disagree with that, are you? ---- Small Victory (talk) 13:37, 19 July 2009 (UTC)

Small Victory, this is clearly a controversial bundle of material you inserted here, and so slowing down seems to be the least we can do. Please first consider two things:

1. Please make sure we only put in material which is uncontroversial and neutral and well sourced, AND which is relevant to this article.

2. Look at the structure of THIS article and consider where this subject might fit, and indeed whether it is not ALREADY covered. For example this article covers a lot of the haplotypes being considered already. BUT this article is NOT broken into geographical source areas.--Andrew Lancaster (talk) 13:43, 19 July 2009 (UTC)

The previous approach to the article has been rejected as discussed in the deletion process. Independent editors viewed the previous material as POV fork. So we need a new approach, I suggest not including any material in this article until we reach a consensus. It is even possible that the a separate article can be created, but it has to be neutral. So I agree with Andrew that we need to slow down. At this stage a draft is probably the best way to go. I suggest someone neutral, other than myself or Small Victory, should lay a foundation to the article. Wapondaponda (talk) 14:52, 19 July 2009 (UTC)

Well, here is the "draft" as it currently appears in the article:

Sub-Saharan African mtDNA (haplogroups L1, L2 and L3) and Y-DNA (haplogroups A, B and E (excluding E1b1b), particularly the ubiquitous Bantu marker E1b1a) are present at generally low levels throughout Europe.

Maternal (mtDNA) lineages are the more common and likely represent gene flow from historical events, such as slavery. They've been found in Portugal (6.9%), Spain (2.1%), Slovakia (1%), Italy (0.87%), Finland (0.83%), Bulgaria (0.71%), Bosnia (0.69%), Basques (0.64%), England (0.6%), Greece (0.44%), Switzerland (0.44%), Czech Republic (0.4%), Russia (0.3%), France (0.3%), Poland (0.18%), Germany (0.17%) and Scotland (0.1%).

Paternal (Y-DNA) lineages occur much less frequently. They've been found in Portugal (3%), Albanians from Italy (2.9%), France (2.5%), Germany (2%), Sardinia, Italy (1.6%), Calabria, Italy (1.3%), Austria (0.78%), Italy (0.45%), Spain (0.42%) and Greece (0.27%).

Genome-wide autosomal DNA analyses using the STRUCTURE clustering program, which is designed to accurately detect and quantify admixture, show equally negligible levels of sub-Saharan African admixture in all Europeans, including Iberians.

Please discuss.--Andrew Lancaster (talk) 15:23, 19 July 2009 (UTC)

I think that putting aside the various statistics pasted in there are only a few short sentences. Basically these sentences are stating a theory. The theory has the following points...

• Certain Y and mt haplogroups are "sub Saharan", and clear well-defined lists of these can be made
• The haplogroups in these lists are not common at all in Europe, and where they appear this is because of slavery
• Mitochondrial types in this sub Saharan classification are more common than Y lineages in this classification in Europe
• (The link, as I understand it is that in some versions of the story being proposed earlier by the same editors on the deleted article it was being argued that slaves who have children are more likely to be women than men.)

Not one of these proposals can be read in any of the sources cited, or in any other source, unless we draw conclusions based on synthesizing the data ourselves. The sourcing, if I understand correctly, is supposed to work like this (based on extensive discussion over on the now deleted article where all this stuff was cut and paste from)...

• In order to get the near lists of which haplogroups are sub Saharan, comments from genetics papers calling a lineage sub Saharan are cherry picked. This raises the question of whether calling a lineage sub Saharan in one context, means it is always sub Saharan; and the even more controversial point in practice of whether this mean other lineages are known NOT to be sub Saharan. Geneticists simply do not write this way, and it is a gross misunderstanding of the literature. NOTE: There is no source which gives clear well defined lists, and no source which explains in a clear way how you would even define "sub Saharan" in a way which is going to be consistent for every type of discussion. So this is clearly original research.
• Concerning the slavery claim, again there are some sources cherry picked who mention slavery as a POSSIBLE explanation for unexpected looking results here and there in isolated studies. There is absolutely no source stating that slavery is responsible for the lineages designated (in Wikipedia) as sub Saharan all over Europe. This is original research.
• There is not even any attempt to source any statement that mitochondrial sub-Saharan lineages are more common in Europe than sub Saharan male lines. This is original research.

So I see nothing in this proposed section which should be kept. This is the same original research which was recently deleted from another part of Wikipedia. It is compressed only.--Andrew Lancaster (talk) 06:23, 20 July 2009 (UTC)

I concur with Andrew. Essentially this is the same POV material that was in the article and the article was deleted because it was a POV fork. Small Victory and Co, rejected my contributions. They also rejected the compromises that Andrew offered. So the deletion process was a referendum on the approach used by Small Victory et al. Andrew has highlighted how the data in the article was used to present a POV that is actually quite unpleasant. Since this approach was rejected by the community, a new approach is warranted. It is only fair, that others who were not given a chance to contribute have their chance to present the material and subject it to the scrutiny of the community. Wapondaponda (talk) 13:06, 20 July 2009 (UTC)

If anyone cares

Regarding the draft, this is what I have picked up. But my experience so far, is nobody cares about verifying content, so some editors are adding content that may be inconsistent with the sources that they add. I will waste some of my energy to illustrate this, because I have some energy left to waste.

Sources not about Europe

The first four references are.

• Martinez et al Admixture estimates for Caracas, Venezuela, based on autosomal, Y-chromosome, and mtDNA markers.
  • This has nothing to do with Europe but Venezuela.
• Abu-Amero, 2007, Eurasian and African mitochondrial DNA influences in the Saudi Arabian population, once again, not about Europe but Saudi Arabia
• Richards et al, Extensive Female-Mediated Gene Flow from Sub-Saharan Africa into Near Eastern Arab Populations , Near Eastern, not Europe.
• Goncalvez et al, Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers Cape Verde is off the coast of West Africa, not Europe.

It seems that the editor is trying to find definitions of admixture from sources not related to Europe. This potentially could be original research. Much better to deal with sources that deal directly with Europe and not other places.

Exclusion of E3b from African admixture

The sources cited by footnotes Richards et al, and Goncalvez et al do not exclude E3b from Sub-Saharan Africa. Goncalvez et al state:

E3b, characterized by mutation M35, probably has an east African origin. The group occurs among Ethiopians (Semino et al. 2002) and Sudanese (Underhill et al. 2000) and appears at frequencies 12%–23% in various Jewish populations (Nebel et al. 2001).

and

The total frequency of haplogroups A and E covering 100% of the 276 Guinean Y-chromosomes is 48% in CVN and 46% in CVS. These values represent the maximum proportion of the west African lineages in the islands. However, since E3b has a significantly higher frequency in north Africans and Middle Eastern populations (12%–22% in Jews; Nebel et al. 2001) than in west Africans (6%), it seems likely that the E3b lineages arrived in Cabo Verde largely from a different source.

So the authors acknowledge the African origin of E3b, but assess two possible routes to Cape Verde. Either via West Africa, but most likely via Jewish immigrants from Iberia. In short, we cannot exclude e3b from Sub-Saharan admixture in such a simplistic manner.

I propose including a quote from Shriver et al, 2008, where they state:

We observed patterns of apportionment similar to those described previously using sex and autosomal markers, such as European admixture for African Americans (14.3%) and Mexicans (43.2%), European (65.5%) and East Asian affiliation (27%) for South Asians, and low levels of African admixture (2.8-10.8%) mirroring the distribution of Y E3b haplogroups among various Eurasian populations.

and

In Mediterranean and Middle Eastern populations, African admixture increases proportionately farther south into North Africa and Southeast into Asia. This distribution appeared to mirror that for the ‘‘African’’ Y chromosome E3b haplogroup (Underhill et al., 2001; Jobling et al., 2003; Cruciani et al., 2004)

. Wapondaponda (talk) 05:21, 20 July 2009 (UTC)

Slavery

The is an overly simplistic statement

"Maternal (mtDNA) lineages are the more common and likely represent gene flow from historical events, such as slavery.

This is sourced to Pereira et al 2000 and is somewhat accurately sourced as they argue that the widespread presence of L lineages in Iberia is due to the slave trade. Firstly the authors state

The geographical distributions of both haplogroups were quite different, with U6 being restricted to North Portugal whereas L was widespread all over the country.

So I don't think it is accurate to describe Sub-Saharan admixture as Negligeable. But back to slavery. Pereira et al 2000 state:

The introduction of L sequences in Portugal was tentatively imputed mainly to the modern slave trade that occurred between the 15th and 19th centuries. Both the great number of slaves that entered Portugal and their very diverse African geographic origin are consistent with the data set now reported. However, we cannot exclude some North-African contribution to present-day Portuguese L lineages.

In general many scholars have started to reassess the overly simplistic almost stereotypical assumption that the presence of L lineages anywhere outside of Africa represents the slave trade. A more recent study by Gonzalez et al 2003, actually contradicts Pereira et al's theory of predominantly slavery era admixture. They state.

However, with respect to the sub-Saharan Africa lineages, the recent history of the Black slave trade carried out by the Portuguese (mainly in the 15th and 16th centuries), with a well-documented import in southern Portugal, also be a plausible alternative to explain the presence of these African haplotypes in this region (Pereira et al., 2000). To test this possibility, we compared the proportion of sub-Saharan Africa haplotype matches between the Iberian Peninsula and northwest Africa (0.75%) with those of the Iberian Peninsula and a sample of sub-Saharan Africans from the Gulf of Guinea. The sample includes 45 Bubis from Bioko and 49 individuals from Saˆo Tome´, 32 Yoruba 1, and 72 Equatorial Guineans. The percentage obtained (0.35%) is roughly half of the former, and in addition, the majority of them (97%) are also shared with northwest Africa, although matches between sub-Saharan and North African samples are only 0.95%. These results suggest that, although both prehistoric and historical influences likely contributed to the sub-Saharan African haplotype pool present in the Iberian Peninsula, the former seems to be more important. Our results are in agreement with the gene flow (19.5%) from northwest Africa to the Iberian Peninsula estimated in a recent study of variation in the autosomic CD4 locus (Flores et al., 2000b), and with the evidence of northwest African male input in Iberia calculated at around 20%, using the relative frequency of northwest African Y-chromosome- specific markers in Iberian samples. Furthermore, our results clearly reinforce, extend, and clarify the preliminary clues of an important mtDNA contribution from northwest Africa into the Iberian Peninsula. On the basis of the L1b frequencies detected in Spanish and Portuguese samples (2–3%) and those found in western Africa (10–30%), a significant influence (at least 10%) of North Africans in the Iberian gene pool has also been admitted

Summary, they argue that L in Iberia is actually of prehistoric origin and not from the recent slave trade. This is not reflected in the current draft, or was not reflected in the deleted article. Wapondaponda (talk) 05:21, 20 July 2009 (UTC)

I agree that the Pereira article is not a valid source for the much stronger claims being put into this article. It does not even claim to be about all of Europe, or all mitochondrial haplogroups. It is about a specific haplogroup, and only in Portugal. But even then it only it is likely that a part of these lineages were due to slave trade. I also agree that looking at the literature more broadly, even this one citation starts to look over-blown and inappropriate.--Andrew Lancaster (talk) 06:00, 20 July 2009 (UTC)

Percentages

Maternal (mtDNA) lineages are the more common and likely represent gene flow from historical events, such as slavery.[90] They've been found in Portugal (6.9%), Spain (2.1%)or (0.36%)[91] , Slovakia (1%), Italy (0.87%), Finland (0.83%), Bulgaria (0.71%), Bosnia (0.69%), Basques (0.64%), England (0.6%), Greece (0.44%), Switzerland (0.44%), Czech Republic (0.4%), Russia (0.3%), France (0.3%), Poland (0.18%), Germany (0.17%) and Scotland (0.1%). Paternal (Y-DNA) lineages occur much less frequently. They've been found in Portugal (3%), Albanians from Italy (2.9%), France (2.5%), Germany (2%), Sardinia, Italy (1.6%), Calabria, Italy (1.3%), Austria (0.78%), Italy (0.45%), Spain (0.42%) and Greece (0.27%).

Andrew refers to such as "Accurate sounding" figures. Wapondaponda (talk) 05:21, 20 July 2009 (UTC)

There is also no source being given for saying that maternal lineages are more common than paternal ones. Apparently Wikipedians are coming to this conclusion themselves based on looking at particular datasets. This is OR.--Andrew Lancaster (talk) 06:01, 20 July 2009 (UTC)

Structure, Negligeable African admixture

Genome-wide autosomal DNA analyses using the STRUCTURE clustering program, which is designed to accurately detect and quantify admixture,[94] show equally negligible levels of sub-Saharan African admixture in all Europeans,[95] including Iberians

The sources cited include

• Pritchard et al. I could not find in this article, anywhere that states that Sub-Saharan African admixture is negligeable.
• Genetic_history_of_Europe#cite_note-95 states that Auton et al, say the following

Auton et al. 2009 note higher haplotype diversity in Southwestern Europe, and in particular a higher number of haplotypes shared with the Yoruba, for which they propose four possible explanations: 1) West African admixture, 2) North African admixture, 3) the recolonization of Europe from Iberia after the Ice Age, and 4) a combination of two or all three of these, stating that further research needs to be done. However, in Figure S3 A of the supplementary material, which shows the results of a STRUCTURE-based admixture analysis, neither the Spanish nor the Portuguese have any significant membership in the Yoruba (YRI) cluster.

This is a very dangerous case of original research, because this is not what the authors say. They specifically state, and this is a direct quote, so their is no chance of misinterpreting them.

Our analyses also have direct relevance to current debates in human population genetics regarding the extent of historical gene flow among Africa, Europe, and the Middle East Our observation of a north–south gradient in diversity with the highest estimates of diversity in the southern part of the continent is consistent with the initial founding of Europe from the Middle East, the influence of Neolithic farmers within the last 10,000 yr, or migrations south followed by a recolonization of Europe after the last glacial maximum. The unusually high number of haplotypes in South Western Europe is indicative of recurrent gene flow into these regions. Furthermore, when we considered the extent of haplotype sharing with the HapMap YRI population in Europe, we found that the South and South-Western subpopulations showed the highest proportion of shared haplotypes. If gene flow had occurred solely through the Middle East, we would expect the South-Eastern subpopulations to have the highest haplotype diversity and sharing of YRI haplotypes. These two results therefore suggest that while the initial migrations into Europe came via the Middle East, at least some degree of subsequent gene flow has occurred directly from Africa. A potential concern is that the HapMap YRI are not representative of diversity in North Africa, and the levels of haplotype sharing must be interpreted with this in mind. It is currently unclear how patterns of genetic diversity in the Yoruba are representative of the wider region, although genetic similarity appears to decline with distance. Nonetheless, the haplotype sharing between Europe and the YRI are suggestive of gene flow from Africa, albeit from West Africa and not necessarily North Africa. Future studies will hopefully be able to better resolve this question by comparing haplotypes from further populations around the Mediterranean.

My proposal is to include excerpts from this quote, per Wikipedia:PROVEIT#cite_note-1, to avoid confusion or even misrepresenting sources. Wapondaponda (talk) 05:21, 20 July 2009 (UTC)

---

You think that because the 'Sub-Saharan African' article's talk page is gone you can pretend that you weren't proven wrong on these issues? Not a chance.

Re: Sources not about Europe

Those sources don't have to be about Europe because they're not being cited in reference to admixture in Europeans. They're being cited in reference to the haplogroups that they use (and don't use) as evidence Sub-Saharan African admixture. But of course, you already knew that. You just needed an excuse to dismiss them all because you don't like the consensus they arrive at. Too bad the excuse you came up with is beyond lame.

Hi Small Victory, I had understood that you were using these articles as a source for building up a case. These sources show which haplogroups are to be called "Sub Saharan". Right? And from these definitions, you put together a case using other information from other articles.--Andrew Lancaster (talk) 14:30, 20 July 2009 (UTC)

Re: Shriver et al. 2008

That study is co-authored by one of the founders of DNAPrint Genomics, and it applies that organization's methodology (AIMs), which has been harshly criticized for "involv[ing] loci that have undergone strong selection, which makes it unclear whether these markers indicate shared ancestry or parallel selective pressures." That alone bars the study from inclusion in the article.

Hi Small Victory, that article making the criticism is making a much bigger argument which basically means a lot of what you are citing and arguing should not be cited and included. You should be careful not to cherry a criticism and only apply it to some data you want to delete.--Andrew Lancaster (talk) 14:36, 20 July 2009 (UTC)

On a side note, the authors' E3b explanation for their (already unreliable) findings makes no sense. They found more West African admixture in Iberians than in Greeks, yet Greeks have much more E3b than Iberians. And they totally ignore E3a and L mtDNA, which are actually West African in most cases and much higher in Iberia than in Greece. So maybe, just maybe, they're barking up the wrong tree with their E3b reference, which would be characteristic of the low level of their DNAPrint-style "research".

Yes, indeed these published authors might have made mistakes. This is something we can argue about any source, which would then lead to Wikipedia needing to be a research institution, or else unable to function, and so Wikipedia came up with some policies about things like that.--Andrew Lancaster (talk) 14:36, 20 July 2009 (UTC)

Re: Auton et al. 2009

The note I added (as a compromise to you, btw) perfectly summarizes what that study says about the haplotypes shared between Southwestern Europeans and West Africans:

The high number of samples spanning Europe allowed us to investigate geographic patterns of haplotype diversity at a more localized level. We see a North-South gradient in the number of haplotypes present for both H10 and H25 (Figure 3A) with the highest levels of diversity being found in the Southern regions. In particular, South Western Europe has a higher mean number of haplotypes than South Eastern Europe and Western and Central Europe. This is unexpected, as many current models of historical human migration predict numerous migrations into Europe from Africa via the Middle East, and one would therefore expect the highest diversity in the South East, with decreasing diversity moving North and West [Hellenthal et al. 2008, Chikhi et al. 2002, Barbujani and Goldstein 2004]. The excess haplotype diversity in South Western Europe has at least two possible explanations. First, it may reflect direct migration from North Africa across the Mediterranean. Alternatively, it may represent a recolonization of Europe after a period of glaciation during which the Southern areas of Europe became a refugium for the prehistorical human population [Barbujani and Goldstein 2004, Willis and Whittaker 2000].

To address this issue, we investigated the level of haplotype sharing between African and European populations. In the absence of 500K data from North African populations (the HGDP having been genotyped on a different platform), we investigated patterns of haplotype sharing with the HapMap Yoruba (YRI) population. Using the 25 SNP haplotype windows outlined above, we found that South West Europe had the highest proportion of haplotypes that are shared with YRI (Supplementary Table S5). Furthermore, there were significantly more shared haplotypes between South West Europe and YRI relative to South East Europe and YRI (p-value 0.0072; Mann-Whitney U test), which suggests that the unusually high haplotype diversity in South Western Europe is indicative of gene flow from Africa. However, it is perhaps worth noting that this does not preclude the refugium hypothesis from also contributing to the pattern.

A potential concern is that the HapMap YRI are not representative of diversity in North Africa, and the levels of haplotype sharing must be interpreted with this in mind. It is currently unclear how patterns of genetic diversity in the Yoruba are representative of the wider region, although genetic similarity appears to decline with distance [Conrad et al. 2006, Jakobsson et al. 2008]. Nonetheless, the haplotype sharing between Europe and the YRI are suggestive of gene flow from Africa, albeit from West Africa and not necessarily North Africa. Future studies will hopefully be able to better resolve this question by comparing haplotypes from further populations around the Mediterranean.

So no, the authors are not at all clear about how to interpret their finding. Whenever they mention gene flow from Africa, they say "suggestive of". Then they propose the alternative explanations of North African admixture and the Iberian postglacial refugium, pointing out that further research needs to be done.

And they don't indicate a direct YRI contribution either. They indicate haplotypes that are shared between YRI and Europeans, which is not the same thing. Open your eyes and look at Figure S3 A in the supplementary material. It shows virtually none of the YRI component in any of the European samples. ---- Small Victory (talk) 13:06, 20 July 2009 (UTC)

But you admit that the authors do not say as you propose, that gene flow from Africa is negligible, as they suggest gene flow from Africa. You are focusing on their alternate hypothesis, not their main hypothesis. Their main point is that pattern of haplotype diversity is consistent with gene flow from Africa. Their alternate hypothesis is that it is due to the LGM refugium. I have no problem with including their alternate hypothesis. But if you genuinely look at the data, African admixture in Iberia, is consistent with the several independent studies, Pereira et al, Gonzalez et al etc. So the alternate hypothesis is a less likely explanation for the presence of haplogroup L lineages in Iberia. The YRI haplotype sharing is clearly shown in the YRI table in supplementary materials which is about 5%, so they may not even be referring to YRI in this specific case but to haplotype diversity in general.

Secondly, you highlight their argument that YRI diversity may not be representative of North African admixture and the wider region. This is precisely what I had been discussing. YRI admixture is not necessarily representative of Sub-Saharan admixture. But YRI is always Sub-Saharan. In short YRI admixture will always represent a minimum of Sub-Saharan admixture. The absence of YRI doesn't imply the absence of Sub-Saharan admixture. But the presence of YRI implies the presence of Sub-Saharan admixture. If say, the study were to incorporate admixture from say indigenous East African populations, Central Africans and Nilotic populations. We would expect the proportion of Sub-Saharan admixture to even be greater than YRI. Recall that African populations are genetically very diverse, and YRI is only one population in Africa.

So I suggest not sidt-tracking from their main argument, and highlighting their alternate hypothesis as their main hypothesis. Rather their main hypothesis should be given prominence Wapondaponda (talk) 13:47, 20 July 2009 (UTC)

Wapondaponda, I think that these studies look only for similarities and what their words mean is "we do not know which migrations happened we just see these similarities and think they must be caused by something interesting". For example the Yoruba and Iberian might both have a lot of North African admixture. It is the same point I was making on the deleted article talkpage about Ethiopians. When "admixture analysis" clusters Ethiopians as a "mix" between Western Eurasians and "Black Africans" this does not mean the geneticists are saying that there were two source populations who were mixed together to give a cocktail. It means that they pretended something like this in their mathematical analysis, in order to get a perspective. Many different types of migrations can explain a single result like these. Obviously my point applies to Small Victory as well because what I am saying is that any attempt to take one admixture analysis and make big claims about directions of migrations is something we have to be very careful of.--Andrew Lancaster (talk) 14:44, 20 July 2009 (UTC)

I agree in that, the precise details of prehistoric migrations are not known. The purpose of the Hapmap, was simply to take samples from a "representative population" in each continent, and make their DNA profiles available to the public for study. The hapmap project specifically state:

These samples were collected in a particular community in Ibadan, Nigeria, from individuals who identified themselves as having four Yoruba grandparents. It is important to include a reference to "Ibadan, Nigeria" when describing the source of these samples out of respect for the community's wishes. Including the name of the city and country where these particular Yoruba samples were collected also reinforces the point that the sample set does not necessarily represent all Yoruba people, whose population history is complex. These samples should not be described merely as "African," "Sub-Saharan African," "West African," or "Nigerian," since each of those designators encompasses many populations with many different ancestral geographies. Note that the adjective form is "Yoruba," as in "the Yoruba samples," not "Yoruban." The accent is on the first syllable (YOR-u-ba).

So in this case YRI is a stand-in for Sub-Saharan Africa, albeit an imperfect one. We can say, with some degree of confidence, that it wasn't Yoruba people who migrated into the Iberian peninsula in pre-Neolithic times, since the expansion of people from West Africa is a fairly recent event, coincident with the Bantu Expansion around 5,000 years ago. However, as I have previously posted, pre-Neolithic North African populations, were probably related to the ancestors of Yorubas and other Sub-Saharan Africans. Over time these North Africans seem to have admixed with incoming peoples from the Near East as hypothesized by Rando et al 1998, and Arredi et al 2004 creating the current genetic structure of Modern day North Africans. The Berbers have a genetic structure of >70% E-M81, which is East African and up to 48% haplogroup L and M1 lineages. Traditionally these L lineages have been ascribed to the slave trade. But this view is changing now, because many of these L lineages are unique to North Africa, per Gonzalez et al 2003. We can therefore state, that the emerging consensus is that the prehistoric North African immigrants to Europe, especially through Iberia, were not contemporary West African peoples, but they were related to them. The Shriver study, basically found the exact same pattern as Auton et al by also using YRI/West African samples. Science is based on replicability. If numerous independent studies converge on the same finding, then we approach a mainstream consensus. Wapondaponda (talk) 15:59, 20 July 2009 (UTC)

As usual, you have no idea what you're talking about. E-M81 and M1 subclades are indigenous North African markers that arose in populations who had migrated from West Asia. They're no more "East African" than any other haplogroup on earth. And no, Shriver and Auton didn't produce the exact same pattern. Auton's admixture analysis found virtually no Sub-Saharan African admixture anywhere in Europe. Shriver's found elevated levels of admixture that are undoubtedly a product of the faulty methodology used. ---- Small Victory (talk) 13:18, 21 July 2009 (UTC)

Auton et al.'s main hypothesis was given precedence in my note. Out of the four possible interpretations, I listed it first. What more do you want? Should we just ignore the other hypotheses and the results of the admixture analysis? I'll bet you'd like that, but it's not going to happen.

Also, you're still misunderstanding what Auton actually found. Haplotypes shared between the Yoruba and SW Europeans means exactly that, and nothing more. It does not necessarily mean that one population is admixed with the other. They could both be admixed with a third group (such as North Africans, who weren't tested in the study) or it could simply be the result of genetic drift linked to human migrations that ultimately trace back to Africa (hence the Iberian refugium hypothesis).

It isn't up to us to decide which hypothesis will turn out to be correct. All we can do is report what's in the study, which is what I did. ---- Small Victory (talk) 13:01, 21 July 2009 (UTC)

Yes you did mention it, but the text mentioned a lot more of the other hypothesis than the main one.

If two populations share a similar haplotype, then three scenarios apply

• Convergent evolution
• Common ancestry
• Admixture

It is standard for scientists to consider all three scenarios when comparing two populations.

• Convergent evolution does occur but due to the randomness of mutations, it is usually the least likely scenario.
• Common ancestry is also possible because humans are apparently something like 99.97% alike. But for two populations to randomly converge on similar frequencies of rare traits is unlikely. Most likely if two populations converge to have similar frequencies of a haplotype, then they face similar selection pressures.
• Admixture-If there is evidence of contact or gene flow.

Typically the scientists will chose one of these as their main hypothesis by weighing the evidence at hand. So you are right in that haplotype sharing between Yoruba and SW Europe, may indeed be a coincidence. But in this study, they hypothesize in the discussion when the say

Nonetheless, the haplotype sharing between Europe and the YRI are suggestive of gene flow from Africa, albeit from West Africa and not necessarily North Africa.

The acknowledge that they would like to investigate North African populations as well. But my sentiment, is that won't change much. Genetic Diversity is clinal, so most likely there will be a cline from West Africa across North Africa to Iberia of YRI haplotypes. This has already been demonstrated by studies of Berbers which show they occupy an intermediate position between Sub-Saharan Africa and Eurasia. Wapondaponda (talk) 13:40, 21 July 2009 (UTC)

Please Make it easy

Please tell (on this talk page) me how many people where studied to get the 2.1% figure for Spain if you are going to revert my edit The Count of Monte Cristo (talk) 02:21, 20 July 2009 (UTC)

Most of the mtDNA data comes from Achilli et al., which is a comprehensive survey of Europeans. It includes a large sample of Spaniards from all over the country. Here's the breakdown:

Spain-North-West ... 8/216 ... 3.7%

Spain-North-East ... 3/179 ... 1.68%
Spain-Center ....... 1/148 ... 0.68%
Andalusia .......... 2/114 ... 1.75%
---

TOTAL ............. 14/657 ... 2.1%

--- Small Victory (talk) 13:15, 20 July 2009 (UTC)

I'll make a general point about this kind of problem, because I have come across it before. If this was a key point for the article, for example if the article was about Iberian DNA, then it might be a good idea to put in more data, but given that this article is about the whole of Europe I think if anything we need less detail. In practice, these are small percentages for these haplogroups and you are talking about the difference between finding 1, 2, or 3 people. If you think the % will mislead people why not write "3 out of 179"?--Andrew Lancaster (talk) 14:26, 20 July 2009 (UTC)

The 95% Confidence intervals for rows are:

8/216 - 3.7%.. 1.9% to 7.3%

3/179 - 1.68%. 0.61% to 4.9%

1/148 - 0.68%. 0.016% to 3.8%

2/114 - 1.75%. 0.054% to 6.3%

14/657 - 2.1%. 1.27% to 3.6%

PB666 ^yap 22:50, 21 July 2009 (UTC)

Not fair unless you include Basques and data from rhouda et al. The Count of Monte Cristo (talk) 15:55, 20 July 2009 (UTC)

I have moved the posts so they can be read properly. SOPHIAN, please take more care where you insert words on talkpages. This is not the first time you inserted right in the middle of someone else's posting. People have to be able to read this. Doesn't Basque country come under North East normally? Surely we don't need a statistic for every region in Europe.--Andrew Lancaster (talk) 17:04, 20 July 2009 (UTC)

Rhouda et al. Studied 844 Spanish people and 3 had L (0.355%) Achilli et al. Studied in addition to what you say 156 Basques and 1 had L Leaving 18 cases of L in 1657 Spanish people or 1.09% The Count of Monte Cristo (talk) 21:48, 21 July 2009 (UTC)

Draft

I have started a draft here Talk:Genetic history of Europe/ Sub-Saharan African admixture in Europe. I am just throwing some ideas out and nothing is concrete. But if anyone has some good ideas we can incorporate them into the draft. Wapondaponda (talk) 06:10, 20 July 2009 (UTC)

I fail to see why the old article had to be deleted only to start over with a new article on the topic. If the content of the old article was flawed, the standard appoach would have been just to fix it. I also fail to see the relevance of the topic as a standalone article. As in many of our genetics articles, we are mostly looking at random detail cobbled together from academic papers directly (as opposed to via a secondary or tertiary, encyclopedic source). This makes for a "better than nothing" collection of factoids, but nothing that can be used to draw any sort of conclusion. Of course there is genetic flow everywhere, even across the Sahara. It is just a matter of "more" vs. "less" admixture. Prehistoric Sub-Saharan admixture in Europe will be practically impossible to measure without (extremely difficult) recourse to ancient DNA because it is so weak that it can hardly be distinguished from Early Modern admixture.

The result of the AfD is to eliminate the article as it was principally opinion and junk science, and retain a very small bit of the article in the merge to this article, the delete and merge was part of the consensus opinion. I have no great problems with what was written with this regard and I was for the articles deletion.PB666 ^yap 22:23, 21 July 2009 (UTC)

In a nutshell, I do not see the point of such an article. --dab (𒁳) 13:20, 21 July 2009 (UTC)

A more fruitful approach imho would be an attempt to compile a discussion of the major barriers to human gene flow. The Sahara will feature very near the top in that, probably just second to the major Oceans. This would be a topic very relevant indeed to prehistoric human migration and one that I think could be made into a coherent, meaningful article. --dab (𒁳) 13:24, 21 July 2009 (UTC)

I think recent prehistoric admixture can be measured because it is still present in the European gene pool. Overtime, as the genome gets sliced and diced and people migrate back and forth, it would become impossible to discern. But presently, patterns of prehistoric African admixture are apparent. Wapondaponda (talk) 14:35, 21 July 2009 (UTC)

Luigi Luca Cavalli-Sforza

Once again I have been invited to come over and see what my fellow wikipedians are up to. Folks, y'all need to put the coffee cups down (or what ever source the caffiene is injected from) and slow down your discussion and remember the talk page guidelines.

Regarding this author - he was a prominent author back in the 60s - 80s. The basic problem is that most of the work came before the age of precise genetic methods. He used serological techniques and a whole slew of methods that are clearly out-of-fashion now. A.C. Wilson and company really introduced the age and genre of information we are now in, and much of ACs conclusions have effectively replaced Cavalli-Sforza's early conclusion, including the OoA and timing of the OoA issues. This article focuses way to much on C-Ss work, it sort of reminds me of the types of discussions that came from books in sci.anthropology.paleo in the mid 1990s. He is still somewhat active with Y chromosome interpretations but alot of the things I have seen him suggest lately are pretty much off by a factor of 50% anyway. I really do not like articles with alot of 'this famous guy' name dropping. Name dropping IMHO is a form of propoganda and excessive use violates WP NPOV guidelines.PB666 ^yap 14:20, 21 July 2009 (UTC)

I agree that CS's work is relatively dated, but it was one of the first comprehensive analyses of human genetic diversity. Yes apparently, he only used a few markers to synthesize his principal components. Since the sequencing of the whole genome, it is now possible for more detailed scientific investigations. My impression is that CS's studies have not been completely invalidated by recent studies, rather recent studies have refined much of CS's work. What is great about CS's work, is that it is fairly easy for lay people to understand, which makes it ideal for wikipedia, because wikipedia tends to have a general audience. Of course other's may argue that if it's for lay people, then it is an oversimplification, but we have to live with this dichotomy. Wapondaponda (talk) 14:29, 21 July 2009 (UTC)

The difference is much like the difference between the Bohr atom and the Heisenberg/Quantum mechanical Atom. Unfortunately one is wrong, the other is not.

Despite the simplicity of his conclusions, the approach is rather wrong. And if NPOV is to be employed why is Wilson's work not covered. Here is the basic problem, and I apologize if I seem to insult anyone here, this is not my intent. There was a first person who left Africa as such or a group, there is archaeological evidence that this might have occurred 125 kya (both from the levant, but supported by Liujiang). There are archaeological sites in India that date to about 80kya that also support this. These migrations are occurring ealier than the earliest fixation dates for the Y-chromosome, and given the 2N rule we can estimate that a TMRCA for Y chromosome is occurring and constrictive evolution that fixes it for at least 30ky after the TMRCA it places Y-chromosome in a constrictive context in Africa to 90kya which is rougly about the time people are reaching East Asia. While the mtDNA does not suggest migrations this early its confidence interval allows such early migrations. So the discussions about Y-chromosome and timings of migrations as seen in Journey of Man are basically idealizations, not reality. Either there are some mistaken assumptions with molecular clocking of the Y chromosome, or Y-chromosome underwent a post exodus selective sweep, and therefore it is an unreliable marker for early migrations anywhere. Frankly, I think exit dates which include the previous interglacial period (up to 131 kya). In addition, the dates archaeology generally agrees upon is that humans had reached Eastern Europe by 40kya, and that by 34 kya there was occupation within central Europe, by 30 kya they had reached Iberian and were affecting the tool industries of the region (therefore the dates in the article are not correct). There is molecular evidence that there was early geneflow from Africa, and although there is little archeaological support, at least by the epipaleolithic most of the archaeological evidence comes from coastal regions of iberia, suggesting a shift from open range hunting, which could indicate the dominance of one culture during the glacial period which favored eastern migrants but a shift to coastal foraging which favor migrants from the south. There appears to be a meshing of African and Eastern DNA in Iberia.

Here is my basic problem, migrations and the alleles or haplotypes that these migrations introduce are not general or diffuse, particularly when one talks about crossing bodies of waters. Molecular studies now clearly indicate that many founding or settlement events are quite discrete, both in size and within a temporal context. HLA studies of Iberians and Europeans indicate quite clearly that discrete contributions from Africa have occurred in the past. The problem is not that these discrete events occurred, the problem is how do we create a context which is correct (this was my problem with the Subsaharan page). A recent study of Eastern Islanders for example showed not native American mtDNA or Y chromosomes, but 2 individuals had HLA that came from South America, reproting the fallibility of both analysis. When did this admixture occur, before Europeans or after Easter Island became part of Chile. The result is not unexpected because HLA is under heterozygous selection and mtDNA and Y are haploids with tendencies to undergo fixation. Effectively HLA preserves about 3 times the added diversity of mtDNA and Y combined in real time.

There is a problem when using mtDNA and Y is that the fix rapidly often leaving the impression that an event occurred once and from a single source(and yet mtDNA will give a date of say 60 kya and Y for the same date 20kya, and the HLA studies will indicate that both dates and other dates might be correct). Scientist compound the problem with what is statistically known as B-error (type-II error), that means not to collect enough data to show a significant separation when a significant separation exists (a major problem I have with C-Ss work). Consequently, the mtDNA people claim there was a single event for exodus, when in-fact, there were multiple events. This is pertinent to European claims because certain mtDNA that appear to have arrived into Iberia are either contemporary to this migration (60 to 130 kya) or different. The archaeology makes no claim that AMHs were in Iberia before 35 kya which leaves 'silent' period of 25 to 70 kya. It is imperative to look at the potential flaws of every claim. So that many discrete events may occur, we often don't have enough data, the proper tools to 'parse' that data objectively, or we don't have a means of properly calibrating the molecular clocks to time the events (For example, these new Mitogenomic clocks have a huge problem with selection at coding sites that corrupts the clock, removal of these sites makes a less precise clock that is more accurate).

• Every claim should be critiqued, the weakest claims, no matter how historic, popular should be pruned from the article. I can give an example of this, the Topper archaeo-philes are presenting now that humans came from Europe to the New World (preclovis) and this is gaining popularity. THere have been claims of sites in S America that Africans came across the atlantic and settled 50 to 60 kya. Even some claims that Homo erectus or Neandertals made it first to the new world. There is no apparent molecular evidence from mtDNA, HLA, or Y supporting these beliefs. In addition these claims are based on tools that are not obviously of human origin.
• Speculative genetic claims, and I know most of them, really cannot be founded in archaeology and the molecular clocking makes some rather large assumptions. It is very difficult to assign migration to a specific paleoanthropological context, and even if one can, the variance on these clockings are -50/+75% about a relative range.
• Equity in speculative claims, if two claims are equally speculative, don't add more speculative claims, instead cite the reasons for why a speculative claim should be removed here, bring in the most recent literature in support of its speculation and remove it.
• Molecular anthropology is what it is. It cannot be dressed up to be made more than it is, the tools we have are frequently abused to create speculation. Many papers from the 80s, 90s and even some recent papers make conclusions that cannot be supported by their data or statistics, many of these have proven to be incorrect. What happened to MREH? What became of Ayala's "Myth about Eve"? The mhc16 study? The recent AfD highlighted the questionable conclusion of an individual who works on HLA, and the situation between Africa and the Greeks. For the mtDNA folks here, be aware the from 2000 to 2004 there were a number of papers published with a fantastice number of sequencing errors, particularly papers dealing with Europeans [Search Bandelt in pubmed]. From every perspective there are errors in the data set.

mtDNA has a number of supervariable sites such as 16129 and 16183-16192 that are not useful. 16183-16192 and some other sites have been noted to change from different samples of the same individual. The mtDNA genomic clocking on rarely mutated sites...I simply do not trust, these sites may be variably selective and disappear as soon as people migrate or a culture shift occurs. As stated above there is a rather large history of sequencing errors. Historic comparisons are based on assumptions between HVR mtDNAs and genomic mtDNAs may introduce inaccuracies.

Y chromosome. It is good to see a refinement of Y chromosomal SNP typing, the STRs had been used in the past and these often betray ancestry. Some older schemes of ancestral typing may not be comparable to the most recent schemes. Beware studies that rely on molecular clocking of Y chromosome, there are assumption errors in the clocking that cannot yet be explained. Y-chromosome may be heavily influenced by cultural selection and fixation could be much more rapid in certain instances that is currently believed. The 2N rules are based on variable selection, if selection is positive for any length of time the 2n rule cannot be applied.[See Kimura 1952]

HLA. HLA suffers from similar historic problems. Early studies typed A9 for instance that then became A23 and A24 and then evolved to A*23 and A*24 which then resolved into A*2301, A*2302, A*2303, ...,A*2402, A*2403, ..... and one has to be very careful when conclusions are made based on old typing technology or typing kits. Cross references need to carefully resolved, for instance why A24 can be called A*2402. There is another problem with HLA, and that is haplotype frequencies are frequently reported as 1 or 2 occurances. The relative frequencies that can give rise that can give rise to 1 to 5 observations have a wide relative variance. This fact also needs to be applied to frequencies based on Y and mtDNA. Let say A paper finds the haplotype A*3108-B*5112 and this is deemed to be of native american origin, how can we be sure unless all A31-B51 that exists in Asia has had the same degree of typing.

• Be critical of research that might be speculative or synthesis based on limited or partial evidence, with comparisons have the proper background work on all possible contributing populations been carefully done. How will the results reflect reality if new mutations in a sequence are found, or if another population it typed with more individuals and thus showing more haplotypes that give it better statistical power.

[Sorry to junk up this page with even more writings]PB666 ^yap 17:54, 21 July 2009 (UTC)

North Africa

This section needs some clarification. North African admixture in this case, should strictly speaking consist of E-M81 and U6. These are the only clades that are specific only to contemporary North African populations. E-M78 has a presence in Sub-Saharan Africa. In addition, and we know that the expansion of E-M35 started in Sub-Saharan Africa, proceeded to North Africa, the levant and then Europe. Currently the initial expansion from Sub-Saharan Africa has been ommitted, and an arbitrary region, North Africa has been selected as the source population. So even E-M81, does also represent the expansion from SSA as well, but its may or may not have involved contemporary North Africans. Wapondaponda (talk) 16:41, 21 July 2009 (UTC)

Pictures of children

A user added a series of photos of children. I don't see what relevance they have in a genetics article, so I have deleted them. Wapondaponda (talk) 18:35, 21 July 2009 (UTC)

Genetics section

I am going to go through the genetics section presenting paragraphs 1 by 1 point out problems with each paragraph.

One of the first scholars to perform genetic studies was Luigi Luca Cavalli-Sforza. He used classical genetic markers to analyse DNA by proxy. [OK] This method studies differences in the frequencies of particular allelic traits, namely polymorphisms from proteins found within human blood (such as the ABO blood groups, Rhesus blood antigens, HLA loci, immunoglobulins, G-6-P-D isoenzymes, amongst others). [Too much information, the techniques is not that good] Subsequently his team calculated genetic distance Subsequyently the genetic distance between populations was calculated, based on the principle that two populations that share similar frequencies of a trait are more closely related than populations that have more divergent frequencies of the trait. and phylogenetic trees were constructed that showed genetic distances diagrammatically.[Provide a reference to the paper(s) or books] His team also performed principal component analyses, which is good at analysing multivariate data with minimal loss of information. The information that is lost can be partly restored by generating a second principal component, and so on.^[1] In turn, the information from each individual principal component (PC) can be presented graphically in synthetic maps. These maps show peaks and troughs, which represent populations whose gene frequencies take extreme values compared to others in the studied area.^[2] [Not appropriate] Peaks and troughs usually, but not necessarily, connected by smooth gradients, called clines. Genetic clines can be generated in several ways: including adaptation to environment (natural selection), continuous gene flow between two initially different populations, or a demographic expansion into a scarcely populated environment with little initial admixture with pre-existing populations.^[3] Cavalli-Sforza connected these gradients with postulated pre-historic population movements based on known archaeological and linguistic theories. However, given that the time depths of such patterns are not known, “associating them with particular demographic events is usually speculative”.^[4] [This section is about techniques, where are the results?]

Rewrite.

Luigi Luca Cavalli-Sforza performed studies on classical genetic markers to assess the geographic relationships between peoples in order to analyse DNA by proxy. Subsequently, the genetic distances between populations were calculated and phylogenetic trees were constructed that illustrated the genetic distances. These studies indicated relationships between geographically populations with modes and anti-modes connected generally by smooth gradients called clines.

This is all that is encyclopedic with regard to this page, the remainder of information belongs on a techniques page as it pertains to typing and phylogenetic techniques in general. For passages the need special emphasis please use footnotes.PB666 ^yap 19:09, 21 July 2009 (UTC)

Studies using direct DNA analysis are now abundant use utilize mitochondrial DNA (mtDNA), the non-recombining portion of the Y chromosome (NRY) or autosomal DNA. MtDNA and NRY DNA share some similar features which have made them particularly useful in molecular anthropology. These properties include the direct, unaltered inheritance of mtDNA and NRY DNA from mother to offspring, and father to son, respectively, without the 'scrambling' effects of genetic recombination [There are studies that indicate some genetic recombination occurs with mtDNA, emphasized by a recent study which suggest forced recombination of mtDNA goes undetected by many statistical techniques for detection of recombination]. We also presume that these genetic loci are not affected by natural selection [other forms of selection such as cultural selection for alpha males or by surname may also effective passage, also selection of those who bring or make technologies], and that the major process responsible for changes in base pairs has been mutation (which can [be] calculated).[5] [There is no doubt that selection is acting upon mtDNA, inaddition selection is acting upon certain coding sites, at least in humans passage of mtDNA cannot be considered neutral, see Gonder et al 2007] The smaller effective population size of the NRY and mtDNA enhances the consequences of drift and founder effect relative to the autosomes, making NRY and mtDNA variation a potentially sensitive index of population composition.[4][6][7] [There is a founder bias for mtDNA and a migration bias for Y chromosome. If A is a population about twice the size of B then Ya will exhibit a fixation curve about the same size as Xb, despite the same ploidy, the effective size of the male population is about half that of X.] However, these biologically plausible assumptions are nevertheless not concrete. For example, Rosser suggests that climactic conditions may affect the fertility of certain lineages.[4] [What about migration and selection on mtDNA? From tropics to glacial SW asia, to tropical India, back to glacial temperate zone, back to austronesia, up the pacific rim, into the Arctic and down to South America, ever looked at the number of nonsynomous coding region mutations in South Americans?] Even more problematic, however, is the underlying mutation rate used by the geneticists. They often use different mutation rates, and therefore studies are frequently arriving at vastly different conclusions.[4] Moroever, NRY and mtDNA may be so susceptible to drift that some ancient patterns may have become obscured over time. [If mtDNA has a founder bias and Y has a migration bias, and both undergo fixation prior to observation, can intermediate admixture events be observed?] Another implicit assumption is that population genealogies are approximated by allele genealogies. Barbujani points out that this only holds if population groups develop from a genetically monomorphic set of founders. However, Barbujani argues that there is no reason to believe that Europe was colonized by monomorphic populations. This would result in an overestimation of haplogroup age, thus falsely extending the demographic history of Europe into the Late Paleolithic rather than the Neolithic era.[8] (See also Genetic drift, Founder effect, Population bottleneck.)

Here the question is do people who understand the complexity of human molecular anthropology produce alot of speculation or are they simply sitting back and waiting for better data to come that produces a non-speculative result. And if we are offering up speculation here what is its future value, here.PB666 ^yap 19:46, 21 July 2009 (UTC)

Whereas Y-DNA and mtDNA haplogroups represent but a small component of a person’s DNA pool, autosomal DNA has the advantage of containing hundreds and thousands of examinable genetic loci, thus giving a more complete picture of genetic composition (eg see Seldin). However, descent relationships can only to be determined on a statistical basis because autosomal DNA undergoes recombination and is liable to the process of natural selection.[mtDNA undergoes natural selection, Y chromosome may have issues of its own, why the distinction?]

Genetic studies operate on numerous assumptions and suffer from usual methodological limitations such as selection bias and confounding. Furthermore, no matter how accurate the methodology, conclusions derived from such studies are ultimately compiled on the basis of how the author envisages their data fits with established archaeological or linguistic theories.[Well of course, you got a reference on this?]

How does all of this pertain to the main? Is it a red flag on a bull's tail.PB666 ^yap 19:42, 21 July 2009 (UTC)

Backward emphasis

Its interesting reading this article that the emphasis on genetics is almost the opposite of the genetic reliability of the markers used. S-Cs work is generally the least reliable, as it uses structure that are not discrete measures of molecular genetics, the Y chromosome which has all sorts of problem is treated as secondary importance, and the mtDNA which probably best represents the process gets a paragraph. Tishkoff's CD4 intron study is not mentioned at all, this was the first study showing some more recent african contribution at the molecular genetic level. HLA studies are not mentioned at all. There is way too much emphasis on old studies proxy methods that can have multiple interpretations, some of the conclusions fly against some of the more recent conclusions based on mtDNA and can be confirmed by HLA.PB666 ^yap 19:55, 21 July 2009 (UTC)

Editors showing their true colors

Now that we're "sharing space" with another type of admixture in Europeans, we can bear witness to the agenda-driven double standard that's applied by certain editors here (namely Wapondaponda and Andrew Lancaster). Notice that neither one of them has any problem whatsoever with the Central/East Asian admixture section, even though it's constructed identically to the Sub-Saharan African admixture section. They haven't laid so much as a finger on it, and it barely even registers on their radar. There have been no "citation needed" links added to it, no concern expressed about neutrality, no questioning the definition of "East/Central Asian admixture", no attempts to include R1a or R1b (whose ancestors, R and P, originated in Central/East Asia, just like the ancestors of E-M78, E-V13 and E-M81 originated in East Africa), no insistence on qualifiers regarding "older connections" or populations not necessarily being "separate entities", no nitpicky rewrites and deletions of material without cause, and no petitions to have the entire section removed altogether. Only the Sub-Saharan African admixture section is subjected to that kind of scrutiny and that kind of thinly-veiled OR and POV-pushing. I wonder why that is. It couldn't possibly have anything to do with Afrocentrism, could it? Perish the thought. ---- Small Victory (talk) 13:51, 21 July 2009 (UTC)

I don't think one would consider Andrew an Afrocentrist. Wapondaponda (talk) 13:57, 21 July 2009 (UTC)

But one would sure consider you an Afrocentrist (which you don't even attempt to deny). And Andrew is turning into your clone. ---- Small Victory (talk) 12:06, 22 July 2009 (UTC)

There are talk page guidelines. Please do not insult people in this manner. Talk pages are for the improvement of the main page, not for insulting people. Secondarily Andrew seems to have a pretty good handle on the literature, ergo if he sees contribution from Africa, it probably indicates he has information that supports his belief.PB666 ^yap 15:21, 23 July 2009 (UTC)

I didn't insult anyone. I simply criticized other editors' approaches, just as Wapondaponda did to me below. Funny how you have no problem with that. ---- Small Victory (talk) 12:49, 24 July 2009 (UTC)

I have no idea what the above means, it is argumentative, a rant and should be refactored. Talk pages are for the improvement of the article, they are not a forum, a soapbox, your psychiatrist, etc.PB666 ^yap 13:59, 21 July 2009 (UTC)

If you have no idea what it means, then don't make assumptions about what it is. I assure you that it's related to the quality of the article, and its implications are perfectly clear, which is why the response has been so underwhelming. ---- Small Victory (talk) 12:06, 22 July 2009 (UTC)

Insults have nothing to do with improving the quality of the Article. I am going to say this same thing here that I said on the E1b1b page. The argumentative and non-cooperative attitude of the editors on the main page have seriously diminished the readability of the page. By creating a combative environment what you have done is created a contorted almost legalistic text which is not of benefit to the general public. The idea that 'my opinion is right and everyone else is wrong, I don't care what author X, Y and Z say' only results in diatribe here and a reflection of diatribe on the main. This is an encyclopedia, it is designed for people with an eight grade reading skill and up, it is not a place where we hammer out which set of authors have their head screwed on strait.PB666 ^yap 15:27, 23 July 2009 (UTC)

I agree with Pdeitiker. From now I will avoid entering into discussions with Small Victory, because they always seem to deteriorate into personal attacks. Similar complaints are seen here User_talk:Small_Victory#Tone_of_discussion Wapondaponda (talk) 17:59, 23 July 2009 (UTC)

Small Victory, I have edited in most sections in this article over time and also given a lot of further comments on this talkpage. When a new section arrives, people watching the article do tend to give that new section a bit more attention. The sub saharan had fundamental technical problems when it was in the deleted article, and I think it is obvious that we should not be keeping anything of that nature. This does not mean that I am a "clone" of all the other editors who agree with me on this basic point. There is certainly no pattern of agreement between me and Wapondaponda concerning anything much. I think your posting above is unjustified and silly. I believe you should explain your thinking in neutral terms, and focus purely on the article and wat should be in it. If I have done something wrong concerning this article, explain it. This constant obsession with perceived Afrocentrism that some editors have is really a terrible distraction to normal work on the quality of Wikipedia. There is no point being obsessed with people's POV. Everyone has a POV, and this is not a problem as long as they follow the normal standards.--Andrew Lancaster (talk) 01:52, 24 July 2009 (UTC)

Well, Andrew, if you weren't so singularly and obsessively focused on the Sub-Saharan African admixture section, you might have noticed (or cared) that the Central/East Asian admixture section is also new. I gave it a major overhaul at the same time that I added the refashioned SSA material. In fact, the two sections are virtually identical in construction and in the kinds of markers they use, which is appropriate since they're reporting on similar phenomena. Yet in your mind, one has "fundamental technical problems" while the other doesn't. Care to explain that? Oh wait, you can't without admitting bias. ---- Small Victory (talk) 12:43, 24 July 2009 (UTC)

References for trans-Mediterranean African genetic contribution

General

• Genes peoples languages CS for genetic distances
• Bowcock; et al. (1991). "Drift, admixture, and selection in human evolution: A study with DNA polymorphisms". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Halder; et al. (2008). "A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Auton; et al. (2009). "Global distribution of genomic diversity underscores rich complex history of continental human populations". {{cite journal}}: Cite has empty unknown parameter: |1= (help); Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Reich (2008). "Principal component analysis of genetic data". {{cite journal}}: Cite journal requires |journal= (help)
• Shimada MK, Panchapakesan K, Tishkoff SA, Nato AQ, Hey J (2007). "Divergent haplotypes and human history as revealed in a worldwide survey of X-linked DNA sequence variation". Mol. Biol. Evol. 24 (3): 687–98. doi:10.1093/molbev/msl196. PMID 17175528. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Tishkoff SA, Dietzsch E, Speed W; et al. (1996). "Global patterns of linkage disequilibrium at the CD4 locus and modern human origins". Science. 271 (5254): 1380–7. PMID 8596909. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Frudakis, Tony (2007). "Apportionment of Autosomal Diversity with Continental Markers". Molecular photofitting. p. 326. ISBN 0120884925. {{cite book}}: External link in |chapterurl= (help); Unknown parameter |chapterurl= ignored (|chapter-url= suggested) (help)

HLA

• Middleton D, Menchaca L, Rood H, Komerofsky R (2003). "New allele frequency database: http://www.allelefrequencies.net". Tissue Antigens. 61 (5): 403–7. PMID 12753660. {{cite journal}}: External link in |title= (help)CS1 maint: multiple names: authors list (link)

Iberia

• Spínola H, Middleton D, Brehm A (2005). "HLA genes in Portugal inferred from sequence-based typing: in the crossroad between Europe and Africa". Tissue Antigens. 66 (1): 26–36. doi:10.1111/j.1399-0039.2005.00430.x. PMID 15982254. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Pacho A, Mancebo E, del Rey MJ; et al. (2004). "HLA haplotypes associated with hemochromatosis mutations in the Spanish population". BMC Med. Genet. 5: 25. doi:10.1186/1471-2350-5-25. PMC 529258. PMID 15498100. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link) [A29-B44 is from West Africa]
• Pérez-Miranda AM, Alfonso-Sánchez MA, Peña JA, Calderón R (2003). "HLA-DQA1 polymorphism in autochthonous Basques from Navarre (Spain): genetic position within European and Mediterranean scopes". Tissue Antigens. 61 (6): 465–74. PMID 12823770. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Sanchez-Velasco P, Gomez-Casado E, Martinez-Laso J; et al. (2003). "HLA alleles in isolated populations from North Spain: origin of the Basques and the ancient Iberians". Tissue Antigens. 61 (5): 384–92. PMID 12753657. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Muro M, Marín L, Torío A; et al. (2001). "HLA polymorphism in the Murcia population (Spain): in the cradle of the archaeologic Iberians". Hum. Immunol. 62 (9): 910–21. PMID 11543893. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Synek V, Reuben JR, Du Boulay GH (1976). "Comparing Evans' index and computerized axial tomography in assessing relationship of ventricular size to brain size". Neurology. 26 (3): 231–3. PMID 1082559. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Grimaldi MC, Crouau-Roy B, Amoros JP; et al. (2001). "West Mediterranean islands (Corsica, Balearic islands, Sardinia) and the Basque population: contribution of HLA class I molecular markers to their evolutionary history". Tissue Antigens. 58 (5): 281–92. PMID 11844138. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

Central Mediterranean

• Grimaldi MC, Crouau-Roy B, Contu L, Amoros JP (2002). "Molecular variation of HLA class I genes in the Corsican population: approach to its origin". Eur. J. Immunogenet. 29 (2): 101–7. PMID 11918634. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Lampis R, Morelli L, De Virgiliis S, Congia M, Cucca F (2000). "The distribution of HLA class II haplotypes reveals that the Sardinian population is genetically differentiated from the other Caucasian populations". Tissue Antigens. 56 (6): 515–21. PMID 11169241. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Contu L, Arras M, Carcassi C, La Nasa G, Mulargia M (1992). "HLA structure of the Sardinian population: a haplotype study of 551 families". Tissue Antigens. 40 (4): 165–74. PMID 1471143. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

Eastern Mediterranean

• Arnaiz-Villena A, Dimitroski K, Pacho A; et al. (2001). "HLA genes in Macedonians and the sub-Saharan origin of the Greeks". Tissue Antigens. 57 (2): 118–27. PMID 11260506. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Petlichkovski A, Efinska-Mladenovska O, Trajkov D, Arsov T, Strezova A, Spiroski M (2004). "High-resolution typing of HLA-DRB1 locus in the Macedonian population". Tissue Antigens. 64 (4): 486–91. doi:10.1111/j.1399-0039.2004.00273.x. PMID 15361127. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• For Romanian HLA as with many recent studies the work of Constantinescu I is presented directly to www.allelefrequencies.net however Reed E, Ho E, Lupu F; et al. (1992). "Polymorphism of HLA in the Romanian population". Tissue Antigens. 39 (1): 8–13. PMID 1542880. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) but the techniques of 1992 were picked up many SSA alleles as nulls.
• Ivanova M, Rozemuller E, Tyufekchiev N, Michailova A, Tilanus M, Naumova E (2002). "HLA polymorphism in Bulgarians defined by high-resolution typing methods in comparison with other populations". Tissue Antigens. 60 (6): 496–504. PMID 12542743. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Arnaiz-Villena A, Iliakis P, González-Hevilla M; et al. (1999). "The origin of Cretan populations as determined by characterization of HLA alleles". Tissue Antigens. 53 (3): 213–26. PMID 10203014. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Uyar FA, Dorak MT, Saruhan-Direskeneli G (2004). "Human leukocyte antigen-A, -B and -C alleles and human leukocyte antigen haplotypes in Turkey: relationship to other populations". Tissue Antigens. 64 (2): 180–7. doi:10.1111/j.1399-0039.2004.00258.x. PMID 15245373. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Arnaiz-Villena A, Karin M, Bendikuze N; et al. (2001). "HLA alleles and haplotypes in the Turkish population: relatedness to Kurds, Armenians and other Mediterraneans". Tissue Antigens. 57 (4): 308–17. PMID 11380939. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

North Africa

• ReviewPiancatelli D, Canossi A, Aureli A; et al. (2004). "Human leukocyte antigen-A, -B, and -Cw polymorphism in a Berber population from North Morocco using sequence-based typing". Tissue Antigens. 63 (2): 158–72. PMID 14705987. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Choukri F, Chakib A, Himmich H, Raissi H, Caillat-Zucman S (2002). "HLA class I polymorphism in a Moroccan population from Casablanca". Eur. J. Immunogenet. 29 (3): 205–11. PMID 12047355. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Arnaiz-Villena A, Benmamar D, Alvarez M; et al. (1995). "HLA allele and haplotype frequencies in Algerians. Relatedness to Spaniards and Basques". Hum. Immunol. 43 (4): 259–68. PMID 7499173. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Hajjej A, Kâabi H, Sellami MH; et al. (2006). "The contribution of HLA class I and II alleles and haplotypes to the investigation of the evolutionary history of Tunisians". Tissue Antigens. 68 (2): 153–62. doi:10.1111/j.1399-0039.2006.00622.x. PMID 16866885. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Ayed K, Ayed-Jendoubi S, Sfar I, Labonne MP, Gebuhrer L (2004). "HLA class-I and HLA class-II phenotypic, gene and haplotypic frequencies in Tunisians by using molecular typing data". Tissue Antigens. 64 (4): 520–32. doi:10.1111/j.1399-0039.2004.00313.x. PMID 15361135. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Hajjej A, Hmida S, Kaabi H; et al. (2006). "HLA genes in Southern Tunisians (Ghannouch area) and their relationship with other Mediterraneans". Eur J Med Genet. 49 (1): 43–56. doi:10.1016/j.ejmg.2005.01.001. PMID 16473309. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)

MtDNA

• Gonzalez; et al. (2003). "Mitochondrial DNA Affinities at the Atlantic Fringe of Europe" (PDF). {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Malyarchuk; et al. (2008). "Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Malyarchuk; et al. (2005). "African DNA Lineages in the Mitochondrial Gene Pool of Europeans". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Pereira L, Prata MJ, Amorim A (2000). "Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation". Ann. Hum. Genet. 64 (Pt 6): 491–506. PMID 11281213. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• McEvoy B, Richards M, Forster P, Bradley DG (2004). "The Longue Durée of genetic ancestry: multiple genetic marker systems and Celtic origins on the Atlantic facade of Europe". Am. J. Hum. Genet. 75 (4): 693–702. doi:10.1086/424697. PMC 1182057. PMID 15309688. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Achilli A, Rengo C, Magri C; et al. (2004). "The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool". Am. J. Hum. Genet. 75 (5): 910–8. doi:10.1086/425590. PMC 1182122. PMID 15382008. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

Y chromosome

• King (2007). "Africans in Yorkshire? - the deepest-rooting clade of the Y phylogeny within an English genealogy". {{cite journal}}: Cite journal requires |journal= (help)
• Cruciani; et al. (2004). "Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out Of Africa". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Underhill; et al. (2001). "The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations" (PDF). {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Lancaster, Andrew (2009), "Y Haplogroups, Archaeological Cultures and Language Families: a Review of the Multidisciplinary Comparisons using the case of E-M35" (PDF), Journal of Genetic Genealogy, 5 (1)

Wapondaponda (talk) 00:29, 22 July 2009 (UTC)

Backflow

• Cherni L, Fernandes V, Pereira JB; et al. (2009). "Post-last glacial maximum expansion from Iberia to North Africa revealed by fine characterization of mtDNA H haplogroup in Tunisia". Am. J. Phys. Anthropol. 139 (2): 253–60. doi:10.1002/ajpa.20979. PMID 19090581. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
• Gonzalez; et al. (2007). "Mitochondrial lineage M1 traces an early human backflow to Africa". {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)
• Ennafaa H, Cabrera VM, Abu-Amero KK; et al. (2009). "Mitochondrial DNA haplogroup H structure in North Africa". BMC Genet. 10: 8. doi:10.1186/1471-2156-10-8. PMC 2657161. PMID 19243582. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)

Comments

I have reorganized your list and added to it.PB666 ^yap 13:35, 22 July 2009 (UTC) I recommend a further reorganization of the top section.

Great. I have also been thinking about how best to organize the material. We have different 3 measures, Y, mtdna and autosomal and at least two distinct periods of gene flow(recent and prehistoric). We also have two points of entry, Iberia and the Mediterranean. Any suggestions.Wapondaponda (talk) 17:27, 22 July 2009 (UTC)

I will be adding references for HLA. I am working on a private page at the moment that drafts the tables from allelefrequencies.net. these Tables will clarify that of A. A-V that is credible and that which is 'not so credible' as a reference his work is referencable as long as more recent work in the field upholds his findings. The best evidence IMHO is from the HLA, far more work has been done with HLA than Y and mtDNA and consequently it is more sensitive, but there are problems.PB666 ^yap 18:15, 22 July 2009 (UTC) BTW, the reason I cite two papers dealing the the Franco-Iberian refuge is that this can be thought of as a conveyor belt, if African alleles make it to the region prior to the end of the YD then they can be conveyed into Europe. What that means is that those haplotypes that make it to Iberia are filtered upward by selection and drift, but once they get into the 'feed' area the conveyor belt can feed them Northward. Some of the haplotypes we see in Europe are from ancient migrations from NW Africa; however minor haplotypes that have undergone extensive recombination overtime are difficult to recognize. So that as the feild progresses and we have more expansive and allele and haplotype sensitive studies, it becomes easier to resolve these. This is the essence of the critique of C-S because his studies are more or less like a far-sighted old man look for fleas on a dog. As for suggestions, look at the box on the top of the page.PB666 ^yap 18:22, 22 July 2009 (UTC)

Malyarchuk et al seem to be in agreement with the Franco-Iberian refuge theory as the conveyor belt of L lineages into Eastern Europe. Wapondaponda (talk) 20:19, 22 July 2009 (UTC)

BTW, why do we want to retain this name for the section SubSaharan Africa. Although there is some trace evidence that some of these haplotypes originated in Subsaharan Africa most of the composite evidence suggests that the Transmediterrean gene flow was mediated by North African components. The only evidence I have for any Subsaharan migration into Eurasia, directly was via the horn into Arabia, and possibly from eastern Sudan, Erithrea or Ethiopia toward the Indus Valley. Having gone over a considerable number of markers it looks as if North Africa (Tunis) was a source of African markers in Portugal, that other sites contributed to the make-up of Sardinia, and there was NW source that contributed to Iberia, A nile source that contributed to the Aegean and Black Sea region. Should this whole line of thought be treated under a North African contribution section?PB666 ^yap 02:21, 23 July 2009 (UTC)

I agree that all gene flow from SSA to Europe had to pass through North Africa. However there seems to be a notion that North African gene flow is completely distinct from Sub-Saharan gene flow which I believe is an incomplete oversimplification. The very notion of Sub-Saharan Africa itself is not realistic in those prehistoric times when the Sahara desert wasn't a desert but a savanna.During the wet phases, people from SSA would expand northwards and occupy much of savannas of the Sahara. Gonzalez et. al. 2003 suggest a neolithic expansion of Subsaharan L lineages into the Sahara as the possible source population of Iberian L. I was thinking of renaming the article just African admixture so that we don't have to limit ourselves to direct SSA admixture. Wapondaponda (talk) 05:33, 23 July 2009 (UTC)

There is a difference between actually what is in the data and what people say in discussions. The basic problem here for you is that the Egyptian and Sudanese peoples are poorly analyzes. I have only recently seen Sudanese HLA show up in the HLA literature. And the Egyptian resource that I have, still useful, is very old was not used by A A-V in his analysis of the Greeks. According to that study of Egyptians some of the nodal haplotypes may have come from ancient Egypt as with the modal haplotypes within the Sardinians. The www.allelefrequencies.net (see HLA references) database has the most recent allele typing including many new papers from Africa. In addition the format has been reorganized so that one can search haplotypes.

• The obvious connections at the moment are between Tunisia and Portugal (I have an HLA reference for this)
• There is a connection between the Berbers and Iberia. However I have to offer a stong word of caution on this connection, the recent work indicates backflow from Iberia to North Africa, the paleoclimatologist are saying that during the LGM, 24 to 18 kya, conditions in Iberia were severe, and the finding of Neanderthals on Gibraltar, the last N find, is an indication of the severity of the climate. This back flow from Iberia carries European alleles backward, one author claims that A2-B7-DR15 as evidence of gene flow into Iberia, the reverse is probably the case, A2-B7-DR15 probably recombined in Iberia and moved backwards into NW Africa. Other genes moved the other direction, either prior to the LGM or immediately after the LGM as climate improved in Iberia. Another haplotype A24-B8-DR3-DQ2.5 could be the progenitor to A1-B8-DR3-DQ2.5 however A24 did not come from W.Africa. A24 is a gene convertant of A23 which was a minor allele in East Africa and expanded asymmetrically into SE Asia, its presence in Iberia may be the consequence of gene conversion between A24-B35 and A1-B8-DR3-DQ2.5 and the A24-B8 haplotype is found in Tunisia and Morocco. Therefore we have a problem of deducing direction.
• With regard to what A A-V has claimed, I found 2 additional papers (different authors) that support his claim, and a paper that makes no mention on the association but provides even better support. The Subsaharan origin of Attica Greeks falls in the backdrop of extremely poor typing in Muslim North Africa (particularly Egypt and proximal regions) consequently it is drawing a conclusion from a partial vacuum of information. When good studies have been done, such as in Tunisia and Morocco we find the Subsaharan alleles that are found in Europe are often found at levels intermediate between the European levels and the Africa levels. For example A*41 in Tunisia (Cited in the literature). We need to consider this with regard to N.Africa absence of evidence is not evidence of absence and apply this summarily to any N. Africa population that has not been genetically typed.
• With regard to ancient genetic contributions, while there is a tendency for allele associations to decline from south to north in some instances because of the way people expanded after the LGM, it is simply not possible to discriminate this. The evidence at hand is that DR3-DQ2 and DR7-DQ2 which are nodal in West Africa (DR7-DQ2 is also high in the mid east) are very high along the Atlantic coast. A29-Cw16-B44-DR&-DQ2 is but one component of putative west African origin, there are other DR7-DQ2 that could have easily come from the middle East were DR7-DQ2 is high. Because of the nature of diffusion/migration and because of the cyclical occupation of Europe it is very difficult to define when exact alleles arrived, and with back migration the picture becomes muddled even more. I would argue that the same logical constraint also applies to mtDNA and Y chromosome studies.
• Let us take an example of genetic contributions. According to archaeology Sardinia was initially occupied ~9000 years ago, I would contend it probably occurred earlier. By HLA we have one haplotype in strong linkage disequilibrium indicating a founder affect, this haplotype A30-cw5-B18-DR3-DQ2 (I credit this haplotype as of Africa origin and the consequence of a founder affect, probably N or NE Africa) occurs in 15% of Sardinians and is the highest frequency 4 locus haplotype in Europe. A second haplotype A2-Cw7-B58-DR16 is believed to also be of African origin. So that in this instance we have the blazing set of markers in Sardinia, but what about Europe. 13,000 Germans (26,000 chromosomes serotyped) typed A30-B18-DR3 = 0.16% IOW a 100 fold decline in haplotype frequency over a distance ~1000 kilometers (800 miles from Sardinia to Berlin -other frequencies- Basque 8.1, Spanish = 2.6%, French = <0.6%, Italian = 0.4%). This contrasts with A3-B7-DR15, a classic example of W.Eurasian marker is found over 1000s of miles east west. A2-B58-DR16 is not found in the German (chromosomes typed = 26000). So that we have evidence here just how quickly this recent African contribution drops into Europe. I want to emphasize the point, the evidence we have of genetic contributions is not (wide - as in a hand waving motion), it is rather local, punctuated, or from a point to a point. This nature of the evidence needs to be conveyed in the description. And to reiterate the point, from what place did a people contribute these Subsaharan influences to the Greeks? Consider if the haplotype is in the Basque and the proto-Basque were the Proto-Atlantic Europeans why isn't this hap more frequent now in other Europeans? (Answer) because the Basque are an admixture of more recent migrations and their previous genetic makeup. A few areas of Europe have been receptive to recent African contribution in the Mesolithic/Neolithic periods, but most areas of Europe have not. In contrast France has been heavily influenced by migrations from Italy, Greece, Anatolia, and Middle East and these areas. When we see markers of recent Africa input, it is difficult in instances were there is a trace, whether this influence is local (Basco-Sardinian), via the Eastern Mediterranean or direct. Occam's razor suggests often the simplest answer is the best answer, in which case these alleles appear to be carried with measurable gene flow from Ionian, Aegean, Northeastern Mediterranean regions. [And HLA bring forth a greater body of literature, a large set of genetic diversity, and considerable number of people typed (between serotypes and genotypes almost a million chromosomes typed in the region), ergo the problem is not data, its how best to interpret the data, all the typing studies in Europe aren't worth much if N. Africa is poorly typed].

Something to be considered as you read the conclusions of these HLA papers.PB666 ^yap 13:54, 23 July 2009 (UTC)

Refining the analysis of Y-chromosomal diversity in Alentejo (Portugal), This particular article failed to detect Y lineages of "Sub-Saharan African descent", yet they report significant frequencies of (HBB*S) and glucose-6-phosphatedehydrogenase (G6PD) deficiency, which are known to be of Sub-Saharan descent. The alternatives could be that these alleles entered through females, or very simply that "North African lineages" of e3b, that were detected, are basically "Sub-Saharan". Wapondaponda (talk) 19:19, 25 July 2009 (UTC)

STRUCTURE

SOPHIAN has been blocked for a week for several recent infractions, including edit warring on this article.

Small Victory writes in the article, and I quote

Genome-wide autosomal DNA analyses using the STRUCTURE clustering program, which is designed to accurately detect and quantify admixture,[93] show equally negligible levels of sub-Saharan African admixture in all Europeans,[94] including Iberians;

I challenge him to provide a direct quote from the reference cited, [8] to verify this claim. This is an official wikipedia policy per WP:PROVEIT which states

The burden of evidence lies with the editor who adds or restores material. All quotations and any material challenged or likely to be challenged must be attributed to a reliable, published source using an inline citation. The source cited must unambiguously support the information as it is presented in the article. The source should be cited clearly and precisely to enable readers to find the text that supports the article content in question

and more specifically Wikipedia:PROVEIT#cite_note-1, which states:

When there is dispute about whether the article text is fully supported by the given source, direct quotes from the source and any other details requested should be provided as a courtesy to substantiate the reference.

I am officially disputing Small Victory's claim and requesting direct quotes. If Small Victory has integrity, then he will either provide such a quote, if it exists, or withdraw his claim if it doesn't. I also ask that independent editors verify Small Victory's assertion. In the meantime, I will proceed to remove the quote, because I cannot verify it. Should a direct quote that supports this claim be found and independently verified, then I will not object to its inclusion in the article. Wapondaponda (talk) 17:56, 25 July 2009 (UTC)

This is not the way to go about solving the disputes. If you guys cannot manage to bring forth a neutral point of view I recommend this page be deleted or restarted from scratch. It does not matter if you cannot find evidence at one locus in one people. The nature of drift and founder bias means that sometimes the evidence is going to be glaringly obvious, for example A30-B18 in Sardinia. On other occasions the evidence is going to be hard to detect. Imagine all the possible scenarios in Europe. You have African females as founders (Iberia), eurasian females as founders, male Africans and recent immigrants, male Europeans as recent immigrants, there are potential population events (like LGM and YD) and there are repetitous migrations. Sometimes you get lucky, for example the Pas lie exactly on a node of E1b1b1b in N Iberia. What is interesting in the Pas is that outside of the valley all A29-Cw16-B44 are basically in strong linkage disequilibrium, particularly at the high resolution typing level. The Pas are the only exception, they show numerous other haplotypes of Cw16 indicating that they are closer to the site of entry into Iberia. In addition the HFE locus is the result of gene conversion between A29-Cw16 and A*0301-Cw*0702, the highest level of both of these is within this area of Iberia. As I was telling you previous, much of the evidence for gene flow from Africa into Europe is very punctate, it is not diffuse. I will have the A30-B18 page up soon and you can see what I mean. From an observational perspective scientist are supposed to explain the observation and come up with more accurate interpretations, that means combining evidence against a hypothesis with evidence for a hypothesis.

The critical feature that you keep forgetting is that recent migrations did not contribute greatly to European genetic makeup. However all humans are originally from subsaharan africa, and non-recent contributions, particularly those before the LGM but after the first wave of humans from Africa are not easy to detect because there is a huge confidence range associated with any molecular genetic data. If I take a very strict statistical interpretation on many loci favored by scientist, the null hypothesis is only disproved with great refinement of technique and large samplings in Europe and Africa. Many areas of africa are very poorly typed, and there has been subsequent scattering of peoples prior to and after the post-glacial climate optimum. PB666 ^yap 01:58, 26 July 2009 (UTC)

I agree that recent migrations did not contribute greatly to the European genetic make up. But what is unclear is the role of Ancient migrations. Certainly the migration of haplogroup E seems to have had a significant impact, since it reaches frequencies as high as 50% in the Balkans. Whether it was only one man who introduced his genes into Europe or many men, remains to be elucidated. How much autosomal DNA remains in Europe from the migration of Haplogroup E is also not yet known. Of course population differentiation and no gene flow is the null hypothesis. But we consistently see hints of gene flow, that tend to differentiate Europeans from other non-African populations, in that Europeans seem to have slightly more common ancestry with Africans, than say East Asians or Native Americans. Maybe much of this DNA is no longer in LD, so it is harder to detect, and because Europe is the most mixed continent, DNA is scattered around the continent, causing the someone disjunct distribution of certain African haplotypes. Wapondaponda (talk) 03:33, 26 July 2009 (UTC)

I don't know how true this is or not. I see putative evidence of Ancient contributions from both direct and Indirect sources. MtDNA groups X appears to move into Europe from the East, there is the potent migration of A1-B8-DR3 from Iberia. We can't even say at the moment whether these haplotypes and groups underwent extreme assymetric expansion. What I have examined is the rectangular occupation that was bordered by the Alps, Mediterranean, Atlantic and Retreating glaciers. Within that context there are a handful of haplotypes 2 of which are potentially of more ancient NW African origin. The problem is both are in acute linkage disequilibrium 12,000 years after the fact, how badly were they in linkage disequilibrium 12 kya. Ergo we have alot of room for random drift and binomial probability puts a pretty wide distribution of frequencies that can produce 1/4 or 2/4. In terms of Gene flow from the East, from tribes of peoples of middle eastern ancestry that accumulated African genes as a consequence of climate driven migrations or transcontinental nomadic behaviors in peoples. I cannot reiterate the point, there are clines in Europe, this is true, but they are not radial clines from mode to antimode, they are highly assymetric. AH8.1 declines along a slope from Ireland to Yugoslavia, there is a rapid drop in SE England and NE France and a rise going into Scandinavia a drop in Poland and a rise into the Hungary and a drop going into Romanian and another rise going into Serbia. The dips and rises are the consequence often of specific migration events. The drop in Paris is due to migration from Italy and Greece, the cline across N. Europe may be due to Negative selection since the Neolithic, which both suppressed but may have also promoted migrations from the South. The was a specific migration from Anatolia to SE France that appears to have touched Tuscan region and Switzerland, but all but moved through France without leaving a trace. You have to get out of you head C-S, that is old school. This specific injections of Y chromosome, they are not as these clines painted on the map, there is a blotch here, a big blotch over their, and places with very sharp frequency drop offs. The only reason that AH8.1, AH7.3, AH7.2, AH2.44 have produced the appearance of clines because they seeded an immense area of northern Europe with a founder affect. Consequently as the produce migrations in different direction this gives the appearance that there is a cline, but if you take a look at the end of the Haplotype, the DP loci, you will find that these haplotypes did not expand from a single point. One of the biggest problems right now with genome-wide surveys is the following: One large scale study will pick up an association in one region and another study will pick up another association in a different regions, we have had two large scale genome studies of Celiac disease and both studies managed to find loci with stupendous linkage, neither study found the same linkage (Except DQ2.5). How does one go about reconciling these inconsistencies. Easy human genetics does not serve scientist or clinicians, it serves the dogma survive and reproduce. There are all kinds of underlying regional factors that promote the ability to migrate into and the desire to migrate out of regions we don't understand, but what we can gather is that these regional selections are involved in regional survival, so that we have a basketwoven Eurasia particularly in interior and well traveled regions. I have read in history books this group invaded and wiped out this other group. And yet we find no evidence in the HLA that group X was wiped out or the the genes in place are overrepresented by group Y. We look at Arabia and how history tells about all the population events, but then look at certain HLA allele frequencies and haplotypes, and we find patterns suggestive of strong isolation, and then go 500 miles over to a parcel of land virtually ignored by history and it looks like an LA Freeway at 5:30PM. Apriori assumptions have got it so wrong so many times, it best to wait for thorough studies using the best available data and tools.

The problem is that Wapondaponda doesn't understand how the STRUCTURE program works (or he's pretending not to, as he seems to have no problem with it in the 'Central/East Asian admixture' section). Here's a very clear, easy-to-follow explanation from its creators, which shows that it's perfectly acceptable -- indeed ideal -- for quantifying Sub-Saharan African admixture in Europeans:

We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci.

http://pritch.bsd.uchicago.edu/publications/structure.pdf

Results are displayed in a color-coded chart like this one that shows population affinities and admixture proportions for each of the populations tested. A look at Figure S3A of the supplementary material from Auton et al.'s study will reveal an identical chart showing virtually no Sub-Saharan African admixture in any European groups. ---- Small Victory (talk) 09:00, 26 July 2009 (UTC)

No text supporting your claim, as I expected. The above quote is not from Auton et al but is a general statement about STRUCTURE program. This is WP:SYNTH. Find specific unambiguous text supporting your claim, and I will agree to include your statement. WP:No original research states,

This includes unpublished facts, arguments, speculation, and ideas; and any unpublished analysis or synthesis of published material that serves to advance a position. This means that Wikipedia is not the place to publish your own opinions, experiences, arguments, or conclusions.

In other words, Wikipedia editors shouldn't analyze data to advance a position, especially if the authors of the study have not done so. Your statements are an unpublished analysis. Wapondaponda (talk) 12:15, 26 July 2009 (UTC)

Since STRUCTURE results are most often presented visually, the chart is in effect a "direct quote from the reference cited". Therefore, your request is nonsensical and betrays either a poor understanding of the method, or a ruse to have material you don't like removed from the article (or both). And btw, the reason there's no text reference to African admixture is that none of the populations tested had any to speak of. ---- Small Victory (talk) 13:46, 26 July 2009 (UTC)

The outputs from the STRUCTURE simulation depend on the input parameters that are used. So while admixture can be inferred from it, we require the authors of the study to interpret the results for us. We should not read their charts and come up with conclusions. For example, one structure input is the number of clusters, in this study they used k=2 to 5 clusters. With each value of K we get a different chart. As a result we get a complex pattern which is best left to the authors to interpret. So the first chart has only two clusters, East Asian and European. There is no YRI at all which is unrealistic. YRI is instead represented by a mixture of East Asian and European. Native american only appears when K=5. Native americans show no crossover, with East Asia which is somewhat absurd given that they share recent ancestry. The authors state

While the global STRUCTURE analysis reveals broad patterns of population �differentiation (Supplementary Figure S3), the method is limited to using a small fraction of the available SNPs due to high computational cost. Furthermore, as the number of specifi�ed clusters is increased, the patterns of population structure become increasingly difficult to interpret.

So if the authors of the study say they are having difficulty interpreting the data, I don't see how a wikipedian could ace it. Wapondaponda (talk) 21:58, 26 July 2009 (UTC)

OK guys, knock it off. This is really not the place to go about this, these types of discussions belong on your talk pages, not here. Muntuwandi you act like you're seeking attention, this is not the place. Small Victory, are you professionally familiar with how the program works that generates these admixture diagrams, those I have seen reported for the global population used k = 14 clusters to achieve the best results and those levels were particularly important for establishing subdivisions within Africa? I want to remind you guys that although the human genome has been sequenced, there are still alot of variation, undetected variation in the human population and there is still considerable amount of sequencing errors and artifacts. Resolution between different populations and establishing admixture ratios work best when 2 populations have been separated for a period of time, and admixture occurs only once. Constant geneflow between groups over time does not give the best resolution. Populations that exist in genetic clines frequently have undetected alleles that when treated as one create false assumptions about population. The methodology they are using maybe sound but the data they are feeding into the program may not be perfect (or to state otherwise, not good enough to resolve contributions between to groups that were historically more closely related). I have a piece of advice, before placing this material on the Main, why don't you, Small Victory, have some respect for the people here and bring the material here first, both the conclusions you want to add and the tables or figures they are based on, so that we can see how reliable these maybe. Molecular anthropology is full of examples, perfectly sound logic, from the literature in which the data set or population sample was so incomplete that the conclusions drawn were diametrically opposed to reality. Therefore even drawing a conclusion based on what authors say in the conclusion (speculation) section of published literature is risky.PB666 ^yap 00:36, 27 July 2009 (UTC)

Auton et al. use the results depicted in Figure S3 to quantify admixture in different populations. Of course, they only discuss it in the text when admixture is actually present, which makes Wapondaponda's request for a quote ridiculous. Here they are discussing European admixture in Mexicans based on the above chart (note that they don't mention African admixture for the obvious reason that the Mexican sample they tested doesn't have any):

The results are shown in Supplementary Figure S3D. At K = 2, the Mexican individuals appear admixed between a predominately European cluster and a predominately East Asian cluster, with slightly greater membership in the former cluster. However, at K = 3, the Mexicans form their own cluster and no longer share East Asian admixture, but retain a 'European' admixture component. The average proportion of European admixture in Mexican individuals with K = 3 is 32.5% with a standard deviation of 17.4%.

--- Small Victory (talk) 10:22, 27 July 2009 (UTC)

Pdeitiker, you are right, I am seeking attention, because I recognize that this specific problem can only be resolved by the community.Wapondaponda

The community will fix this page when the COIs back away from the page. Who do you think is going to repair this page in this environment? The hostilities are creating an excess amount parenting peers and almost no time working on the page.PB666 ^yap

Small Victory and I alone will not be able to resolve this. This is a very specific and simple issue. Should Wikipedians, in this case Small Victory, be reading, analyzing or interpreting charts, especially in ways not specified in the articles from which they are sourced.Wapondaponda

That is your issue, that is not the specific problem to wikipedia. While NOR is a pillar the basic problem here is how you three cannot see things from the other persons perspective, it is about neutral point of view. Let me make a brief synopsis, you added a collection of content, he considered it bunk, tossed all of it out, inserted his own content, and this has been going on different pages for quite a while. These content oscillation is not encyclopedic. The two contents needs to be merged together, with your content he is allowed to respond with information from the literature (such as Tishkoff et al, 1996) which find no evidence of excessive gene from SSA outside NE Africa or Eurasian as occurred during the first migration.

Academic consensus-The statement that all or most scientists or scholars hold a certain view requires reliable sourcing. Without a reliable source that claims a consensus exists, individual opinions should be identified as those of particular, named sources. Editors should avoid original research especially with regard to making blanket statements based on novel syntheses of disparate material. The reliable source needs to claim there is a consensus, rather than the Wikipedia editor. For example, even if every scholarly reliable source located states that the sky is blue, it would be improper synthesis to write that there is a scientific consensus that the sky is blue.

— WP:RS

Since there is no consensus on how much genetic input came from North Africa or from sub-saharan Africa we have a situation in which multiple reliably-sourced opinions can be provided.PB666 ^yap 04:38, 28 July 2009 (UTC)

From what I can tell, the HAPMAP data is only piggybacking here into the analysis of structure, and it does not constitute the main analysis. Specifically the only subcontinental analysis presented is for East Asia, South Asia, Mexico and Europe(Nelson 2008). There is no subcontinental analysis for Africa(YRI)(page 2 supplementary material). I am still trying to understand what actually the STRUCTURE analysis constitutes. I agree with Pdeitiker, in that the results of structure depend on the inputs. The Tishkoff paper identified 14 clusters worldwide. Each value of K yields different levels of admixture, so admixture results from structure are not absolute values.Wapondaponda

It is in the developemental stage, as they presented in the paper the statistic provided the most reliable interpretation at k = 14. Interestingly the program divided the younger exoafrican groups before dividing older sub-Saharan groups, indicating distance of separation of is a factor in the capacity to recognize admixture. Admixture is most easily recognized in haplotypes if each common mutation or shared source of variation is border on both side by private mutations. Constant geneflow does not allow this. As the number of relevant SNPs increases the ability for these programs to parse out ancestral clusters will also increase. If you are testing the Guarachi against Western Irish, there is a relatively good spatial separation that prevents admixture except through greatly indirect transmigratory genetic exchange. However if the Sengalese have gene flow from the Berbers and Iberians have gene flow from the Berbers it is less easy to find a markers that clearly distinquishes Iberians from Senegalese.PB666 ^yap

In any case Small Victory is contending that Sub-Saharan admixture is negligible based on his own reading of the chart. However this directly contradicts what is in the text, when they specifically discuss YRI haplotype sharing and West African gene flow into Southern Europe. That Small Victory is willing to ignore the main conclusions of the study and instead subjectively interpret a chart is at the core of this dispute. Wapondaponda (talk) 12:46, 27 July 2009 (UTC)

Yeah, Tishkoff tested Africans from all over the continent, including the Horn, yet the Europeans they were compared to still didn't have any admixture to speak of.[9]

And you're the one ignoring Auton's conclusions, pretending that West African gene flow is the only interpretation for the shared haplotypes. My version is more neutral because it mentions all possible interpretations, plus the results of the admixture analysis. ---- Small Victory (talk) 13:58, 27 July 2009 (UTC)

[Sigh] I am not going to get in an argument between you two. You are wrecking the Main, neither of you are doing anything to improve the quality, or more important the encyclopedic nature of that page. If you are not here to provide encyclopedic content in line with WP:MOS then don't screw with the Main page. I have asked you, Andy has brought this to the attention of the Admins, and Admin told you guys a couple of days ago to work together. You must learn to work together. Small Victory you have a snide attitude and you blow off these indications of gene flow and others like myself who have papers suggesting gene flow know what is significant and what is not. If you live in Sardinia, then the contribution of African sources of DNA other than the migrations from East Africa is highly significant. If you live in Portugal or Spain the contribution is highly significant. Muntuwandi you cannot invent results that are not there, even if you suspect they are there, you have to go by the science that is out there, and _if anything_ you need to restrict presenting all interpretations because some of the results are not studied in a thorough manner. I have yet to see any result that suggest unequivocable evidence of gene flow from sub-saharan africa into Europe (I have repeatedly told you this), the critical issue is the nature of poor genetic studies done in NE Africa to date. I have 100s of paper on HLA sitting right next to my leg here, many that corroborate what Arniaz-Villena stated in the 2001 publication, but I am not convinced this comes from sub-Saharan Africa. The HLA studies offer the best evidence. But (at some point I will have a page that deals with this issue) when one dives into the issue, one begins repeatedly hitting N. African populations (e.g. the Berbers). How do you discriminate gene flow from Berbers into West Africans (like Senegal) from gene flow of equitorial Africans into Berbers. This is the problem with the YRI HapMap, they did not test a bunch of African groups, they are holding up a single group as a surrogate for whats going on in Africa. By just about every credible molecular anthropologist out there is critical of sampling issues within Africa, sample within Africa should equal or exceed sampling out of Africa. Here is the trouble with Arniaz-Villenas conclusion, There is about 2000 miles betweeen where these genes he called SSA were found, and the first Nile dwelling people to be sampled. Vast empty space of NE Africa that has not been studied according to modern methods of HLA genotyping. Egypt, untyped, Libya, untyped, Sudan, no formal papers presented, some typing, Algeria, typing only of the berbers.

This is all very simple, what is spoken of within the literature, that which best methods show to be reliable and there isn't that much, and every thing else needs to be kept off the Main. IMHO the Sub-saharan african issue should get a couple of sentences in North Africa. I think Arniaz-Villena needs to be introduced along with subsequent papers that support the position and then we can discuss the problems in NE Africa (I have the publications from Egypt and Sudan) to provide NPOV and that is all we need to introduce. Simply because L1, L2, L3 are found in SSA does not mean that they could not have spread slowly northward into N.Africans indigeonous peoples, the same is true with the Y chromosome. As long as you three continue to lock horns on the main page, the main page is not going to attract expert editors to fixe the page, and folks are not going to be able to read the page, so that whatever pearls of wisdom you add are basically thrown in a pigpen.PB666 ^yap 04:38, 28 July 2009 (UTC)