Talk:African admixture in Europe/Archive 1

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Does the article NAME make sense?

I'd like to ask whether this article name makes sense. Admixture of what? Biodiversity? Languages? Music styles? If the subject is human genetic diversity then doesn't it need some more words?--Andrew Lancaster (talk) 11:26, 26 August 2009 (UTC)

I would prefer to hear from others before starting to move the article to a better name.--Andrew Lancaster (talk) 15:00, 28 August 2009 (UTC)
Suggestions,
  • African DNA admixture in Europe
  • African genetic admixture in Europe

Wapondaponda (talk) 16:37, 28 August 2009 (UTC)

  • I agree the name is sub-optimal. African-European human genetic admixture is a bit of a mouthful, but is probably reasonable. One goal of a good article name is that it's easy for somebody to find it directly by knowing what to type into the search box. It's unlikely that's going to happen with this article no matter how the name gets tweaked; the only likely way I can see for somebody to get here is by clicking a link from a more generic article, dab page, category page, etc, so I'm not worried too much about the exact name being easy to guess/predict. I assume there are other articles on similar topics (Geographic area X admixture into geographic area Y), and it would be nice if there was a common naming scheme for all of them. -- RoySmith (talk) 16:53, 28 August 2009 (UTC)
Google gives some insights, and it reminds about some of the things we have to be careful of too. Admixture is often a word used to describe a sort of statistical simulation which is not always even meant to imply causality. It is a technical term I fear many people misuse. We are talking about good old fashioned "mixture" to speak, because if I understand the intention we ARE talking about real movements of people. For example when a study describes Ethiopians in terms of Middle Eastern and Sub Saharan "admixture" they are not necessarily meaning to say that Ethiopians descend from the mixture of two migrations which came from those places.
To use a bit of jargon there is a difference between Population Structure and Population History. Is this article not about the latter, i.e. "population movements"? Please opine.--Andrew Lancaster (talk) 17:03, 28 August 2009 (UTC)
Admixture originally refers to non genetic mixtures. However it seems to have recently entered the genetics lexicon. One more suggestion
  • African gene flow into Europe.
Wapondaponda (talk) 06:53, 2 September 2009 (UTC)
Maybe better than what we have but...
  • It treats genes as things that flow. I like to avoid such metaphors in this subject because people get confused enough already.
  • No mention of humans.
African contributions to human genetic diversity in Europe is not catchy, but does it need to be catchy?--Andrew Lancaster (talk) 08:28, 3 September 2009 (UTC)
Hoping this question will not be forgotten.--Andrew Lancaster (talk) 10:01, 7 September 2009 (UTC)
The current name accomplishes a lot in just three words. It is easy to wikilink, for people to search for the term and for search engines to find the article with just a few keywords. However its brevity may be an oversimplification and the current name may not be able to characterize the complexity of Afro-Euro history. The name you proposed is probably the most appropriate description of the content in the article. The problem is, it is a mouthfull, 8 words. Wapondaponda (talk) 20:52, 8 September 2009 (UTC)
Note the constant STRUCTURE debate from Small Victory, claiming that if this article is about "admixture" then it has to be all about those types of studies (or his interpretations of them). I think it is nonsense, but these comments certainly cause some distraction? Maybe your African gene flow into Europe is preferable to what we have now. What do others think?--Andrew Lancaster (talk) 08:11, 9 September 2009 (UTC)

Opening sentences

I'd like to go through the opening sentences and raise some issues I think need addressing...

African admixture in Europe refers to the European presence (via admixture) of human genetic lineages typical of the peoples of Africa including Sub-Saharan Africa.

First, this is a definition, presenting itself as a well-known one from outside Wikipedia. Is it one?

This evidence pertains to geneflow suspected after humans left Africa via Arabia more than 40,000 years ago.

Is it really appropriate to put this very specific migration down in the intro without any discussion of it? I think not. A casual reader will get the impression that there is no debate about this, and they'll also probably tend to guess why this migration is being distinguished. Will they think this was the first migration for example? I am not sure we need this sentence.

The evidence suggests that there has been gene flow between Africa and Europe in both prehistoric and historic times.[1]. In more recent history, the peoples of Europe and Africa came into contact during the, the exploration and colonisation of Africa and as a consequence of the Atlantic slave trade.[2] As a result of these recent contacts, lineages of African descent have also been detected in Europe. In general, African admixture is distributed along a South-to-North cline, with peaks in the Mediterranean region and Iberia.

How about...

This article summarizes what is known or proposed concerning the presence of African genetic lineages in European populations. The first anatomically modern humans in Europe are thought to have had African ancestry, and genetic evidence suggests subsequent movements from Africa to Europe in prehistoric and historical periods.

I think the rest is for the body of the article, and the article should be divided into time periods. I see no reason to exclude any time period from the first anatomically modern humans in Europe onwards.--Andrew Lancaster (talk) 11:39, 26 August 2009 (UTC)

I definitely agree that the lead needs some refinement. However I also find a brief timeline of events important as it helps to define admixture. The OOA migration is the time=0, the reference point. However, I am open to a suggestion that incorporates this information into the body of the article. Wapondaponda (talk) 22:57, 26 August 2009 (UTC)
And which OOA migration is "the" one? Is this concept really so simple that you can pass it off quickly in an intro?--Andrew Lancaster (talk) 05:55, 27 August 2009 (UTC)

Merger proposal

The issue of merging was specifically dealt with at Wikipedia:Articles for deletion/African admixture in Europe and the decision was to keep a separate article. So I will remove the tag. Wapondaponda (talk) 06:57, 2 September 2009 (UTC)

Please allow reasonable time for discussion with more editors. Abductive (reasoning) 08:24, 2 September 2009 (UTC)
Given how much discussion there has been already, including very recently, shouldn't you as the proposer give some explanation about what new issues you want to raise?--Andrew Lancaster (talk) 11:57, 2 September 2009 (UTC)
The subject of the AFD was specifically whether to have a separate article or merge into Genetic history of Europe. this comment specifically addresses the issue. I feel a discussion about merging is redundant, and means going through the process all over again. I agree with Andrew in that unless there is some new information, there is no need to go through what was discussed just last week. Wapondaponda (talk) 06:35, 3 September 2009 (UTC)
I assume that this is a content fork. Aren't you guys on opposite sides? Abductive (reasoning) 06:46, 3 September 2009 (UTC)
Andrew prefers not to take sides in disputes, so we are not on opposite sides or on the same side. Wapondaponda (talk) 06:59, 3 September 2009 (UTC)
Interesting. Still a content fork. Abductive (reasoning) 07:05, 3 September 2009 (UTC)
Not necessarily a CFORK, actually the genetic history of Europe article may have more problems than this article. Wapondaponda (talk) 07:08, 3 September 2009 (UTC)
But a better title. Abductive (reasoning) 07:14, 3 September 2009 (UTC)
The contesting content on Genetic History of Europe has been removed, therefore it is no longer a content fork. The better way to describe it is as divide and conquer, get this material of another page so that the other page can evolve, and this page, well we shall see if the editors take their role as wikipedians seriously or not.PB666 yap 16:21, 3 September 2009 (UTC)

My current feeling is that this article should be given a chance to see if editors can find enough non controversial and properly sourced material to make a non controversial and properly sourced article. The deletion debate about this article went "my way" in the sense that I argued there was enough of a change of subject to make it unclear whether this article would necessarily have the same problems as the last one. But actually I did not vote. I therefore believe it is critical that this article sets itself a clear title and direction. See the subject above, which I believe is not being handled with sufficient seriousness.--Andrew Lancaster (talk) 08:22, 3 September 2009 (UTC)

Agreed with AndrewPB666 yap 16:17, 3 September 2009 (UTC)

Work to do

Back to the main issue, there is actually a lot more information that will be added to this article. The autosomal markers, for which there is a lot more detail, are only briefly mentioned here. If we had to merge back, Genetic history of Europe will have too much information about Africa. Already there are suggestions to delete the admixture sections on Genetic history of Europe as there are already articles that deal with them, such as this article. Wapondaponda (talk) 07:59, 3 September 2009 (UTC)

Intro

I have changed the intro quite a lot in the way I already implied I thought necessary. Now the article starts by laying out the basics of what mainstream archaeology says about the chronological starting point. This gives a basis which can be built upon rather than leaving everything to vaguely implied assumptions. Leaves things between the lines might end up getting accused of being a way of quietly pushing a POV, and we now that such accusations do tend to fly around this subject!--Andrew Lancaster (talk) 09:25, 3 September 2009 (UTC)

COI heads up

Just a note to say I have cited myself in a trivial way. The article seemed to need a comment about the age of E1b1b1b (E-M81), but the primary literature is all over the place. Rather than taking a position myself (I think it is North African Neolithic more likely than not, but frankly there is very little to go on and it certainly probably split from the other major clades before the Holocene), we at least need a reference to a review saying that there are big variations in the approximations, and there is only one such review I think.--Andrew Lancaster (talk) 10:49, 3 September 2009 (UTC)

See below, I think we need to combine implications, such as recent gene-flow from NW Africa into SW Europe. You have now a collection of references on how best to deal with ambiguous implications (Schaffner 2004 for instance, Takahata 2001) and that the most effective way is to have evidence from a variety of sources such that one is not leaning to much on a single locus, such as Y.PB666 yap 16:11, 3 September 2009 (UTC)
On this I agree, but I've worked on what I know best today.--Andrew Lancaster (talk) 16:13, 3 September 2009 (UTC)

Getting things going

I have a couple of recommendations here, before we fix the name, let's first think how best to get the published materials into the article, particular stuff that was removed from the Genetic History of Europe. Since these names were drawn of usage on other pages, they are fine for now.

-Critical problems of the page. How material is introduced.

1. This articles topic is constrained by the following:

That ancient Europeans arrived primarily from Asia, not Africa, that to the best of our knowledge this first migration occurred 32 to 40 kya. And that these people had evolved since leaving africa (both with regard to selectable markers and with regard to neutral markers-neutral evolution)
That the evidence presented in this article pertains to gene-flow from Africa, indifference to previous gene-flow into SW Asia ~50,000 years previous, that is in a more recent time frame.'

2. That broad patterns of gene-flow, such as from the Middle East or from SSA via unknown paths or from the middle East need to be conditioned into a section of Alternative explanations, such that these are set aside from items that have more obvious connections. EV-13 might fall into this category.

3. The Lead should be a synopsis, the basic facts and refer to section leads, keep it short and free of opinion.

Describing information

1. Lets not make the mistake of Genetic History of Europe with long boring discussion of techniques, if people what to read on techniques they can read the various pages.

2. Contain information that pertain to single sources, for example, information about NW africa contribution should be presented in one section, if there is alot of information with Y or mtDNA than break it down into subsections, otherwise it should be combined. Figures, diagrams, maps are key to making a nice page.

3. Why is this information important, for example, what distinguished the EM-81 in northern Iberia from theories concerning Moorish migrations? Opinions are less important than style, this is an encyclopedia such that the reader needs to be coaxed to read.

4. Small sections at a time, work on each section so that when it is complete it is close to the final product, avoid opinion, even author opinion, each section should be validated with facts and conclusions from several sources.PB666 yap 16:11, 3 September 2009 (UTC)

I'll go through your comments...
  • First whatever points you raise, I see no reason to stop thinking about what the real title should be. Focus has been a big problem with this article, and I think we can be pretty sure that delete debates have not stopped. I think it is fine to ask "what is the body of sourced material we are trying to put together" but this question can not be separated from the question of what it is that links these materials. We do not just want a mass of loosely relevant information.
  • Intro. I lengthened the intro today and this may be one thing you are addressing. When I read your comment I went and snapped off what I added into a new section which lays out the basic timeframes involved. I stick by saying that not doing this will leave a gap where edit wars will put down roots.
  • Your point about African routes going through the Middle East is an interesting one this article has to face. From a point of view of Europes genetic makeup is the disctinction being made between Africa and the Middle East perhaps even a little artificial? (Shock horror.)
  • Long boring discussions. So far I think the article length is OK? What do you think?
  • Are you arguing that it is better to break the main part of the article into regions than into types of DNA?
--Andrew Lancaster (talk) 16:26, 3 September 2009 (UTC)
No major complaints with the current content. My only concern is, as Andrew has pointed out, focus. Personally I don't mind detail and even prefer it, but the POV and OR police are always looking for excuses to slap fact tags. The more compact and direct the content is, the less opportunity is given for tagging.
The section "examples of gene flow" was originally "Defining African admixture". The reason was to address some of the controversies or misunderstandings that are currently prevalent concerning the origins of certain markers. Specifically that certain markers may have moved back and forth between Eurasia and Africa. Wapondaponda (talk) 07:12, 4 September 2009 (UTC)

E1

I am looking to add more information on Haplogroup E1 (Y-DNA). Though less frequent, it is an interesting haplogroup as it is found all over, including Italians, Albanians, Turks, Iberians, Canarians, Middle Easterners and North Africans. Haplogroup U6 also needs some mention as it has been detected in Iberia.

Wapondaponda (talk) 07:24, 4 September 2009 (UTC)


I have not specifically collected much E1 data, but I have collected at least some Y haplogroup data from these regions that might help:

Regards--Andrew Lancaster (talk) 08:16, 9 September 2009 (UTC)

Elephant in the room

Based on the latest autosomal DNA evidence using the STRUCTURE program, Europeans don't have any African admixture to speak of:

So there's absolutely no justification for an entire article on this subject. It can only be a POV fork. ---- Small Victory (talk) 13:49, 4 September 2009 (UTC)

The thread was refactored, it was declared by NOR noticeboard to be original research. The NOR tag was also removed since the NOR here was removed.PB666 yap
Editing or deleting other people's comments is a big no-no. And nothing was "declared" by anyone. There's a discussion that's still ongoing, but no one has been able to demonstrate that citing a clearly explained chart is OR, because it obviously isn't. Besides, this is just the talk page. Deleting material from here that's under discussion takes information suppression to a whole new level. ---- Small Victory (talk) 12:06, 7 September 2009 (UTC)

Overtagging

According to the essay at WP:OVERTAGGING, no more than two or three tags are normally necessary. Furthermore reasons for adding a specific tag need to be articulated on the talk page. As I have not seen any reasons for some of the tags, I suggest removing some or all of the tags. If the details regarding any disputed content are expressed, then the tags can be readded. However, it should be noted that other means of resolving content issues should be attempted before adding tags. Wapondaponda (talk) 06:42, 5 September 2009 (UTC)

POV forking by SOPHIAN

Just fresh out of a month long block SOPHIAN has created Black African genetic contribution to the population of the European continent. Wapondaponda (talk) 06:53, 5 September 2009 (UTC)

Moorjani et al , new study

Abstract, is available. Confirms African ancestry in many southern Europeans, though percentages are not high, but they are nonetheless statistically significant, approx 2%. Furthermore the spanish admixture is estimated to have occurred 1700 years ago. Wapondaponda (talk) 12:44, 5 September 2009 (UTC)

We'll have to wait and see what these "methods that can infer admixture proportions in the absence of accurate ancestral populations" turn out to be, and if they have any validity. It sounds very dubious to me. Anyway, I don't know what you're getting so excited about. The study shows that admixture is extremely low and occurred in historical times, pretty much disproving everything you've ever claimed and confirming that this article is nothing but Afrocentric POV. ---- Small Victory (talk) 12:16, 7 September 2009 (UTC)
Wow. You even complain when Muntuwandi's African claims seem too unambitious. Anyone would think you are just looking for an argument.--Andrew Lancaster (talk) 12:27, 7 September 2009 (UTC)
The presentations are next month, don't know what the actual publication date is. Many of the authors are faculty in the Department of Genetics at Harvard. Reich who is already cited for Principal component analysis of genetic data is a coauthor. I don't know what methods they used, who knows may be even STRUCTURE. Don't know if I will even be agreeable to the results of the study. The abstract of Characterizing the history of sub-Saharan African gene flow into southern Europe states

Recent analyses of whole-genome SNP data sets have suggested a history of sub-Saharan African ancestral contribution into southern Europe but not in northern Europe, consistent with previous analyses based on the Y-chromosome and mitochondrial DNA. However, there has been no characterization of the proportion of African admixture in southern Europe, or of its date. Here we analyze data from ~450,000 autosomal SNPs in the Population Reference Sample, ~650,000 SNPs from the Human Genome Diversity Panel, and ~1.5 million SNPs from the HapMap Phase 3 Project, and studied patterns of correlation in allele frequencies across populations to confirm the evidence of African ancestry in many southern European populations but not in northern Europeans. Using methods that can infer admixture proportions in the absence of accurate ancestral populations, we estimated that the proportion of sub-Saharan African ancestry in Spain is 2.4 +/- 0.3%, in Tuscany 1.5 +/- 0.3%, and in Greece 1.9 +/- 0.7% (1 standard error). We also studied the decay of admixture linkage disequilibrium with genetic distance, which provided a preliminary estimate of the date of African gene flow into Spain of roughly 60 generations ago, or about 1,700 years ago assuming 28 years per generation. This date is consistent with the historically known movement of individuals of North African ancestry into Spain, although it is possible that this estimate also reflects a wider range of mixture times.

Firstly the authors attribute this sub-saharan influences to the movement of individuals of North African ancestry. This addresses the fact there has not been a clear cut distinction between North Africa and Sub-Saharan Africa, especially in prehistoric times. I don't know yet whether they address the migration of e1b1b lineages. Though the admixture levels are not high, they are still significant. In Spain, for example admixture of 2.4% was detected. With a current population of 46 million, 2.4 percent is equivalent to 1.1 million Africans, which is not a small number. Wapondaponda (talk) 14:06, 7 September 2009 (UTC)

STRUCTURE and admixture

According to SV's most recent posting on this talk page, SV has disputed this article based on results from the software program STRUCTURE. SV has argued that the presence of "discrete clusters" produced by STRUCTURE, means that no admixture exists between discrete clusters. Though STRUCTURE can be used to measure admixture, none of the studies cited by SV have published any data that directly concerns African admixture in Europe determined by STRUCTURE. As a result, the consensus from original research noticeboard has been that unpublished analysis of published facts constitutes original research. SV has been unsatisfied with this assessment and now it seems his whole argument centers on this software simulation.

I have been researching the apparent paradox as to why the authors of STRUCTURE say that it can be used to measure admixture but yet almost nobody has published a direct admixture analysis based on Structure. Despite the fact the STRUCTURE is used extensively, so far I have only seen one study, that used STRUCTURE to directly quantify admixture, and that is Auton et al for Mexicans. In the same study STRUCTURE was run on the global level and with K=5, five clusters which correspond to the major continents. A visual analysis of the chart indicates some discrete looking green and blue clusters, which SV has argued imply no admixture. However in the same study the authors have decided to address the "current debates in human population genetics regarding the extent of historical gene flow among Africa, Europe, and the Middle East". To do this, they do not use STRUCTURE, but instead use another method they call "haplotype sharing" which I think simply means counting the number of mutations shared by Yorubas and Europeans. It is interesting that they use STRUCTURE to measure admixture in Mexicans but not to measure Yoruba admixture in Europe. Furthermore they also perform a principal component analysis which revealed an African, Middle Eastern and European cluster, this runs contrary to the chart from STRUCTURE, that revealed separate discrete looking clusters of Europeans and Africans.


The simple reason for these apparent paradoxes, I believe is to do with how STRUCTURE is designed. There are two reasons, I believe, one is the assumption that the number of clusters, K is real and the second is the assumption of complete linkage equilibruim.

Value of K

The creators of STRUCTURE, Pritchard et al state:

here are also biological reasons to be careful interpreting K. The population model that we have adopted here is obviously an idealization. However we pointed out in our discussion of data set 3, clusters may not necessarily correspond to “real” populations.

This is illustrated with the study by Li et al and Li et al 2008 supplementary materials. They performed Structure using 650k SNPs on the global HGDP samples. When K=5, Druze have small amounts of African admixture, when K=6 this African ancestry disappears and the amount of South Asian ancestry increases in the Druze. When K=7 a new cluster, dark brown, which is prominent in middle eastern populations emerges. Interestingly not a single individual has 100 percent membership in this dark brown cluster. As can be seen, the value of K significantly changes the proportion of admixture. What value of K to use will depend on the specific study and any assumptions. Rosenberg 2003 and Auton 2009 used k=5, Li k= 7, and Tishkoff 2009 used k=14. Which K is correct is anyone's guess. Because of the subjective nature of K, it is understandable why STRUCTURE has not been used extensively for admixture mapping

Linkage assumption

The second assumption for Structure is that all loci within a cluster are in linkage equilibrium, Pritchard et al state that their model assumes that "loci are unlinked and at linkage equilibrium with one another within populations". Recent admixture introduces linkage disequilibrium into the receiving population and STRUCTURE will detect this and assign the markers in LD to the admixing population not the admixed population. In short, STRUCTURE is better equipped to measure recent admixture than more ancient admixture. This is because older admixture is thoroughly mixed in the population and as a result structure assigns it an indigenous status.

Summary

Basically STRUCTURE is a computer program that the phrase Garbage in garbage out applies. If all the assumptions are correct, then Structure will produce accurate data. But it seems this is not often the case because STRUCTURE isn't commonly used for admixture mapping. Wapondaponda (talk) 21:26, 6 September 2009 (UTC)



Will this never end? You're like a creationist trying desperately to discredit evolution, but failing miserably. A few replies:
  • There has been no "consensus at the original research noticeboard". You wish.
  • All STRUCTURE studies that conduct admixture analyses directly quantify admixture. And every study I've cited contains published data that directly concerns African admixture in Europe determined by STRUCTURE. Each includes African and European samples, and the authors make clear that the charts show continental ancestry and admixture proportions:

Rosenberg et al. 2005: We utilized the unsupervised clustering algorithm implemented in STRUCTURE [12,13] to group individuals into genetic clusters in such a way that each individual is given an estimated membership coefficient for each cluster, corresponding to the fraction of his or her genome inferred to have ancestry in the cluster. [...] Each individual is represented by a thin line partitioned into K colored segments that represent the individual's estimated membership fractions in K clusters.

Auton et al. 2009: In order to quantify patterns of population structure and admixture, we utilized STRUCTURE [Pritchard et al. 2000], a commonly used Bayesian clustering method. [...] Setting the number of clusters (K) to five revealed structure largely corresponding to continental regions (Figure 1A).

  • The reason only Mexicans are discussed by Auton is because they're the only sampled population that has admixture. How many times am I going to have to explain the obvious to you? And how many times are you going to ignore it?
  • Haplotype sharing is not a "method", and it isn't the same thing as direct admixture. Auton gives other explanations for it, including North African admixture in both SW Europeans and Sub-Saharan Africans, and simple genetic drift due to Iberia's role as a population refugium. But you know this very well because you're trying to suppress that information.
  • There is no analysis that reveals an African, Middle Eastern and European cluster. That's just this plot viewed from a different angle (PCs 3 and 4 rather than PCs 1 and 2). And it's the first two PCs that Auton (and everyone who knows anything about PCA) says show continental ancestry and admixture that corresponds to the STRUCTURE charts:

The first two principal components (PCs) of the combined dataset separate individuals into clusters largely determined by geographic origin (Supplementary Figure S1A), which is consistent with a previous analysis of the HGDP dataset [Li et al. 2008].

We repeated the analysis using the 'supervised' STRUCTURE mode, having pre-assigned European and East Asian individuals to their respective populations. A K = 3, we found this method to give similar results to the unsupervised mode, with a European admixture component of 35.0% (standard deviation 16.8%) in Mexican individuals. The first two principal components of the same individuals demonstrates a similar pattern (Figure 1B), with Mexican individuals forming a distinct cluster between the European and East Asian Clusters in the first principal component. However, the second PC further differentiates the Mexican individuals from the East Asian individuals without substantially increasing the separation from Europeans.

  • As you've noticed, increasing the value of K often reduces admixture. That's because STRUCTURE assigns individuals to clusters adding up to 100%, and if there aren't enough clusters to represent the true genetic structure, then you get false assignments. So there have to be at least as many clusters as continental groups studied. For example, in Wilson's analysis, no Native Americans were tested, so 4 clusters were enough; this wasn't the case in Rosenberg's analysis, where at least 5 clusters were needed to differentiate the Oceanians, who showed exaggerated Asian, European and African admixture prior to that. Therefore, STRUCTURE may overestimate African admixture in Europeans, but it won't underestimate it, despite what you're hoping. ---- Small Victory (talk) 12:51, 7 September 2009 (UTC)
There was a consensus at the noticeboard, a very stark one. And you are not understanding what people are saying to you, because you do not want to, and because as usual you have lost track of your own tortuous efforts to argue with people about every little thing. You have your hands over your ears. Anyway, this article is not about STRUCTURE, and it does not need all the OR you want to put in because if all you want to argue is that analyses tend to show admixture to be small, then who is arguing with you? You don't need a debate about STRUCTURE for that. Everyone seems to agree on that? Indeed you just posted a sarcastic message on this talkpage to point our how un-impressively Afrocentric Muntuwandi's recent edits were. You apparently have no point worth making.--Andrew Lancaster (talk) 13:02, 7 September 2009 (UTC)
Well according to Auton et al, they state the STRUCTURE, underestimated admixture in their study,
To investigate the level of admixture in the Mexican population, we combined the Mexican samples with a sample of European and East Asian populations. Using structure with K = 3 we estimated an average of 32.5% European ancestry in Mexican individuals which is lower than some previous estimates based on microsatellite or "ancestry informative" markers
Increasing the value of K does not necessarily reduce admixture, because new clusters emerge. As in the case of Li et al 2008, ancestry in the south Asian and middle eastern cluster increased from k=5 to k=7, whereas African and European ancestry reduced.
It seems that SV has adopted a one-dimensional approach based only a STRUCTURE. It seems the only reason SV clings to STRUCTURE, is because it is the only method that you believe supports your position. Better to look at the bigger picture, which includes, y-DNA, mtDNA, HLA, PCA, genetic distances, archeology, anthropology and linguistics, which are all quite consistent with each other. Wapondaponda (talk) 14:28, 7 September 2009 (UTC)
We've already been over why Auton's results differed from previous estimates:

However, it should be noted that the variability between individuals is high, and that the Mexican samples in our study originate from a single location (Guadalajara).

That has nothing to do with what I'm talking about. Obviously, when new clusters emerge, ancestry in those clusters increases. It's the ancestry in the preexisting clusters that decreases, as misclassified individuals get assigned to the correct new clusters. Do you understand any of this stuff?
And I don't "cling" to STRUCTURE. It happens to be the latest, most widely used method of genetic testing, and the only one designed specifically to quantify admixture, which is what this article is supposed to be about. Rather, it's you who's clinging to outdated, deprecated and irrelevant methods because you believe they support your position, and you know that STRUCTURE analysis doesn't. ---- Small Victory (talk) 11:55, 8 September 2009 (UTC)
Auton et al state in the supplementary material

While the global STRUCTURE analysis reveals broad patterns of population differentiation , the method is limited to using a small fraction of the available SNPs due to high computational cost. Furthermore, as the number of specified clusters is increased, the patterns of population structure become increasingly difficult to interpret. As an alternative means for analyzing population structure, we conducted a PCA of the genotype data [Patterson et al. 2006]. This method has the advantage of being able to analyze many more SNPs and can flexibly summarize patterns of both discrete and continuous spatial population structure.

Wapondaponda (talk) 20:45, 8 September 2009 (UTC)
Do you have any actual arguments or are you just going to keep ignoring what I say and citing random passages out of desperation? Btw, this is what Auton says about that PCA:

The first two principal components (PCs) of the combined dataset separate individuals into clusters largely determined by geographic origin (Supplementary Figure S1A), which is consistent with a previous analysis of the HGDP dataset (Li et al. 2008).

I'm sure you'll ignore that too. ---- Small Victory (talk) 12:58, 9 September 2009 (UTC)

Going through the current article - "First settlers"

The majority of inherited genes found in modern Eurasians were carried by a small number of individuals that left a constrained area of East Africa more than 70,000 years ago.[2][3] Currently accepted models suggest migrations from Arabia into SW and South Asia. Over time some peoples migrated northward and westward into South Eastern and Eastern Europe (See Peştera cu Oase) after 45,000 years ago. At this time Neanderthals lived in Europe and areas of Southwest and Central Asia. While there is still a possibility that some Neanderthal genes entered modern humans in the past, most of the genetic makeup of Europeans can be traced to the early migrations Out of Africa.

— Version right now

I see a lot of problems with this.

  • First settlers as a title leaves a lot of explaining to do. Who decided who the first settlers are? In other words why are Cro Magnon the first and not the Neanderthals or other archaic humans? In order to help readers understand this the distinctions between archaic and anatomically modern needed to be mentioned but this has been removed.
  • First sentence implies consensus in the literature which does not exist. Many authors think the genetic landscape of Europe results largely from things happening when farming was introduced or after. The sources given are two Tishkoff articles, one from 1996, and one about a different subject.
  • The third sentence then goes on to explicitly imply there is consensus opposite to what the first sentence demanded!
  • The second sentence implies that there is consensus that the Sinai was unimportant. Why?
  • Last sentence does not define "the early migrations Out of Africa" which people who know the subject will know is unrealistic, and which will mislead people who do not know the subject.

Several of these problems keep getting inserted into the text and have been pointed out before. (Or perhaps it is more correct to say that important information keeps getting removed leaving big holes.--Andrew Lancaster (talk) 05:49, 7 September 2009 (UTC)

What text do you suggest. Wapondaponda (talk) 06:16, 7 September 2009 (UTC)
It might be easier to just start editing, because we are not in an edit war, but I see the first and second sentences as basically needing to go (exact migration routes between Africa and Asia not relevant anyway) ; and then some extra information has to be inserted to make some points more clear.--Andrew Lancaster (talk) 07:09, 7 September 2009 (UTC)

Looking ahead at questions that might be raised

For the time being, this subject now has a chance to settle into an article and justify its existence. (Small Victory and SOPHIAN managed to get themselves blocked for those who don't realize.) We do not know how it will look after a month or so, but it is possible that the subject matter will substantially overlap with Genetic History of Europe. I thought it worth already stating that my thinking about the questions this raises would be like this:

  • If the content could be merged in Genetic History of Europe with creating big diversions, then I think everyone should be happy that we had a chance to polish up this material and merge it back into a presumably better article? The extra discipline of having to work on one theme might even lead to this article containing preferable materials for some sections, and indeed I suggest that anyone editing either article should look to the other every now and then for ideas.
  • If it is not possible to insert whatever this article becomes without substantially messing up the Genetic History of Europe article with diversions etc, then I guess this here article (with a better name?!) should stay.

Is this also how others see it?--Andrew Lancaster (talk) 10:10, 7 September 2009 (UTC)

Eventually some content will have to be merged back into Genetic history of Europe. But it should follow the format of WP:Summary style. In other words, we should have a summary of this article in Genetic history of Europe, and we can maintain this article. The main reason for maintaining this article has to do with space. In general the content in GHOE should be proportional to the proportion of admixture, so we cannot have too much information about African admixture on GHOE. But there are no limits to how much information we can place in this article, as long as it is directly relevant and notable. Wapondaponda (talk) 10:32, 7 September 2009 (UTC)
In terms of parts of these two articles being merged, this can always happen and indeed I did some edits to both today, based on comparing them, and I can see more. But what if we come up with an article which is essentially covering subjects which are ALL covered in the other article, and could be merged back in without making the other article worse in any way including length? What I guess I am saying is that if this does happen I see no problem merging it back in.--Andrew Lancaster (talk) 11:07, 7 September 2009 (UTC)

STRUCTURE charts show continental ancestry and admixture proportions

These are descriptions of the STRUCTURE charts from the studies they're used in (and the paper by the program's creators that all the studies reference):

We describe a model-based clustering method for using multi-locus 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. [...] 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

We utilized the unsupervised clustering algorithm implemented in STRUCTURE [12,13] to group individuals into genetic clusters in such a way that each individual is given an estimated membership coefficient for each cluster, corresponding to the fraction of his or her genome inferred to have ancestry in the cluster. [...] Each individual is represented by a thin line partitioned into K colored segments that represent the individual's estimated membership fractions in K clusters.
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010070

In order to quantify patterns of population structure and admixture, we utilized STRUCTURE [Pritchard et al. 2000], a commonly used Bayesian clustering method. [...] Setting the number of clusters (K) to five revealed structure largely corresponding to continental regions (Figure 1A).
http://genome.cshlp.org/content/early/2009/02/12/gr.088898.108.full.pdf

The PCoA clearly identifies four widely dispersed groupings corresponding to Europe, South Asia, Central Asia, and Africa [...] A complementary Bayesian approach that uses the program STRUCTURE [14,15] supports the PCoA findings (fig. 1C). This method generates admixture components from individual genotype data without consideration of previous population labels, essentially with the use of departures from Hardy-Weinberg equilibrium. When the number of putative populations (K) is set at four, the groups largely correspond to the same four regional divides apparent from the PCoA.
http://www.anthro.psu.edu/Student/graduate/docs/marc%20bauchet%20Measuring%20Population%20Stratification%20with%20Microarray.pdf

At K = 5, the 938 individuals segregate into five continental groups, similar to those reported in a microsatellite-based study of the same panel. [...] In many populations, ancestry is derived predominantly from one of the inferred components, whereas in others...there are multiple sources of ancestry. [...] Mixed ancestries inferred from genetic data can often be interpreted as arising from recent admixture among multiple founder populations. In the current setting, however, the estimated mixed ancestry can be due either to recent admixture or to shared ancestry before the divergence of two populations but without subsequent gene flow between them.
http://www.sciencemag.org/cgi/content/abstract/319/5866/1100

We applied a model-based clustering algorithm that, loosely speaking, identifies subgroups that have distinctive allele frequencies. This procedure, implemented in the computer program structure (14), places individuals into K clusters, where K is chosen in advance but can be varied across independent runs of the algorithm. Individuals can have membership in multiple clusters, with membership coefficients summing to 1 across clusters. [...] At K = 5, clusters corresponded largely to major geographic regions. [...] In several populations, individuals had partial membership in multiple clusters, with similar membership coefficients for most individuals. These populations might reflect continuous gradations in allele frequencies across regions or admixture of neighboring groups.
http://pritch.bsd.uchicago.edu/publications/RosenbergEtAl02.pdf

The apportionment of individuals (the average per-individual proportion of ancestry) from each of the eight populations into the four STRUCTURE-defined clusters (Table 2) broadly corresponds to four geographical areas: Western Eurasia, Sub-Saharan Africa, China and New Guinea.


http://www.ucl.ac.uk/mace-lab/macepdf/Wilson-NatGen-01-GDR.pdf

And of course, these studies often discuss admixture in different populations when it's present (obviously, they rarely discuss it when it's absent):

Notably, 62% of the Ethiopians fall in the first cluster, which encompasses the majority of the Jews, Norwegians and Armenians, indicating that placement of these individuals in a 'Black' cluster would be an inaccurate reflection of the genetic structure. Only 24% of the Ethiopians are placed in the cluster with the Bantu and most of the Afro-Caribbeans; however, 21% of the Afro-Caribbeans are placed in a cluster with the West Eurasians (presumably reflecting genetic exchange with Europeans). Finally, China and New Guinea are placed almost entirely in separate clusters, indicating that the ethnic label ‘Asian’ is also an inaccurate description of population structure.


http://www.ucl.ac.uk/mace-lab/macepdf/Wilson-NatGen-01-GDR.pdf

Mexico: As discussed in the main text, we quantified the admixture in Mexicans using a STRUCTURE analysis of Mexicans, Europeans and East Asians. We extracted 778 individuals from the POPRES, comprising of 107 Mexican individuals, 400 randomly selected European individuals with known European grandparents and 271 East Asian individuals (including 90 HapMap individuals). We used 6,557 SNPs with MAF in these populations of > 0.2 (within Mexico) and spaced at least 400kb apart. 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%. Further increasing K only reveals further admixture among European populations or separates the Japanese and Chinese populations.
http://genome.cshlp.org/content/suppl/2009/05/01/gr.088898.108.DC1/Supplementary_Material.pdf

In many populations, ancestry is derived predominantly from one of the inferred components, whereas in others, especially those in the Middle East and South/Central Asia, there are multiple sources of ancestry. For example, Palestinians, Druze, and Bedouins have contributions from the Middle East, Europe, and South/Central Asia. Burusho, Pathan, and Sindhi have an East Asian contribution. Hazara and Uygur share a similar profile of combined South/Central Asian, East Asian, and European ancestry. In East Asia, only the Yakuts share ancestry with both Europe and America, although these contributions are small. Although much of sub-Saharan Africa, Europe, and East Asia appears to be homogeneous in Fig. 1A, finer substructures can be detected when individual regions are analyzed separately. For example, we identified two components that separate the 16 East Asian populations and correspond to a north-south genetic gradient (fig. S2A). Han Chinese can be divided into a southern and a northern group. A similar analysis for South/Central Asia is shown in fig. S2B. Mixed ancestries inferred from genetic data can often be interpreted as arising from recent admixture among multiple founder populations. In the current setting, however, the estimated mixed ancestry can be due either to recent admixture or to shared ancestry before the divergence of two populations but without subsequent gene flow between them. For example, the European and Asian ancestries seen in Uygur and Hazara populations are likely due to relatively recent admixture, whereas the inferred Native American ancestry in Yakuts and Russians likely reflects shared ancestry before the predecessors of the Native Americans crossed the Bering Strait. The Middle Eastern populations may have experienced both continuous gene flow and shared ancestry with the rest of Eurasia.


http://www.sciencemag.org/cgi/content/abstract/319/5866/1100

--- Small Victory (talk) 12:54, 8 September 2009 (UTC)

From your chosen quotes:

Mixed ancestries inferred from genetic data can often be interpreted as arising from recent admixture among multiple founder populations. In the current setting, however, the estimated mixed ancestry can be due either to recent admixture or to shared ancestry before the divergence of two populations but without subsequent gene flow between them. For example, the European and Asian ancestries seen in Uygur and Hazara populations are likely due to relatively recent admixture, whereas the inferred Native American ancestry in Yakuts and Russians likely reflects shared ancestry before the predecessors of the Native Americans crossed the Bering Strait.

I think you have to actually make clear what you are arguing. No one has said articles using STRUCTURE can not be cited. No one denies that this is one tool of the trade. And yet you seem to see yourself arguing against such arguments. The only debate clear in my mind is about a specific interpretation of a specific graphic from a specific article. You were unable to find words in the article to say what you wanted the graph to say so you wrote them yourself and failed to convince anyone that this was not original research. Is there any other subject being discussed?--Andrew Lancaster (talk) 13:14, 8 September 2009 (UTC)
Whether it's "recent admixture" or "shared ancestry", Europeans have virtually none of it from Africans, and that's the whole point. And yes, Muntuwandi is trying to deny the validity of STRUCTURE and have it barred completely for precisely that reason. Where have you been? ---- Small Victory (talk) 13:10, 9 September 2009 (UTC)
I won't engage in the STRUCTURE debate any longer until there is some new information that hasn't already been discussed. If SV can provide unambiguous information from reliably sources that says based on STRUCTURE, we conclude that there is no African admixture among Europeans, then we can include such information alongside the other reliable sources that say otherwise. What I have stated are requirements stated at WP:PROVEIT and WP:NOR. Until then it is pointless to go around in a circular debate. Wapondaponda (talk) 17:05, 9 September 2009 (UTC)
I do not know if I am saying the same thing but I would suggest, SV, that you make concrete proposals and we discuss those. It seems pointless to argue about a theoretical general disagreement like "the value of STRUCTURE" or "Afrocentrism" when disagreements are really just about specific practical wording proposals as far I see. Let's learn from the pointless conversations of the past.--Andrew Lancaster (talk) 17:25, 9 September 2009 (UTC)

It's very simple. The two of you just don't want to accept the facts. STRUCTURE analysis is the only method of genetic testing that's designed specifically to show continental ancestry and admixture proportions, as stated clearly in all of the sources cited above. These same sources show virtually no African ancestry or admixture in a representative sampling of Europeans. Therefore, this article is an Afrocentric POV fork and should not exist. Period. ---- Small Victory (talk) 12:50, 10 September 2009 (UTC)

That is still very vague. Just saying "it is all about other editors" is actually a useless accusation because it is not about the subject we are supposed to talking about, making an encyclopedia. What precise text are we debating about? Do you have a concrete proposal? The only proposal I know about are your personal interpretations of articles which have been criticized as OR. Is there anything else?--Andrew Lancaster (talk) 17:18, 10 September 2009 (UTC)
I'm writing in plain English, Andrew, and I've cited numerous sources. If you think what I'm saying is "vague", then the problem is with you. ---- Small Victory (talk) 13:26, 11 September 2009 (UTC)
So put an ANSWER in clear English please. What Wikipedia text changes are you proposing? Really this is not the place to be defending STRUCTURE or complaining about Afrocentrist plots. Is all of this just a very indirect way of trying to defend the same stuff which has already been taken to several other forums of discussions and found to be OR? Or do you have some new proposal? Who knows, maybe if you make your proposal clear there will be an agreement that will come out of it.--Andrew Lancaster (talk) 13:38, 11 September 2009 (UTC)

Small medium or a lot

There are many ways to characterize the African contribution to European genetic diversity. If we looked at E3b alone, according to Cruciani it accounts for 7.2% which places it in the top 3 most common haplogroups in Europe, by some reports. Maybe top 6. That is quite significant. However, mtDNA levels are quite low, less than 1%. Most importantly, the autosomal levels are difficult to analyze. Cavalli-Sforza's simulation from the 1990s predicted 35% though occuring 30,000 years ago. These older methods have of course been updated, and those figures are not frequently reported, however these figures are consistent with the presence of e3b lineages. The complication with E3b lineages is that it only involved a few African males, because only one African lineage dominates. These males brought some pre-Agricultural technology from Africa, which mixed and matured in the Near East, after which their y-chromosomes proliferated in Europe. However, this seems to have been a one off event, and afterwrds the links to Sub-Saharan Africa were cut off, or significantly curtailed. Because this was a one off event, the admixture of these Africans was over time, diluted, however evidence remains in the y-chromosome because it remains intact and is not subject to dilution as is the case with Autosomal markers.

A further complication is the time depth. E3b lineages entered Europe sometime after 11kya. This is recent relative to the OOA migration 50-70kya, but it is still a long way back. Most importantly both Africans and Europeans have undergone important demographic changes due to the impact of farming. In Europe, it seems, that paleolithic lineages were replaced by Neolithic lineages and in Africa the Bantu expansion significantly reduced diversity. These demographic changes make it difficult to determine the genetic profiles of ancestral populations to determine admixture. The exponential population expansions that occurred after farming have exaggerated the effects of natural selection, sexual selection, drift and founder effects. The result is that even though an initial admixture event may be high, over time, the forces of evolution would act to modify genetic profiles so as to make admixture harder to detect.

In short, there are several different ways to characterize admixture and percentages may be an oversimplification. Wapondaponda (talk) 20:51, 14 September 2009 (UTC)

I think time-frame is what makes this subject awkward, and so that must probably be where you have to find the solution to how best to structure this. I know it is like a cracked record to keep saying that all lines are African if you go back far enough, but it still seems to be something you are not keeping in mind enough. If you do not keep in mind things get very confusing because you are not comparing apples with apples, and the term African becomes meaningless.
For example, for discussion here is a step wise version of what I mean, which accepts the common idea that the Neolithic is the single biggest event in the formation of Europe's modern genetic make-up.
  • At a certain time depth, 100% of genetic diversity in Europe was African. The time depth itself is controversial but I suppose it is not controversial to say that it is "close to" 100% at the time when the earliest anatomically modern humans were still in Africa. In other words, if you go back that far all or almost all European ancestors were in Africa, give or take a few possible Neanderthals or other archaic interbreeding.
  • The next big "almost replacement" phase is perhaps when the more gracile types of homo sapiens were in Africa, on their way to replacing Cro Magnon man more or less. In the Mesolithic just before the Natufian perhaps, we can probably still say that the majority of European ancestry might be in Africa, and therefore "African"? [Later edit: not really. The Neolithic in the Middle East was not clearly not just African.]
So I guess I am thinking that if it is ever going to succeed the article needs this stuff laid out early like a set of rules. Then if you take this approach most Eb1b in Europe is only African in what we can perhaps think of as the last wave out of Africa. I think you really have to say that, sure, but be careful not to exaggerate how African that is, given that there might be a lot of European genes that are African in this sense.--Andrew Lancaster (talk) 21:24, 14 September 2009 (UTC)

New HLA study

A new study

  • Lulli; et al. (2009). "HLA-DRB1 and -DQB1 loci in three west African ethnic groups: Genetic relationship with sub-Saharan African and European populations". doi:10.1016/j.humimm.2009.07.025. {{cite journal}}: Cite journal requires |journal= (help); Explicit use of et al. in: |last= (help)

Not much detail in the abstract, but the title is suggestive. Wapondaponda (talk) 17:49, 15 September 2009 (UTC)

Comment and advice

Some of the discussion above, and the apparent uncertainty about the state of the science in this area concerns me. Part of the problem, which is no doubt related editing disputes, seems related to the reliance on data from individual scientific articles, and the attempt to put together a full picture of the topic from these. As we have seen, there is a strong danger of original research with this approach. Are there no update-to-date review articles discussing the evidence? A chapter or paragraph from a book? These should form the foundation of the article rather than the individual studies. I realize that this is not a medical article per se, but these guidelines may prove helpful when thinking about what sources should be used here. [1] --Slp1 (talk) 17:54, 18 September 2009 (UTC)

Many genetics articles have the problem that whatever books are out there are probably poor and out of date. There just isn't enough secondary literature, and so it is hard to avoid. However concerning this particular article, I personally think that Muntuwandi is falling into a similar trap to the one Small Victory got into - obsessing about the latest findings concerning details, when actually, for this particular article the details are not the subject and a fairly uncontroversial broad outline is possible to build up. At least I think it should be easier than in some of the other cases we've had.--Andrew Lancaster (talk) 18:02, 18 September 2009 (UTC)
Interesting. But might not recent scientific articles have good reviews of the state of the scientific literature/knowledge about the issue that could be used as a basis? I can't judge the specifics here, because I can't make head or tail of the article, which is in itself a problem, because articles here are supposed to be written for a general audience. I would support your suggestion that a broad uncontroversial sweep is going to be better than a mass of detail. Muntuwandi, what do you think? --Slp1 (talk) 18:25, 18 September 2009 (UTC)
I can understand the concerns, particularly when it comes to using a specific book that forms the foundation of an article. The problem so far, is that peer reviewed studies do not have a format that is wikipedia-friendly. Popular science books are more wiki-friendly. The seminal popular science books included Cavalli-Sforza's History and Geography of Human Genes, and Genes Peoples and Languages which both discuss African Admixture, however these books are great for wikipedia, but they are somewhat dated. These books were succeeded by a wave of popular science books concerning genetic genealogy (The Real Eve, The Journey of Man, The Seven Daughters of Eve, etc), but there has since been a lull in new publications. So unfortunately we have to use peer reviewed studies and much of what they have is raw data. Furthermore most books are publications, focus on only one type of genetic marker. That is either the y-chromosome, mtDNA or a particular microsatellite locus or HLA. It would be great if someone could compile all this information in a book and cross reference the information. There is a similar discussion Talk:Y-DNA_haplogroups_by_ethnic_groups#Mission_impossible. However, I must state, that most of the information is an accurate representation of the sources. The only thing is that the format of presentation is different.Wapondaponda (talk) 18:29, 18 September 2009 (UTC)
If you look at medical articles, you will see that brand new information from one or two articles is not allowed, all by itself, to change the focus and direction of an article. The conclusions of the most recent review articles form the core, and newer, potentially contradictory information is given little or no place until the scientific community (not WP editors) determine the relevance and importance of the study's results to the subject at hand. I would recommend a similar approach. The danger of striving to be up to the minute up-to-date is that anonymous WP editors end up doing evaluations that are better done by named scholars.--Slp1 (talk) 18:45, 18 September 2009 (UTC)
There is always a conflict with genetics articles between including detail and making articles accessible to a general audience. So I can understand some of the confusion. What I would suggest, is that if you could pin point specific issues that are problematic, then we can attempt to address them. As for controversies, I don't see a major paradigm shift with regard to the specific genetic lineages discussed in this article. We are just likely to see more sampling of populations and more detail, but the new information is likely to be consistent with what is already known. The content of this article is controversial in the blogosphere, and it is controversial on Wikipedia, but there doesn't appear to be any controversy amongst the scientists themselves.Wapondaponda (talk) 19:39, 18 September 2009 (UTC)
In this particular article Muntuwandi, can you honestly say that most of the basic insights from the Cavalli Sforza works and similar have been destroyed by newer material, such as STRUCTURE methods, or bigger surveys of more genes? Honestly I do not see that? In the Genetic History of Europe article we now start with CAvalli Sforza and give a few uncontroversial updates, and I tend to think that this may also work here?--Andrew Lancaster (talk) 20:01, 18 September 2009 (UTC)
Actually, I have been a supporter of including Cavalli-Sfoza's earlier works. It has been Pdeitiker who believes that they are obsolete. What I have found most interesting is that despite the older technology, their results are still consistent with what is known now. CS used 120 markers, but the results are still similar when half a million markers are used. The main issue with CS, is that his studies were done before most of the y-chromosome and mtDNA lineages were sequenced. Otherwise CS's works are still considered classics. Wapondaponda (talk) 20:08, 18 September 2009 (UTC)
My basic proposal is that you try to build a VERY solid foundation that is as uncontroversial as possible, and what I am arguing here is that I think this is possible. This is an area you are interested in and really it is up to you to see if this article can be become lasting material in Wikipedia right now.--Andrew Lancaster (talk) 20:11, 18 September 2009 (UTC)

I think what we have already is pretty reliable information that is sustainable in the long term. I am interested in this subject, but it is not the only subject I am interested in. There is no guarantee that I will always be around to edit this article. So the community has a stake in this article and future of the article depends on how the community feels. So far the community's response has been positive, with some even finding the article interesting. However, most editors who read or comment on this article only have a passing interest, and therefore I don't expect a lot of new contributions from editors in the near future. The trouble has been that SV's presence on wikipedia is almost exclusively about this article and its previous incarnations. It started at White people, then Sub-Saharan DNA admixture in Europe, then Genetic history of Europe and now this article. Based on his/here editing history, SV is a SPA who is fully devoted to this article, s/he has the time and effort to force POV material into the article. If this were to occur, chances are that nobody will oppose, not because they are agreeable, but because it takes time and effort to research the subject matter. Consequently, I would love to step aside and focus on other subjects, but because of editors I perceive to be " POV pushers" I will have to maintain an interest. Wapondaponda (talk) 23:51, 18 September 2009 (UTC)

Sickle Cell in Europe

There are five different mutations that can cause sickle cell, four of which are thought to have emerged in Africa, where as one is thought to have emerged somewhere between Arabia and India. The Sickle Cell genes are believed to have proliferated in areas affected by Malaria. Due to heterozygote advantage, a person with one copy of the sickle cell gene is resistant to Malaria, whereas a person with two copies, will be affected by anemia. Balancing selection applies. This Benin Sickle cell trait has been observed in Portugal, Sicily and in Israel amongst Arabs and Jews. There was once a section entitled "Adaptive autosomal markers" that dealt with it. I think this information is useful from a medical perspective. Sources include

Wapondaponda (talk) 22:32, 21 September 2009 (UTC)

GM immunoglobulin allotypes

The following I put in bold is incorrect. You simply need to look at the source.

"Further studies have shown the presence of haplotype GM*1,17 23' 5* in southern Europe. This haplotype is considered a genetic marker of subSaharan Africa, where it shows frequencies of about 80%.[34] Whereas in non-Mediterranean European populations that value is about 0.3%, in Spain, the average figure for this African haplotype is nearly eight times greater at 2.4% and it shows a peak at 4.5% in Galicia[35]. Values of around 4% have also been found in Huelva, in the Aran valley in the Pyrenees[36] and the large islands of Sicily (ranging from 1.56% at Valledolmo to 5.5% at Alia), Corsica and Sardinia.[37]. According to Calderon et al. 2007, although some researchers have associated African traces in Iberia to Islamic invasions, the presence of GM*1,17 23' 5* haplotype in Iberia may in fact be due to more ancient processes as well as more recent ones through the introduction of genes from black slaves from Africa.[35]"


The source:

"The GM*1,17 23' 5* haplotype shows a peak in Galicia (0.045), although values of around 0.04 have also been found in the Aran valley in the Pyrenees [25] and the large islands of Sicily, Corsica and Sardinia [24]. In Spain, the average figure for this African haplotype is 0.024, whereas in other non-Mediterranean European populations that value is nearly eight times lower (0.003). Although some researchers have associated African traces in Iberia to Islamic invasions [12,13], the presence of GM*1,17 23' 5* haplotype in the Galician population may in fact be due to more ancient processes as well as more recent ones through the introduction of genes from black populations from America. Other evidence of African genetic influences in western Iberians has been provided by analysis of variation of Y chromosome [26] and mtDNA [27]. In the latter paper, the authors hypothesise that haplogroup L was introduced in Portugal through the recent Black African slave trade, while U6 lineages were associated with the Muslim rule of Iberia."


This ENTIRE WIKI article is filled with lies, distortions and all forms of manipulated information. It is disgraceful for WIKI to allow some of the information psoted. Any competent, unbiased geneticist would be shocked to read this trash in this section. It's time for all the insecure, mindless, sociopathic racists to grow-up and find a real job. —Preceding unsigned comment added by London Hawk (talk • contribs) 16:26, 28 January 2010 (UTC)

Thanks for taking an interest in this article. I hope you can help make it better. Please sign your postings, and please if you see an error which can be shown simply from the sources, make the change required. Don't waste your emotional energy by making angry speeches, because normally no one on Wikipedia will recognize your speech as applying to them. The article is the result of various edits and does need more work. But Wikipedia is not an organization. In fact, one could argue that you are Wikipedia too now, because you posted here. :) --Andrew Lancaster (talk) 20:05, 30 January 2010 (UTC)

I fixed it and some jack off changed it back despite the evidence I provided here that it was incorrectly quoted. 96.240.7.118 (talk) 07:45, 16 January 2012 (UTC)God

mtDNA

A recent study has not found mtDNA L in Spain in a 686 sample :

http://biotech-events.ifrance.com/CONFERENCES2006/037%20LOPEZ_PEREZ.pdf —Preceding unsigned comment added by Genetic truth (talk • contribs) 15:40, 19 March 2010 (UTC)

Other European countries

In another study on Norwegians, an L2 Sub-Saharan African sequence was found in the sample of 74 Norwegians (1.4% Sub-Saharan admixture) :

Giuseppe Passarino et al., Different genetic components in the Norwegian population revealed by the analysis of mtDNA and Y chromosome polymorphisms, European Journal of Human Genetics10, 521 - 529 (23 Aug 2002)


AUTOSOMAL :

Rosenberg et al. 2002 and Wilson et al. 2001 found 1% of autosomal in Norwegians.


Needless to say, your suspicious claims contradict STRUCTURE studies, which do not find any peculiarly higher admixture levels, sub-Saharan or otherwise, in Southern Europeans than among Northern Europeans. In fact, some of these studies have found lower admixture levels in some Southern Europeans, including Spaniards: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852743/ http://i34.tinypic.com/ekm6h1.png

González-Pérez et al. (2010) have analyzed populations from the northern and southern shores of the Mediterranean, with Central Europeans and West Africans as external references. They estimate Sub-Saharan African admixture using two methods that yield vastly disparate results. In the Discussion section, they admit that the inflated "Alu/STR estimate might be artefactual" and favor the estimate based on the Alu loci set alone because it's consistent with previous mtDNA, Y-chromosome and 500,000-SNP structure data. According to the more accurate latter method, Sub-Saharan African admixture is ~13% in North Africa and "imperceptible" (~0.01%) in Southern Europe: http://img684.imageshack.us/img684/847/gonzalezperez2010admixt.png

A similar study by Auton et al. 2009, which also contains an admixture analysis chart but no cluster membership coefficients, shows little to no sub-Saharan African influence in a wide array of European samples, i.e. Albanians, Austrians, Belgians, Bosnians, Bulgarians, Croatians, Cypriots, Czechs, Danes, Finns, Frenchmen, Germans, Greeks, Hungarians, Irish, Italians, Kosovars, Latvians, Macedonians, Netherlanders, Norwegians, Poles, Portuguese, Romanians, Russians, Scots, Serbians, Slovakians, Slovenians, Spaniards, Swedes, Swiss (German, French and Italian), Ukrainians, United Kingdom and Yugoslavians. —Preceding unsigned comment added by Genetic truth (talk • contribs) 15:49, 19 March 2010 (UTC)

Move

Per Andrew I am moving this article to African contributions to human genetic diversity in Europe Sir. Yorkshire (talk) 04:47, 20 March 2010 (UTC). Of course if this is a stupid move correct me Sir. Yorkshire (talk) 04:49, 20 March 2010 (UTC). Since Anatolia,Cyprus the Levant and Arabia are not in Europe and in this article I am moving this article to African contributions to human genetic diversity in Eurasia.Of course if this is a stupid move correct me. Sir. Yorkshire (talk) 23:38, 20 March 2010 (UTC)

No consensus for a move. Anatolia, Cyprus the Levant and Arabia are discussed because they are en route to Europe, there is no discussion of Iran, Iraq, Yemen, Afganistan, Pakistan and India for which African admixture data exists. Anatolia and Cyprus, depending on the context, can be considered as part of Europe. What is discussed is mainly in the context of Europe.

Requested move

The following discussion is an archived discussion of a requested move. Please do not modify it. Subsequent comments should be made in a new section on the talk page. No further edits should be made to this section.

The result of the move request was: page moved. Closing discussion since the move was already done Vegaswikian (talk) 01:09, 2 April 2010 (UTC)


African contributions to human genetic diversity in Eurasia → African admixture in Europe — African admixture in Europe was yesterday moved to African contributions to human genetic diversity in Eurasia. There is no consensus yet for such a move, request a move back to the original name, while discussions are ongoing. Wapondaponda (talk) 07:33, 21 March 2010 (UTC)

  • There was no consensus reached for a move, so I have moved this back to the original name and protected it against further moves. Please continue to discuss this, and if consensus is reached for a move, myself or any other admin will be happy to assist in the rename. Happy consensus-building. -- RoySmith (talk) 14:22, 21 March 2010 (UTC)
The above discussion is preserved as an archive of a requested move. Please do not modify it. Subsequent comments should be made in a new section on this talk page. No further edits should be made to this section.
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