Pdeitiker

As a fellow member of the WikiProject HGH may I ask for opinions on this accusation?--Andrew Lancaster (talk) 12:09, 27 June 2009 (UTC)Reply

I hope you don't mind that I've just raised a bit of discussion about the reference formats. I just want to get it straight in my mind what we are heading towards, and I think other potential editors will need this also. Look at other Y haplogroup articles and you know why I am cautious.--Andrew Lancaster (talk) 11:55, 30 June 2009 (UTC)Reply

Thanks for your work on the E1b1b article. I keep editing on what you do, but this does not mean I don't appreciate the leads you are giving. We have tended to accrete too much justification of every word and sentence due to the history of editing. Once you start cleaning up, I can sometimes see ways to go further. Anyway, we got off-topic concerning the sub Saharan issue and I wanted to mention that I think the article I mentioned is headed to deletion unless someone can make something encyclopedic out of it, and I tend to think that the scientific literature is just not clear enough to provide a foundation. My reason for writing now is to suggest that you look at an article which has more promise but suffers from some of the same problems: Genetic history of Europe.--Andrew Lancaster (talk) 06:50, 11 July 2009 (UTC)Reply

E1b1b1a as a separate article is just a matter of time I think. Just needs time. Have already done one of course on the haplowiki: http://www.haplozone.net/wiki/index.php?title=E-M78. --Andrew Lancaster (talk) 21:07, 13 July 2009 (UTC)Reply

I kind of agree. It depends a lot upon the edit war factor! Look how much work it is sometimes to change a couple of words on this article. Of course the edit would not need to concern sub Saharan Africa and races, so maybe there is hope! But there could be disagreements about what should stay in E-M35 and what should move on. Would we leave everything in E-M35 in the first stages? I'd suggest we make the new article before starting to delete any big chunks. People might start reverting out of surprise.--Andrew Lancaster (talk) 13:28, 14 July 2009 (UTC)Reply

What do you know? I started splitting and now we have a problem with reverts on the original page with several of the reduction of detail edits being reverted. This can get confusing!--Andrew Lancaster (talk) 17:00, 15 July 2009 (UTC)Reply

Wondering if you'd be interested in commenting on any of the specific discussions on Sub-Saharan DNA admixture in Europe and Genetic history of Europe. The latter is the "keeper" but some of the debates on the former are likely to rage on to other articles.--Andrew Lancaster (talk) 14:10, 17 July 2009 (UTC)Reply

I agree, and I think that your agreement to my deletion proposal says all that needs to be said on the biggest problems of this page. What I was more interested in was getting your input on some of the specific discussion going on on that talkpage. Presuming the article gets deleted, these arguments will probably migrate to Genetic History of Europe. BTW I think Tishkoff came up with a homeland of human genetic diversity, so to speak, near Angola. Quite interesting.--Andrew Lancaster (talk) 14:33, 17 July 2009 (UTC)Reply

FYI, some discussion of Europe-Sub Saharan DNA links has continued on Genetic history of Europe. --Andrew Lancaster (talk) 05:26, 21 July 2009 (UTC)Reply

Hi, in response to your messages, yes I can imagine further improvements on E1b1b. I had already reduced the size of E1b1b1a in the most obvious ways. I don't have a lot of time right now and I don't remember anything needing urgent fixing, but by all means keep looking at it. You seem to see things I don't notice, which is good.--Andrew Lancaster (talk) 23:27, 23 July 2009 (UTC)Reply

I would very much like you to write a draft here, rather than leaving it as a ping pong match: [1]--Andrew Lancaster (talk) 14:39, 26 August 2009 (UTC)Reply

I get your point but if you would write one paragraph on the talk page of the article, and if I can follow it, then I can use it to try to develop a compromise. I fear any draft by Small Victory or Wapondaponda is doomed, and my own draft is not going to please because it misses a lot. It is not an area I have looked at closely yet.--Andrew Lancaster (talk) 06:05, 27 August 2009 (UTC)Reply

Maybe relevant to some comments you made recently: http://www.miller-mccune.com/science_environment/the-ancestor-hunter-1372 --Andrew Lancaster (talk) 19:31, 1 September 2009 (UTC)Reply

Have had a reasonably serious effort today on the African admixture in Europe article. Yesterday I also deleted the edit war ground sections in the Genetic History of Europe article. Comments welcome.--Andrew Lancaster (talk) 11:01, 3 September 2009 (UTC)Reply

Hi PB666, I've left a reply to your message on my talk page -- Marek.69 ^talk 01:49, 5 August 2009 (UTC)Reply

  Hello, Pdeitiker. I've noticed that you have taken a step in the Dispute Resolution Process by posting in one of the dispute resolution forums. Please note that it is recommended that you advise the other party of your complaint filing so that they are aware of it, and so that they have a chance to respond.

If you have any questions, check out Wikipedia:Where to ask a question or ask me on my talk page.

In addition, you would be well-served to read the submission instructions on WQA, and remove excessive formatting and quoting, using diffs as directed. Right now, it's not likely to get a response (talk→ BWilkins ←track) 12:36, 15 August 2009 (UTC)Reply

Good to see another person looking at what we can do about frequency maps. I love the look of contour maps and I know they make things easy to understand, but they are also potentially misleading given the importance of assumptions in them. This means using them is always a balance between a copyright problem and OR. Perhaps the least controversial approach would be to use pie charts. I know of a person who collects such data and posts maps on internet forums. Maybe I can convince him to post his latest stuff on Wikipedia.--Andrew Lancaster (talk) 07:05, 17 August 2009 (UTC)Reply

The E1b1b article has a pretty good bibliography.

• Cruciani et al. (2004) is a "must use" and has good data for many of these areas.
• Hassan et al. 2008 is important because it fills the Sudan gap.
• Rosa et al. has Guinea Bissau.
• Robino et al. adds some detail for the Maghreb, as does Arredi et al. and Luis et al.
• There was a recent paper by Kujanova et al with some interesting data for Egypt.

More generally try the Haplowiki I have set up for the E-M35 project: http://www.haplozone.net/wiki/index.php?title=Kujanova_et_al._%282009%29. If you search for a country, you should find papers covering that country.--Andrew Lancaster (talk) 14:19, 17 August 2009 (UTC)Reply

Here is a new one for a very important region: http://dienekes.blogspot.com/2009/08/coastal-inland-differences-in-y.html--Andrew Lancaster (talk) 18:51, 17 August 2009 (UTC)Reply

• Cruciani et al 2007, too
• I agree that contour maps are intuitive. I have been trying to find software that can generate contours, but no luck yet. The frequency maps can work, but it must take a lot of work to make them. Wapondaponda (talk) 18:41, 17 August 2009 (UTC)Reply

The software packages are named in the papers? The method is the Kriging method. But to cut a long story short this method is just a formalization of guessing what is in the gaps. I think crude maps like PD is proposing are a good idea for avoiding the OR problem and the copyright problem.--Andrew Lancaster (talk) 18:51, 17 August 2009 (UTC)Reply

I just got in from work (12:30AM), its going to be a while before I can update those maps. The Dienekes link appears to be a deadlink, not sure why.PB666 ^yap 05:41, 18 August 2009 (UTC)Reply

Cruciani 2004 and 2007 is basically the same data set. I have tried to reconcile a bit here: http://www.haplozone.net/wiki/index.php?title=Cruciani_data . Let me know if you really can not get to the new article about Syria and Lebanon etc. Another one that might be useful is this new one.--Andrew Lancaster (talk) 12:13, 18 August 2009 (UTC)Reply

I should point out that the haplowiki has several data tables already made: http://www.haplozone.net/wiki/index.php?title=Category:Data . See for example the collection for M123: http://www.haplozone.net/wiki/index.php?title=E-M123_data --Andrew Lancaster (talk) 07:47, 19 August 2009 (UTC)Reply

The basic strategy is to create a Template map that has countries (grey bordered by black or blue) and samples (shades of grey) within countries. The big problem is getting the 2nd. An example of the problem is Kenya has 6 regions which speak bantu and 3 regions that speak bantu and other indigeonous languages. When someone states Kenya Bantu one has to make assumptions that these equally represents all bantu speaking areas of Kenya, but not areas were mixed Bantu is spoken. If not the authors need to state explicitily which region they sampled.

I can give you a list of the samples that are going to take time to process through for the map:

• Northern Russians (Is he referring to ethnic russians and what is the dividing line)
• Southern Russians
• Greeks from Aegean Peloponnese was continental,Euboea as part of Lamia
• Asni Berbers A tiny village just west of Marrakesh
• Bouhria Berbers (I assume these are northern most Morrocan Berbers)
• Moyen Atlas Berbers(What country what berber population)
• Moroccan Jews, Libyan Jews
• Mozabite Berbers (Algerian, there are 9 regions with berbers in Algeria)
• Delta Egyptians (What defines the delta)
• Northern Egyptians (What deliniates N. Egyptians?)
• Egyptian Berbers (Where from?)Siwa Oasis
• Egyptians from Baharia (Where?)Baharyia Oasis <-Assume
• Egyptians from Guma Oasis(Where?)
• Southern Egyptians Southern Half of Egypt<-Assume
• Mixed Ethiopians
• Borana/Oromo (Kenya/Ethiopia)
• Wolayta (who?) mispelled found but no map yet.
• Western Africa (which country(s))
• Mandenka Senegalese (nikoloko?)
• Pygmies (YIKES! threre are fifteen+ pygmy tribes scattered bout Africa)
• Southern Africa (what countries, what people)
• Southwestern Turkish,Northeastern Turkish,Southeastern Turkish, Erzurum Turkish, Central Anatolian (What divides these groups?)
• Bedouin (from where? W. Arabia?)
• Adygei (who)
• Portugal Southern (there is a northern portugal map, southern Portugal may be the southern most province or southern most 4 provinces)

Each one of these requires a search, and after they're respective territories are found, (Hopefully as a Map), the map needs to be drafted and repainted, eliminating all accessory color information leaving a simple polychromatin representations. That then needs to be shrunk, streched, skewed such that it overlays exactly with the wikitemplate map. Then it needs to be recolored, rebordered. At this point one needs to decide if the study represents part or all of a color region. So that I need help finding what is a good representative map of a given sampling, or some indicator, for example coordinates X +/- 1degree or 5 minutes (A minute is approximately a nautical mile at the equator). Once I get through these peoples then I will move onto other studies.PB666 ^yap 14:17, 19 August 2009 (UTC)Reply

I do not see a PMID for the new El-Sibai paper with new Syrian data, and this may be because it is an early pre-publication? Anyway the doi does exist: 10.1111/j.1469-1809.2009.00538.x . As a URL maybe this is better: http://www3.interscience.wiley.com/journal/122553140/abstract TI: Geographical Structure of the Y-chromosomal Genetic Landscape of the Levant: A coastal-inland contrast Annals of Human Genetics 2009 DOI: 10.1111/j.1469-1809.2009.00538.x US: http://dx.doi.org/10.1111/j.1469-1809.2009.00538.x --Andrew Lancaster (talk) 07:49, 20 August 2009 (UTC)Reply

I agree that the El-Sibai data gives problems because of the unclear mixture of data sets. They clearly did not do the same tests on all samples, and if we just remove the ones which are most obviously useless this will bias the data. For the haplowiki I only dared to say what % of a/b/c tested E1b1b was a, b and c, because working out what % of the whole population would involve quite a few steps of analysis beyond what we get out of the paper. The paper did however remind me of the older Zalloua papers and I added E-M123 data for Cyprus and Palestinians to the E1b1b article on Wikipedia, and to http://www.haplozone.net/wiki/index.php?title=E-M123 http://www.haplozone.net/wiki/index.php?title=E-M123_data --Andrew Lancaster (talk) 05:38, 21 August 2009 (UTC)Reply

This might be a practical limitation but perhaps it should be mentioned that your base maps are a little Euro-centric, missing some interesting areas like Somalia and Kenya and most of the Middle East. I don't know if there is any alternative?--Andrew Lancaster (talk) 06:26, 21 August 2009 (UTC)Reply

Yes, because originally there were only a couple of points in Africa and Asia (mostlyu no occurrence points) not west Asia, the new map has been expanded in both directions so that now it includes Iran and also includes Kenya. Should there be a multitude of data on the E haplotypes south of Kenya then it can be enlarged. I like to keep the PNG sizes as small as possible for bandwidth regions, plus in Wikipedia they prefer images of thumbnail size which is standard 200px or so across, and at that size visual orientation on the maps is will decrease as the coordinate dimensions increase.

Expanding a map downward is not such a problem as expanding the map sideways when thumbs are created.PB666 ^yap 13:31, 21 August 2009 (UTC)Reply

If it is the Cruciani data which you are stuck on, don't forget that this data is discussed in several articles, so details missing in one might be present in the other.

• Cruciani; et al. (2002), "A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes" (PDF), American Journal of Human Genetics, 70: 1197–1214, doi:10.1086/340257 {{citation}}: Explicit use of et al. in: |last= (help)
• Cruciani; et al. (2004), "Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out Of Africa" (PDF), American Journal of Human Genetics, 74: 1014–1022, doi:10.1086/386294, PMC 1181964, PMID 15042509 {{citation}}: Explicit use of et al. in: |last= (help); Unknown parameter |month= ignored (help)
• Cruciani; et al. (2006), "Molecular Dissection of the Y Chromosome Haplogroup E-M78 (E3b1a): A Posteriori Evaluation of a Microsatellite-Network-Based Approach Through Six New Biallelic Markers" (PDF), Human Mutation, 27: 831, doi:10.1002/humu.9445 {{citation}}: Explicit use of et al. in: |last= (help)
• Cruciani; et al. (2007), "Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-Chromosomal Haplogroups E-M78 and J-M12", Molecular Biology and Evolution, 24: 1300–1311, doi:10.1093/molbev/msm049 {{citation}}: Explicit use of et al. in: |last= (help) Also see Supplementary Data.
• Scozzari; et al. (2001), "Human Y-Chromosome Variation in the Western Mediterranean Area: Implications for the Peopling of the Region" (PDF), Human Immunology, 62: 871–884, doi:10.1016/S0198-8859(01)00286-5 {{citation}}: Cite has empty unknown parameter: |unused_data= (help); Explicit use of et al. in: |author= (help)

--Andrew Lancaster (talk) 06:30, 21 August 2009 (UTC)Reply

I am going to process what I can and leave the map blank for those I have not struck on my list.PB666 ^yap 13:31, 21 August 2009 (UTC)Reply

I do not know why but the E-M78 level for Serbia looks too low in your map.--Andrew Lancaster (talk) 20:34, 24 August 2009 (UTC)Reply

Have you seen this: http://gunn.co.nz/map/ --Andrew Lancaster (talk) 11:09, 28 August 2009 (UTC)Reply

Hi, where is the table you refer to? Concerning how to improve these maps, more data is an obvious request, and mentioning all sourced used is another. In the end I can imagine these will still get some complaints because of the way it makes large countries look homogenous. Not sure how to fix that, but I am also looking around.--Andrew Lancaster (talk) 05:37, 8 September 2009 (UTC)Reply

Looking around, I've also been talking to a fellow "genetic genealogist" whose maps I like. For example http://i88.photobucket.com/albums/k178/argiedude/IberianM817201samples.gif One problem with many of his maps is that he tends to use predicted haplogroups in order to get value from article which only tested STR data, but perhaps it gives some ideas. I am trying to get him interested in loading maps to Wikipedia, suitable for Wikipedia! You can immediately see something with this M81 map which no published article has yet pointed to so clearly.--Andrew Lancaster (talk) 05:47, 8 September 2009 (UTC)Reply

I am asking the maker of this map what he might have that would not be so open to OR accusations. Concerning your question, good M78 data for the Balkans in several papers: http://www.haplozone.net/wiki/index.php?title=E-V13#Journal_articles_which_have_typed_for_V13 --Andrew Lancaster (talk) 18:33, 8 September 2009 (UTC)Reply

Yes, most E-M35* at least in East and South Africa will be E-M293 as discovered in Henn et al. (2008).--Andrew Lancaster (talk) 05:56, 10 September 2009 (UTC)Reply

I see you pasted in a M35* map anyway. I am not sure it is meaningful. You are correct that the Cruciani data on the haplo wiki should say M123 is always part of M35 not M78. Concerning M123, as it is a haplogroup that has only been discussed in bits and pieces in the literature I have made some effort to collect ALL data here: http://www.haplozone.net/wiki/index.php?title=E-M123_data --Andrew Lancaster (talk) 05:55, 11 September 2009 (UTC)Reply

Many thanks! I have corrected the Semino data and the Oman figure from Luis et al. Anything else?

• Please feel free to register and use the haplowiki. We can store data there with a lower level of concern for OR, because as a specialised wiki I believe that what is "obvious" is going to be different than on Wikipedia itself. For example we have allowed analysis based on STR modal haplotypes using the www.yhrd.org database [2] and we have also allowed use of Whit Athey's haplogroup predictor [3] in order to convert from STRs to SNPs.
• Sorry, I have never collected M33 data.
• Concerning the haplowiki a good way to find what you want might be to check the Category pages. For example for the Middle East.
• I think you have better access to articles than me. For R1a I could not look at the data for what might be an interesting article: Wang et al. (2003), "The origins and genetic structure of three co-resident Chinese Muslim populations: the Salar, Bo'an and Dongxiang", Human Genetics. Any chance you could show me a copy?--Andrew Lancaster (talk) 07:26, 13 September 2009 (UTC)Reply

I included information from Sanchez-Mazas in the article African admixture in Europe. I am not familiar with the nomenclature, so I was wondering whether the information is already covered by the other articles. I also found this article [Immunoglobulin allotypes in Southwest Asia: Populations at the Crossroads http://www3.interscience.wiley.com/journal/119054001/abstract]. I don't have access to the full article, but the abstract describes Sub-Saharan gene flow into Arabia. I am not sure whether this is associated with the Arab slave trade or prehistoric migrations. Wapondaponda (talk) 22:08, 17 August 2009 (UTC)Reply

What you write is interesting, and difficult to follow. Most importantly, or at least for what we are working on, what does it mean in terms of what we should put in a Wikipedia?--Andrew Lancaster (talk) 21:30, 22 August 2009 (UTC)Reply

I think there needs to be something explaining what "record longer genetic histories" means.--Andrew Lancaster (talk) 12:49, 24 August 2009 (UTC)Reply

So it comes down to meaning that they give older common ancestor estimates?--Andrew Lancaster (talk) 06:25, 25 August 2009 (UTC)Reply

Thanks for your explanation!--Andrew Lancaster (talk) 17:39, 2 September 2009 (UTC)Reply

Although you did the right thing by explaining your removal of s poorly worded section, you can't just delete what you don't like. Please update the text instead, with references. Note that Dawkins can be referenced (it did say it was a popular source). And please sign your talk past contributions. It's that not hard. --Michael C. Price ^talk 04:03, 23 August 2009 (UTC)Reply

Please stop instantly reverting. I'm trying to imptove the section. We don't even have time to read your talk page inserts before you started deleting the entire section again.--Michael C. Price ^talk 04:39, 23 August 2009 (UTC)Reply

Remember for future reference: do not delete unreferenced material material. Instead add a ^{[citation needed]} tag. If the material is sourced but you feel incorrect, and you don't want to correct it yourself, then add a ^{[clarification needed]} tag or something else. It saves a lot of wasted time. --Michael C. Price ^talk 10:10, 23 August 2009 (UTC)Reply

Sorry, stopped reading when I got to "However, since you refuse to read the guidelines let me make this clear." since I do and have read the guidelines.--Michael C. Price ^talk 18:24, 23 August 2009 (UTC)Reply

Not sure if you were watching this: http://en.wikipedia.org/wiki/Wikipedia:Articles_for_deletion/Eurasian_Adam --Andrew Lancaster (talk) 11:14, 9 September 2009 (UTC)Reply

Does this article Y-DNA haplogroups by ethnic groups, have a realistic chance of accurately displaying the correct information. Wapondaponda (talk) 04:13, 11 September 2009 (UTC) See Wikipedia_talk:WikiProject_Human_Genetic_History#Data_articles_.28tables_collecting_raw_data.29_for_Y_haplogroups --Andrew Lancaster (talk) 08:47, 11 September 2009 (UTC)Reply

Your response on my talk page, is again excessively verbose and most of it is not relevant to the issue I raised (about your posting erroneous information). Thus, I have limited my response, to your additional comments, to the actual issue of your posting erroneous information. If you choose to respond further, PLEASE limit your comments to that issue, without adding reams of comments that are not germane or relevant. EditorASC (talk) 09:08, 11 September 2009 (UTC)Reply

Since I have not left anything on your page in a week I think the best answer here is that I would be best to ignore troll bait. PB666 ^yap 13:44, 11 September 2009 (UTC)Reply

You are excessively verbose. See WP:TLDR.--Michael C. Price ^talk 20:50, 2 October 2009 (UTC)Reply

Thanks for being encyclopedic, PDeitker. JohnLloydScharf (talk) 23:51, 22 August 2011 (UTC)Reply

Thanks for that data table. Any chance you could e-mail me some more? Those for NRY STR markers are not saying much.--Andrew Lancaster (talk) 08:30, 15 September 2009 (UTC)Reply

The there is a mixture of text and tabled information, its real poor quality presentation. They don't even describe what the base is for the STRs, how do these kinds of things get accepted for publication?PB666 ^yap 14:14, 15 September 2009 (UTC)Reply

Any opinions on this? http://en.wikipedia.org/wiki/Talk:Anatomically_modern_humans#Out_of_Africa_versus_Multiregionalism --Andrew Lancaster (talk) 19:44, 16 September 2009 (UTC)Reply

I think I put it in so hopefully correct. Also see http://www.haplozone.net/wiki/index.php?title=Kujanova_et_al._%282009%29 . One thing I have not yet included anywhere is also this one: http://dienekes.blogspot.com/2009/09/y-chromosomes-of-saudi-arabia.html . Once again remember that I try to keep tabs on all data broken down by region in the Haplowiki, so if you search by a country, you'll find articles about those places. I also have a Category called Data which includes all articles that have raw data: http://www.haplozone.net/wiki/index.php?title=Category:Data --Andrew Lancaster (talk) 08:37, 2 October 2009 (UTC)Reply

Hi Pdeitiker,

I noticed that you have been working quite a bit on the LM remains. Some time ago I translated Mungo Man to German for de-WP; currently I extend the article (already doubled). Don't you want to accelerate your work on the English article, so I can get inspiration? :-) I am neither an expert in genetics nor in anthropolgy or archeology; just a dilligently writing author... but I can see you are an expert at least in genetics... txs, :-) schomynv 07:40, 9 October 2009 (UTC) —Preceding unsigned comment added by Schomynv (talk • contribs)

Hiya Pdeitiker, I see you did alot of work on the above and, seeing that you know your onions re DNA, if you have any input re my talk comment, it would be gratefully received. --Þjóðólfr (talk) 21:38, 20 October 2009 (UTC)Reply

Hiya Pdeitiker, thanks for you input, I am guessing that I will be slow to respond to your input simply because there so much more to the subject than I anticipated! Hopefully you will not mind if I link some or you comments to help my understanding. --Þjóðólfr (talk) 14:08, 21 October 2009 (UTC)Reply

Sorry if my comments about R1a came off the wrong way. I know the article needed compression. My background is in language, and not genetics. I just meant that the piece will need some editing at some point. You're doing good work. Thanks. MarmadukePercy (talk) 01:11, 5 November 2009 (UTC)Reply

In this edit from you added a reference <ref name="Takahata1999"/> to Mitochondrial Eve. Could you please go back and fill in the details, or tell me where you found this reference? Thank you, Debresser (talk) 12:42, 6 November 2009 (UTC)Reply

Thank you. Debresser (talk) 15:53, 7 November 2009 (UTC)Reply

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Darren23^Edits|Mail 00:05, 10 November 2009 (UTC)Reply

Maybe you did not notice but the shape of the tree is the same in the new Underhill paper and according to ISOGG. So this gives us something to work with. OTOH, the mutations they are naming are indeed different: L series (as per the ISOGG tree) are discovered by Family Tree DNA which is a lab that works with genealogists (and we make up ISOGG). M series mutations are names given by the Stanford (i.e. Underhill) people. So they may be the same mutations discovered by different labs or different ones that are phylogenetically equivalent. I have written to ISOGG to see if they can work it out.--Andrew Lancaster (talk) 07:58, 10 November 2009 (UTC)Reply

I think for now R1a1a1 etc should all just be redirect pages to R1a? By the way I guess you realize that the Karafet article in 2008 did try to develop a method with SNPs. See the refs for E1b1b1. Maybe Underhill and Kivisild's review article a few years back also made steps in this direction?--Andrew Lancaster (talk) 15:22, 10 November 2009 (UTC)Reply

Yes I believe Underhill et al. typed for at least as many variants as Sharma et al, though the phylogenetic name might be different. Look at the mutation names when in doubt.--Andrew Lancaster (talk) 07:23, 11 November 2009 (UTC)Reply

I am looking at your edits with a certain amount of shock that you went ahead and made major adjustments while clearly in a state of confusion which you had not even worked out in your own mind. But what is the problem you are grappling with? All you need to do when reading these articles (Underhill, Sharma, etc) is read which mutations they tested. What is so difficult about that?--Andrew Lancaster (talk) 21:38, 11 November 2009 (UTC)Reply

Sorry, but with good intentions your splitting of the R1a is a disaster. Can you please fix it back up?--Andrew Lancaster (talk) 21:13, 11 November 2009 (UTC)Reply

Your accusation of article ownership on my talkpage is uncalled for, and does not make sense given the nature of the concerns I raised. It is not a disagreement about any particular facts or formats. You admit yourself that you do these edits in an incompletely thought through way. You have a habit of doing this and hoping others will tidy up. This is difficult at the best of times. (By the way can you please sign your comments?) But when you make really major changes it is a total disaster. My concern is very simple to understand: the articles AND talkpages were chopped up by you in such a chaotic way that they can not be followed even by people very familiar with their editing history. Therefore I told you we must reverse the splits and moves FIRST so we can then discuss things more carefully. You yourself said that you should have first made a draft. Why didn't you? You posted a question on the talkpage, and then went ahead even though both responses to your question were negative.--Andrew Lancaster (talk) 06:52, 12 November 2009 (UTC)Reply

I think you are confusing a lot of issues, and taking offense at accusations that you've gone too far in your normal way of working messily and then hoping others will fix it - something you normally seen to feel no problem admitting to. Can we get past it please and get back to working on making one page make sense first?

In order to try to help understanding I'll reply to a few of the points you posted on my talkpage...

• "I have been cleaning up page after page after page, behind you guys edit warring." This is close to true for what happened on E1b1b, but rather than "cleaning up" I would say you have played a role cutting up swollen texts. After you've done this, there is always a lot of work necessary to rebuild things which can no longer be easily read. Furthermore I think you have the wrong idea about what happened on R1a. I have not been a regular there until recently.
• I think your issue about the Harvcoltxt format is something no-one agrees with you about. Anyway, we have had this discussion before on E1b1b and I think it is not relevant to the current problems on R1a.
• "you created two identically named subclade sections". Sorry. But please note this happened while trying to rebuild the article after your splitting up. You know this.
• "when I came across the article you had a list about 4 time the length of an exceptionally verbose article on a relatively minor subject." Absolutely, and I invited you, and I others said this was good. But we could clean up after that type of edit. The split you now did is a whole new level of deconstruction. You are expecting others to clean up, but making it harder and harder for them.
• "Origin of what R1a or R1a1a?" As I already explained, there is only enough data and enough published opinion, to write about R-M17/M198. For all the other levels we can only make a few side remarks so far. If you think it is not clear enough that the origins sections are about M17/M198, then fixing this would seem no problem. That would be a lot easier to follow than making TWO article which BOTH mix things up.
• "In case you haven't notices there were 10 new mutations added between the two, its you who needs to get your head around this." I think I pointed it out to you? Anyway, the main point is that there is one new level. The exact number of phylogenetically equivalent mutations on each level is not important at all.
• "The origins of R1a and R1a1a as temporally separated by at least 10,000 years." Do we have clear enough sourcing to say this? If so, then I see no reason not to mention it somehow.
• "If you think I am going to go away on this issue you are mistaken, I am going to keep on this issue until these sections are refactored." No one asked you to stop work on this article, and no one else was claiming it had reached the needed level of quality which we were working on achieving together. The ONLY problem is that you leave your edits half done and incomprehensible, and especially when you do this on a grand scale that is totally inappropriate. The solution to texts needing tweaking is tweaking, that means careful writing and not suddenly splitting a whole article into two garbled and wrong pieces. You need to use finer tools sometimes.
• "R1a1a appeared once, at a single point in time, during a single generation, with a single set of STR. The SNPs currently observed are derived from that single founder, and the STR that are observed are derived from that single founder. R1a's coalesce is dependent on this one founder, but also all the other versions of R1a that exist are of equal importance, more so since these have evolved since that founder lived." Actually you are confusing the first person with the mutation and the last common ancestor. These two people could be thousands of years apart, but anyway I do not see any relevance here.
• "You have even recapitulated the R1a* aspect of Underhills table. To perpetuate this myth any longer is a major distraction to the page." Please explain this in detail. If something needs to be fixed, lets please fix it. The only problem was your massive article split.
• "What data is there for a Central Asian origin of R1a [...] How come you took all the effort to destroy the R1a1a page but this remains??" Because it appears in the literature, and it certainly does not require a separate article. What does this have to do with splitting the article??? Please stop mixing up completely different issues.
• "The bronze age has absolutely nothing, I repeat nothing, to do with the origins of R1a, in Underhill." Correct, but it does have something to do with theories which are proposed about R1a in the past, and are still proposed at least about R-M17/M198. Anyway, it is just a question of fixing the wording, not SPLITTING THE ARTICLE.--Andrew Lancaster (talk) 15:43, 12 November 2009 (UTC)Reply

Please forget your idea of setting an ultimatum, and slow down. Please remember that the current round of re-editing is RECENT, arising from the two new articles which have changed the field. Starting mass reverts, or even threatening to do so, would be edit-warring and pointless. Instead, just make the changes you think are needed on the original article, but work more carefully please. These are complex wording issues that are hard to get right. The only thing we ask is that you edit in a way that the article can still be read. The split simply did not work because you were just playing around with ideas and you never seem to have time to work on the details. And anyway it did not address the details you are raising valid concerns about. It was a waste of energy. Work on the article in a normal way instead of by ruining the article to make a WP:POINT. If you see a wording issues you should fix the wording, but NOT MAKE IT WORSE. No one is defending the status quo for its own sake, here. This is not an edit war as far as I can see. There was one suggestion for an article split which people disagreed about and that is it.--Andrew Lancaster (talk) 16:03, 12 November 2009 (UTC)Reply

Responding to your post on my talk page:

• "I believe that R1a1a would make a good article, it is easy to construct, and the nomenclature problems will catch up quickly with new publications." It might be possible, but you did not do this. The easy way to convince people this is possible is something you already suggested yourself: make a draft in a sandbox. I think no one is against the idea in principle, but it would have to be done properly, and there would have to be a reason for doing it. If you end up with two articles which cover the same information, or which can not be understood without constantly flicking between the two, you will have failed.
• "if your not working toward bringing up the articles status, then it is of no real benefit to the page". I absolutely agree, and that is why your split attempt was no good. It kept all the old problems and added some new ones.
• "Show one example of two haplotypes, either 1 R1a and 2 R1b types, or a number of R1a types that point that Central or West Asia is a place of origin for R1a. Show one scrap of evidence that the Central Asian or East Asian origin theory is viable." You are changing the subject again. Wikipedia is not a discussion forum. I'm happy to discuss things for fun but when it comes down to it, we should just try to summarize what the literature says in a neutral way. If you think the current wording over-emphasizes some theories from the literature, lets see what we can do, but splitting the article has nothing to do with this.--Andrew Lancaster (talk) 16:35, 12 November 2009 (UTC)Reply

You have just made your second threat in violation of WP:POINT and WP:DEADLINE. If you want to make the article better no one is stopping you. (And if you want to make concrete suggestions instead of vague remarks, no one is stopping you.) The split was nothing to do with making the article better, because you showed no evidence that you had a plan that would have led to a coherent article, indeed you show little evidence of having thought through the problems that we were all working on, and so please just let that go. You have no right to tell other people to put all their efforts into pleasing you personally.--Andrew Lancaster (talk) 19:24, 12 November 2009 (UTC)Reply

Your latest posting on my talk page is so confused and quickly written that it is hard to see anything relevant to the question at hand, and indeed hard to follow anything. The only comment I can really relate to is about the cladogram. You yourself said that the newer cladogram only made sense in the split article, so if we have no split it is clear we should use the other format.--Andrew Lancaster (talk) 07:28, 13 November 2009 (UTC)Reply

And can you PLEASE not only structure your posts into something logical and worth responding to, but also sign your posts? You make it impossible to have any rational discussion.--Andrew Lancaster (talk) 07:34, 13 November 2009 (UTC)Reply

You latest version of the pre 2009 phylogeny diagram is wrong. Can you please fix it? M420 should not be showing at all, but certainly not over on the side as an alternative clade.--Andrew Lancaster (talk) 16:17, 14 November 2009 (UTC)Reply

  Please remember to mark your edits as minor if (and only if) they genuinely are minor edits (see Help:Minor edit). Marking a major change as a minor one is considered poor etiquette. The rule of thumb is that only an edit that consists solely of spelling corrections, formatting changes, or rearranging of text without modifying content should be flagged as a 'minor edit.' Thank you. Chazchaz101 (talk) 22:46, 10 November 2009 (UTC)Reply

The phylogeny can simply be fixed by adjusting headings. Concerning the data itself there is a fair bit of work, as there was last time I updated it, because the Underhill paper UPDATES many of the same old datasets. So what I've tried to do in such cases (they are common and can not be ignored) is to post ONLY the newest version of a dataset. In other words, for each dataset of Underhill we have to check if it is an update of an old one and edit that old one rather than doubling it. The reference is then always to the newest version, (which should have references to old versions). At least with this new article the supp data actually clearly states which data sets are updates.--Andrew Lancaster (talk) 14:37, 14 November 2009 (UTC)Reply

Yes its a good article but for concurrent not update articles such as Sharma's Saharians, I think its best that we outline why there are two tables and keep them separate.PB666 ^yap 14:40, 14 November 2009 (UTC)Reply

I disagree.--Andrew Lancaster (talk) 07:22, 18 November 2009 (UTC)Reply

I am working on different ideas, possibly including a version of what you proposed. Please warn me if you are aiming to do something else. Otherwise please give me a little time on this to see what is best.--Andrew Lancaster (talk) 20:20, 18 November 2009 (UTC)Reply

Currently I am working on maps,

E1b1b1b -improving

R1a1a* frequency -creating

R1a1a7 frequency -creating

R1a1a STR diversity -creating

I am not going to work on any pages for a while, but if someone has information they think might be useful for the maps, please list below PB666 ^yap 02:34, 16 November 2009 (UTC)Reply

Can you please stop insinuating that all disagreement can be explained my emotional attachment to whatever you think I am attached to? That is in itself uncivil and unconstructive behavior, and not a recommended approach even in cases where it is true.--Andrew Lancaster (talk) 14:15, 17 November 2009 (UTC)Reply

If the shoe fits. Wear it. You own the current problem, it will not be solved until you calm down and stop taking everything so personally. You seem dead-fast on pointing out others errors, but not realizing your complicity to the major problem, areas that you have recently worked on are full of jargon and should be made readable to the common public.PB666 ^yap 20:51, 17 November 2009 (UTC)Reply

I do not have to wear anything. What I am asking you to do is follow Wikipedia policy. I have been trying to discuss particular edits. Interpreting all disagreements as personal attacks, which is what you are doing INSTEAD of good faith editing now, is explicitly an example of uncivil editing according to WP:UNCIVIL.--Andrew Lancaster (talk) 07:21, 18 November 2009 (UTC)Reply

This is a clear example of the black cat calling the kettle black. Andrew. Here is an example of your behavior. What you wrote here is not editing in good faith pb666 going for it. By my standard it is bad faith editing. I asked you to verify the names before altering them. Instead of verifying the names from Redding sources The rs nomemclature is a recognized standard and we have not discussed any "precedent" which says otherwise. however true that may be, that is not what you have been using in your articles, IOW you personally established a precedence, by changing that precedence ad lib may confuse the reader and will make the article more jargonistic. You have not given a good reason yet for changing the name, you are only trying to cover up the fact that you made a possible missassumption about the origin of the name (a page, versus the proper name Page), and I consider this bad faith. We can look at this 2 ways, what I should interpret as good faith, and what is bad faith editing. The title of the section - bad faith, the failure to underscore the precedent you have been using, or the fact you switch nomenclature mid-article and point this as a fault in my understaind of Underhill, bad faith. Was pb666 going fot it, or was he just trying to get you to WP:VERIFY.

I repeat this, you are not going to get me to back off on pushing the readability aspects of the article, I am doing this for your own improvement such that in future you can do this with Y-DNA pages by yourself. I have had the almost same discussions with older editors (3 years back) that you are having with me now. Its about being encyclopedic, you can have all your favorite information in an article (or list) but you must pull from within yourself to make it accessible to others, otherwise for what good reason is it. Science is about 2 aspects:Research and communication. Here is a venue of communication, at some point it may take 5 minutes to create one good sentence, from here on out every sentence will be much more difficult to construct because now it has to make sense at all levels, from the lowest to the highest. I am not your competitor as I told you I really couldn't care less about R1a, OK, its the reader whom you have to be courting.

If you are going to take something and make it more jargonistic, without proper introduction and without graphical explanation, I am going to hold you to the standard, "Why are you doing it?" While I am arguing with you here I could be working on the maps, I could be working in the mtDNA page (which is an interest). While you are arguing with me you could be writing a much more comprehensive lead, improving the readability of the article. PB666 ^yap 14:56, 18 November 2009 (UTC)Reply

I get the picture, and I think you put your finger on the problem you are creating very well: you are trying to teach everyone to do what you prefer; you see your personal preferences, even concerning things you are not good in, to be of a higher rank. You think you do not need to understand the opinions of others. That is the big problem.Andrew Lancaster

I nominated the article for GA status, one of the referees has placed a note on the page saying we need to improve the readability. I am trying to give you advice based on the GA and FA pages I have worked. Andrew its not easy, one editor JFW busted my balls over the edits I introduce. We almost went to arbitration over his insistence that I have a review article verification over something that was midstream in my field of expertise, that I new without doubt was correct. So don't take it personally.

You say "its the reader whom you have to be courting" but in practice you demand that everyone courts you. And you are NOT a typical reader. Let me work on the jargon please. At the moment I have to struggle constantly just to stop your from edits which are designed purely to make a point.

There is a saying, I know what it looks like when I see it, everyone is a great armchair quarterback, but how many of them are actually critiqued. I am singling you out because you want to improve the article, but more importantly if you work hard at it and focus, item by item, you can improve the article. Once you improve this article, you will be much more easily able to improve other articles. However if you keep drawing or waiting for others to step up, it will not get done.

You make a big point above about the "going for it" description. But in fact your own words on talk pages now constantly centre around gung-ho words chosen by you: "I repeat this, you are not going to get me to back off on...". So by your own account you are on a big personal push, and going for it. In contrast, your constant reference to my emotions, starting immediately after I raised concerns with the article split you did, does not have the same excuse: you have never pointed to evidence for the assumptions about my motives which you have made central to your communication with me. I have always explained my preferences in neutral terms, something which you do not even bother to do.--Andrew Lancaster (talk) 15:38, 18 November 2009 (UTC)Reply

The line has to be drawn somewhere, on other pages major contributing editors have done the same thing to me. I am not singling you out. My point is that 90% of the edits at this point need to be directed at making the article more encyclopedic, if you are not familiar you need to review this. I criticize you about your referencing and you blew up in my face, good faith. Click underhill et als Doi: doesn't work, pubmed ID, not present. Tell me, you say you know how to do it, and you wont listen to what I said about how to easily improve the references, and yet the reference you provided does not link. Very unable to accept critique is the way I look at this. Which is more encyclopedic M17 or rs23687894122. How would you like to be called Andrew or ss#987-65-4321? Which is easier for you to read.

By the way, you seem to be saying you can name cases where I have been making the text more "jargonistic" and less accessible. If you are serious about wanting me to fix them can you please point them out so I (and other editors) can look into it? Please do so on the article talkpage. As mentioned many times, I do accept that the article can be improved, and I would like to have the chance to work on that again more than recently.--Andrew Lancaster (talk) 16:10, 18 November 2009 (UTC)Reply

The phylogenetic ("family tree") naming system commonly used for this haplogroup remains inconsistent in different published sources. Although it has not yet used much in published surveys, a more comprehensive survey of the known mutations is listed by ISOGG, and an equivalent tree is given in Underhill et al. (2009) harvcoltxt error: no target: CITEREFUnderhill_et_al.2009 (help).^[1]

Prior to 2009 the mutation SRY1532.2 (or SRY10831.2) defined R1a, and this is also how the term R1a is most often used in publications before 2009.

However the term R1a is also now increasingly used to refer to a broader family including not only this "old" R1a, but also other related R1 (R-M173) lineages which have been found to share several unique mutations with R1a, including M420. In this newer system, the clade defined by SRY1532.2/SRY10831.2 moves from "R1a" to "R1a1".

<--------Starting from this point below I have reworded, not perfect as I said a good correction may take an hour or more to correct--> The family tree of R1a as a whole can be divided into three levels of branching. The following summary is based upon the large survey of Underhill et al. (2009) harvcoltxt error: no target: CITEREFUnderhill_et_al.2009 (help) as follows:

1. R1a* (new nomenclature). Defined as M420 positive but SRY1532.2 negative. (Articles published before the discovery of M420 will not have distinguished these from other R1-M173 lineages.) Underhill et al. (2009) harvcoltxt error: no target: CITEREFUnderhill_et_al.2009 (help) believe this clade or clades to be rare, and have so far found 1/121 Omanis, 2/150 Iranians, 1/164 in the United Arab Emirates, 3/612 in Turkey. Mutations understood to be equivalent to M420 include M449, M511, M513, L62, L63.^[2][3]

Correcting that section First, if it helps break it up into sections as follows

Recently, the labels associated with different branches of the R1a family tree (phylogenetic tree) has been updated. This has resulted in a shift in the names (nomenclature) applied to the branches R1a, R1a1, and R1a1a.

In studies prior to mid-year 2009, R1a was defined by the SRY1532.2 single nucleotide polymorphism (SNP).^{[note 1]} Four additional SNPs between ancestral (basal) R1 and the SRY1532.2 branch-point were described in the late 2009.^{[note 2]} Evaluating anyone of these new SNPs refines the molecular typing method of haplogroup R1, but M420 is preferentially used. Specifically, M420 typing is used to further evaluate Y-DNA that are defined as haplogroup R1 (M173 positive) but not SRY1532.2 or M343(R1b) positive. Underhill et al.(2009) found that this distinction was important as M420 positive/SRY1532.2 negative males exist and indicating that a branch between R1 and SRY1532.2 went undetected.

As a consequence of this oversight, the R1a branch of the R1 clade was shifted 'outward' by inserting a basal branch-point (between the R1 and SRY1532.2 positive clade; See cladogram on right). This required the renaming of all higher branches. The inserted branch-point retains the name 'R1a', and has one defined subclade 'R1a1' as defined by SRY1532.2. Currently, 'R1a*' are M420 positive males that lack SRY1532.2. These individuals do not belong to a defined subclade, and may represent individuals with no new defining mutations relative more basal R1a. Alternatively, these 'R1a*' may have undetected mutations that define a new clade(s), or it is possible that they bear mutations the require the insertion of new branch-points between R1a and SRY1532.2 branch point. R1a* is rare, and found at less than 1% of males in Oman, Iran, United Arab Emirates and Turkey.^{[note 3]}

PD, You do not explain your preferred wording at all, so you force me to comment first. Please believe me that I really do not mean to annoy you but in my honest opinion 999 people out of 1000 will struggle to read this, not just because of jargon. The first sentence is ungrammatical, just to start with. I really can not see anything simpler or clearer about it. It has more jargon, longer sentences, more unusual metaphors, more broken trains of thought, and repetitions, etc. I would like to suggest that because User:Marmaduke Percy is an editor by profession we let him go through questions like this. You have been quite dismissive of him until now, but this is his field. Wording now seems to be the wall we have hit, not a disagreement about facts. Obviously you are going to accuse me of just emotionally defending my own version. Also, please feel free to call in other opinions concerning English. Here are just some comments to show that I am not just making a knee jerk reaction:--Andrew Lancaster (talk) 21:48, 18 November 2009 (UTC)Reply

Not at all, Andrew, this is a process, not an easy process, more importantly I have no expectation that exact wording will be correct or that it will remain the same. First let me say this, I don't know bout you but for me we do not need to pass the GA process, if we do nothing more than learn from the process then the process is well worth it. These are lessons that can be applied to improve all articles. Having said that, to get to something that will pass the review process we have to try, that means make and effort or, likewise go through a process. This process is not a single step, for instance I work on something and walla, its done. Doesn't work like that, even folks who are English editors have their language tweeked from time to time. Reading other article talk pages you will see editors being congradulated for rewording very difficult material because one editor reaches a wall which for that moment they cannot see around.

To get the process rolling we have to unroll the jargon and explain it carefully, assume your reader has no familiarity with any of the Jargon what-so-ever. We have to start with all the information as we have that information rolled out, we can choose better wording, more concise wording, etc.

Notice the key points about the reorganization

• information has not been lost, 'of interest' information has been rolled into notes, that helped to clean-up the structure.
• the un-preferred bullet list " * Thing A (other name for Thing A) " format has been broken out, and replaced by paragraph format, explained as in a paragraph or story, to keep interest, we now are at liberty to expand this structure if we so desire.
• Sentences may be partially redundant to explain material in a step-wise manner, there may be better ways of condensing them, and we might chose to condence 2 sentences to 1 sentence or 3 sentences to 2 sentences. Each concept should be broken out, if that concept
• The information is broken into core concepts. A. why the new branch-point was inserted, B what happened as a consequence. So there is a logic.

Regarding your comments.

• "labels associated with" is a quite weird way to say "names of"

I toyed with it, its not perfect.

• "has been updated" should be "have been updated"

I reworded the structure about 10 times, catching most of these errors. I did not place it into MS Words grammar checker which I will do later.

• using the word updated implies that there is a procedure of updating names (by who?); what happened is that new information came in and this information in itself brings the new family tree. One of the big mistakes intelligent people make in writing is leaving too many things between the lines.

This is an area were specific expertise may require and insertion of information, for example you are more familiar with the ISOGG process, if you were to talk about HLA, then I would be more informed IWHG processes. But remember the paragraph is not about how ISOGG does their business, the paragraph is about why the changes were needed.

• The second sentence means almost the same as the first sentence.

I changed this, maybe it works better maybe it doesn't

• You refer here already to "the branches R1a, R1a1, and R1a1a" but these are going to be defined below:

R1a, R1a1, and R1a1a existed under the old and new terminology, that is why these are leading the discussion. In the section leads we want to hit on what we are going to discuss in the subsection. Whether or not I have lead the subsections or not is something we have to learn to fix. These section leads are the target of a better article lead, such that we really want to get into these section leads things that can be condensed into a stand-alone lead. Not all of the lead have to be in the section leads.

Note: In terms of what defines R1 and R1b will be defined in the lede. and therefore we can choose which nomenclature we want to use, for example R1 or M173, R1b or M343. However it would be preferred to stick to the most user friendly of these when ever possible. In particular there are 3 markers, M334, M343, and M434 that are so similar, that if we use these alot we will certainly confuse most readers. So we need to consider this when inserting 'labels'

The paragraph was partially rewritten, feel free to edit the paragraph to new versions

---

Above written by PB666. (Please sign talkpage posts.) PD, I do not know what to do with this. You can not explain why your text is better. You openly admit it might not be, and you invite me to do my own editing. But in the meantime you are posting comments saying that my writing is crap and you are reverting and rewriting the article into worse English on a constant basis, making it clear all the time that you are not taking the time to even think about what you are doing. You seem desperate to change the lede for example, but you can not explain why in any way that others can follow. This is not a question of scientific knowledge. Personally I think we have gotten the article to a position where it needs finer tools. Your quick way of working is counter productive if your aim is a smoother style.--Andrew Lancaster (talk) 06:45, 19 November 2009 (UTC)Reply

First, the use of 'dirty laundry list' or so-called bullet lists are not preferred.PB666 ^yap 07:26, 19 November 2009 (UTC)Reply

What are you referring to?--Andrew Lancaster (talk) 10:06, 19 November 2009 (UTC)Reply

Second, bolding, except sectional heads, is greatly frowned upon.PB666 ^yap 07:26, 19 November 2009 (UTC)Reply

What are you referring to?--Andrew Lancaster (talk) 10:06, 19 November 2009 (UTC)Reply

Third, while I understand perfectly what you are saying in the text, I have read over 20 times.PB666 ^yap 07:26, 19 November 2009 (UTC)Reply

What does this mean? (Incomplete sentence.)--Andrew Lancaster (talk) 10:06, 19 November 2009 (UTC)Reply

1. R1a* (new nomenclature). Defined as M420 positive but SRY1532.2 negative. (Articles published before the discovery of M420 will not have distinguished these from other R1-M173 lineages.) Underhill et al. (2009) harvcoltxt error: no target: CITEREFUnderhill_et_al.2009 (help) believe this clade or clades to be rare, and have so far found 1/121 Omanis, 2/150 Iranians, 1/164 in the United Arab Emirates, 3/612 in Turkey. 7224 more tests in 73 other Eurasian population showed no sign of this category so far. Mutations understood to be equivalent to M420 include M449, M511, M513, L62, L63.^[2][4]

A. Bullet style list, not preferred. WP:MOS#Bulleted and numbered lists PB666 ^yap 14:40, 19 November 2009 (UTC)Reply

B. Excessive bolding of with the exception of key article words is not preferred. WP:MOSPB666 ^yap 14:40, 19 November 2009 (UTC)Reply

Until now you have never mentioned simple formatting questions as being crucial, and your edits have shown no sign of it either. Such things require none of the actions which have been a source of disagreement between us.--Andrew Lancaster (talk) 16:23, 19 November 2009 (UTC)Reply

Until now we have not undergone GA review. WP:MOSBOLD PB666 ^yap 17:08, 19 November 2009 (UTC) And BTW, I have mentioned the style of the section numerous times, you seemed not to comprehend that I was talking about those sections....PB666 ^yap 17:41, 19 November 2009 (UTC)Reply

I have told you many times that I can not follow most of what you write on talk pages. I am sure many people have told you that. However, when you take the time to write something clearly, it is possible to communicate. It is up to you. Now, can you please state whether you are truly claiming that our editing disagreements recently have involved these formatting details? I do not think so.--Andrew Lancaster (talk) 18:41, 19 November 2009 (UTC)Reply

C. Excessive use of fractions when simpler lingo would suffice. jargonistic. PB666 ^yap 14:40, 19 November 2009 (UTC)Reply

I notice you have no WP citation here. Given the texts we are talking about obviously what you are trying to suggest is that for example 1/100 is more jargonish than 1%, which is clearly nonsense. I have remarked it elsewhere on the relevant talkpage today.--Andrew Lancaster (talk) 16:23, 19 November 2009 (UTC)Reply

This is common sense Andrew, one or two fractions or percents scattered about a section are not going to hurt readability, but we simply cannot have chains of fraction scattered about everywhere. It is simply too easy for the page to get out of hand, for example like the distribution section used to be. Select one or two fractions or percents per section that need to be emphasized. And I will tell the truth, there is no statistical difference between 0/50 and 2/100, or between 3/713. In fact there is little difference between 2/50 and 1/400 at the statistical level, therefore there is no reason to make grand comparisons. In addition combining populations that have 0/N instances would be called cherry picking. First, test two populations, is the difference significant, if not then separating them is not statistically warranted, For example if 0/30 French have R1a* and 2/57 Iranians have R1a* the p-value is = 0.4623 there is no legitimate region from excluding individual all but the largest N, 0/N fractions. Secondarily what is more important is diversity of R1a* to R1 in these regions. However, I will concede on the issue that we can argue that ~70 groups tested had not R1a* as a potentially warranted use of fractions. I don't think we should break down every group that has R1a*, IMHO, its beyond encyclopedic.

I would also ask, before alterning the R1a/Nomen.. is 7224 tests on Y, or R1, or for M420 positives?

PB666 ^yap 17:08, 19 November 2009 (UTC)Reply

OK. There is nothing wrong with you explaining these preferences. Why did you not explain them as personal preferences on the article talkpage originally instead of typing weeks worth of insults and vague threats? If you want to explain this on the article talkpage lets then see what other people think. --Andrew Lancaster (talk) 18:41, 19 November 2009 (UTC)Reply

Its not a personal preference when they clutter the article, the only reason you call it personal is because you have no outside critique. There are two ways to deal with it, overload the article with numeric facts and deal with it, or take a step back, read an article which you are not familiar with that is frontloaded with numbers in the text, and try to empathize with the reader. Of course not having a 16 ton iron weight fall on me is a personal preference. This is a point of discretion which would go by the logic when is too much of a good thing too much of a good thing.PB666 ^yap 23:04, 19 November 2009 (UTC)Reply

I am going to have to cut short these replies for I have other stuff to do, please limit the verbosity of your replies and try to read and familiarize yourself with the WP:MOS. And keep in mind there are common sense issues with regard to readability.PB666 ^yap 17:08, 19 November 2009 (UTC)Reply

You have been writing unformatted and unsigned stream of conscioussness all over my talkpage for weeks, and ignoring all normal methods of shorter, clearer and less verbose communication. Today I have gone out of my way to answer and explain in detail, and suddenly your new excuse for ignoring the opinions of others is that I am verbose.--Andrew Lancaster (talk) 18:41, 19 November 2009 (UTC)Reply

Further information: [[:Manual of Style - Numbers]]

"* Mathematical quantities, measurements, stock prices, etc., are normally stated in figures."

"* The use of words rather than figures may be preferred when expressing approximate numbers."

Clearly not relevant to the case in hand.--Andrew Lancaster (talk) 18:41, 19 November 2009 (UTC)Reply

D. R1-M173, R-M173 and M173 are used on different occasions, use only one terminology. I suggest M173. jargon.PB666 ^yap 14:40, 19 November 2009 (UTC)Reply

R-M173 is standard YCC mutational naming for the CLADE.--Andrew Lancaster (talk) 16:23, 19 November 2009 (UTC)Reply

At what point did we define that, if we define that we can use it, but we never defined it. That is what dejargonizing means, we must clearly and explicity define each obscure meaning.PB666 ^yap 16:41, 19 November 2009 (UTC)Reply

M173 is the name of a mutation. I have no problem with any attempts by any editor to clean up such usage, and I did not realize it was an issue for you. Are you really saying that you have been disagreeing with me about this?--Andrew Lancaster (talk) 16:23, 19 November 2009 (UTC)Reply

I am saying we must put the reader first. If "R-" terminology can be used to create an alternative name for a clade, then somewhere close to the lede of the article we must carefully explain it. It may actually improve the article, but the connection cannot go unexplained. I have not been disagreeing with you, but is one reason for rewritting the text.PB666 ^yap 16:41, 19 November 2009 (UTC)Reply

I believe you'll find that the definition was in the article at some point and removed. I do not recall you ever raising this, and nor do I recall us disagreeing about it. And yet here you are mentioning it as if it explains something we were talking about.--Andrew Lancaster (talk) 18:41, 19 November 2009 (UTC)Reply

E. While I did add the other mutations, I think they belong in notes, not in the main text.PB666 ^yap 14:40, 19 November 2009 (UTC)Reply

I am not sure what this means. What are you talking about please?--Andrew Lancaster (talk) 16:23, 19 November 2009 (UTC)Reply

It means what you agreed with on the notation page when you said:

"Removal of extra SNPs fine by me. It was PB666 who insisted on these." for which I commented Not removal, but noting."

WP:MOS

Forth, I did not say it was easy to write it out. I have created a new page called nomenclature with the talk page.PB666 ^yap 07:26, 19 November 2009 (UTC)Reply

I do not think you have the patience to get this draft you have made to any level of quality even equal to what the article currently has. I think it is much easier to let other Wikipedians work on the main article, not your unfinished ideas. Other Wikipedians are NOT saying that they have problems improving the article. The problem they have is you stopping them.--Andrew Lancaster (talk) 10:06, 19 November 2009 (UTC)Reply

Again this level of critique can be consider an ad-hominim attack and aligns itself with statements you have made which align with WP:OWN.PB666 ^yap 17:08, 19 November 2009 (UTC)Reply

I explained my concerns about your proposal as I see them, and that involved mentioning a problem with your writing not being as good as you think it is. You make it impossible not to mention your editing weaknesses because you make it a basic assumption of your style of communication that all people must accept you as a superior editor, putting his underlings through the hoops. People need to either agree or disagree with you on this demand of yours. That is a logical consequence.--Andrew Lancaster (talk) 18:41, 19 November 2009 (UTC)Reply

Fifth, tis my talk page.PB666 ^yap 07:26, 19 November 2009 (UTC)Reply

I would have thought its purpose was communication? What's your point?--Andrew Lancaster (talk) 10:06, 19 November 2009 (UTC)Reply

Honestly, I'd like you to explain this comment. It sounds super arrogant you know. After all, you've been telling me my tone is poor, so if you want to improve the tone you'd want to clear this up right?--Andrew Lancaster (talk) 18:41, 19 November 2009 (UTC)Reply

Sixth, Happy?PB666 ^yap 07:28, 19 November 2009 (UTC)Reply

With what precisely? You have used many words to say almost nothing. What should I reply to?--Andrew Lancaster (talk) 10:06, 19 November 2009 (UTC)Reply

With the sig after every sentence.

I want to remark that it is surprising to see that even on a complex formatted draft page, which you have set up, here, and after all my requests and complaints, and all the potential confusion you say you want to clean up, that you have started posting in un-signed remarks in a format which makes it unclear who wrote what, when - again. I have therefore had to reformat the page before I could read it and answer it. I hope it is clear that I believe it this approach to editing quality which is precisely the problem with your work on main articles also, especially when you start getting ambitious. These are not two separate problems. Anyway, please respect the fact that I have put a lot of effort into trying to work according to your enormous and absolutely unreasonable demands today, and you have repaid this with absolutely no effort at all to aim at CLEAR writing either on the talkpages or elsewhere. I have given you a lot of feedback and all indications are that you are not going to give serious answers to anything.--Andrew Lancaster (talk) 16:23, 19 November 2009 (UTC)Reply

This is argumentative, my focus is on improvement not discussion, all effort in discussion will not improve the page, you seem to think that the grand effort should be in the argument, I think the grand effort should be in page improvements.PB666 ^yap 16:41, 19 November 2009 (UTC) It could almost be interpreted that by excessive points of discussion you might want to obstruct the improvements or replacement of your text, is this your intent?PB666 ^yap 17:08, 19 November 2009 (UTC)Reply

It seems that trying harder to communicate with you only leads to new diversions. You say you are interested in improvement. Prove it by responding seriously to the very straightforward quality related remarks I have made about your recently posted drafts.--Andrew Lancaster (talk) 18:41, 19 November 2009 (UTC)Reply

I've just spent a whole day trying to respond to your drafts and I have not edited articles in any normal way in the meantime. R1a can certainly be improved but I have to make a choice now it seems as to whether I should edit Wikipedia or else beg for your permission. I choose the former. Your drafts are really not an improvement in any respect as far as I can see, honestly, and I say that having spent a lot of time trying to explain various problems. Most importantly, your responses are not really responses at all and seem to show an enormous lack of potential for any meaningful communication. I feel silly having wasted a day. I am open to good faith attempts to communicate but I do not see any. I am not going to waste time on your drafts at this stage because they clearly aren't going to go anywhere. The final straw is telling me that these wording proposals all still need to be adapted for better wording and then whining that I am being argumentative about details.--Andrew Lancaster (talk) 19:17, 19 November 2009 (UTC)Reply

Again, I do not see it that way, you lace all your comments with ad-hominim attacks. I was simply trying to provide you with a template by which to go forward and you dragged me into this refute that, explain this, why is yours better than mine, and highly nit-picky attitude. This is highly frustrating because you seem to learn nothing and deny everything. You denied I was pointing out stylistic problems with your sections, then you claim I suddenly popped the critiques on you, even though I pointed several times, (the bullet list style is frowned upon, so is bolding, reduce the technical lingo,and numeric stuff and spread out the discussion, I asked you to change the defective reference, you didn't I asked to you fix the most cited reference, and gave the entire citation and you didn't fix it. It just this repeated stubborness that simply will not get these pages to evolve). When I pointed out wiki guides on 'ledes' and presented to you both you and Marmaduke threw it back in my face, you seem genuinely unwilling to start with a block of stone and shape it into a statue, it has to be nearly formed statue or you don't see it, and your strained wooden form is always exception. Either you desire to change the way you are editing or you don't. The thing is Andrew, I neither have the time or the desire to fix every Y-DNA page that pops up, so you cannot rely on me to go through this process for every single page, you have to take the lead, but you have to start by providing a workable framework, which means you need to read MOS, first.PB666 ^yap 22:59, 19 November 2009 (UTC)Reply

No, it is really simple. You have been proposing changes to articles, just like a normal Wikipedian. And then people try to answer you, so far so good. And then communication breaks down, from your side. That's it: time and time again. The fact that you have all kinds of drama to express about others not improving themselves and so on is just smokescreen. It is, to repeat just basic. Concerning ad hominem attacks or whatever else you want to accuse me of, give concrete examples, or else do not make accusations. That's what I do. Your claim that this was about bullet lists and bold types is just amazing coming from a guy who has never mentioned these things, and who never bothers with niceties like signing posts or answering people whose opinion you supposedly wanted to hear. (But if it was correct, then everything is fixed now, because I obeyed your demands.) Your interpretation of what ledes should be like is purely your own, as is the case of many of your pseudo citations of wiki MOS. Did it ever occur to you that if Marmaduke and I were wrong you could make a case back?--Andrew Lancaster (talk) 23:10, 19 November 2009 (UTC)Reply

As I said to you, this is at GA realm, the guides are always there, but at this level these details become important. Whether or not I mention these does not change the fact they have existed.

I am currently going through your comments on the Lede they are very difficult to follow, I had to print them out to understand them, so I am making an effort to go through your comments, but the personal style attacks have to diminish.PB666 ^yap 23:15, 19 November 2009 (UTC)Reply

Making false accusations of ad hominem attacks is in itself uncivil behavior. I have claimed that anything I have written about you has been connected to some clear comment about an editing issue or has been in agreement with your own descriptions of your motives. If you believe my explanation is false, please either state your case or drop it. To repeat if you do not do one of these two things, you are not only impeding any possibility of good communication and cooperation, but you are also in clear breach civility guidelines. Also please stop referring to your own personal preferences as if they are being demanded by a third party. You are simply use this as a way of engaging in discussion.--Andrew Lancaster (talk) 09:17, 20 November 2009 (UTC)Reply

Hello, Pdeitiker. This message is being sent to inform you that there currently is a discussion at Wikipedia:Administrators' noticeboard/Incidents regarding an issue with which you may have been involved. Thank you.. Hello, Pdeitiker. This message is being sent to inform you that there currently is a discussion at Wikipedia:Administrators' noticeboard/Incidents regarding an issue with which you may have been involved. Thank you..

Hey I haven't been on for a while and got your message on my page. Just wanted to thank you and show my appreciation. I've been sitting back watching the page and it's seems Andrew has hijacked the page and is obsessively paranoid. I will start contributing to the article to show my balance and support. I think it's time we balanced the article by expanding the South Asian Origins section and removing alot of the cherry picked, inconsistent, old data being presented as a sealed deal. I'm willing to work with everyone, but they seems hellish on the Linguistic theories...which is 3-4 times the size of the South Asian section. I wrote a big thing on the R1a talk page. Let me know - Thanks!! HonestopL 15:08, 18 January 2010 (UTC)Reply

Hi, I have contributed to the discussion about the page [[4]] and I have not seen any replies or concensus about what to do. I'd apprecite your comment, your views on how to improve those pages. I am willing to do some work. Cheers, rené Renebach (talk) 21:09, 27 January 2010 (UTC)Reply

I have finished a first pass at cleaning up the Haplogroup R1a (Y-DNA) page, which you were also editing until a short while ago. It's still somewhat rough about the edges, and has a pending proposal to split off the origins hypotheses stuff (because that's all speculation and an inevitable magnet for cruft and POV-pushing, so we might as well localize that ongoing edit-war), but in essential outline I think the page is now functionally and logically complete. What do you think? For reference, this is the version I'm talking about. And you may find this thread interesting. rudra (talk) 05:38, 19 February 2010 (UTC)Reply

I have once again removed erroneous information and a photo (not related to the vessels) with an inaccurate caption concerning the aforementioned vessels that were affected by the September 1, 2008 surge in the New Orleans Inner Harbor. I have removed reference links to articles in the Times Picayune newspaper that contained inaccurate information, including inaccurate information about Southern Scrap and the Army Corps of Engineers and what happened during Hurricane Katrina.

The Courier, American Explorer, and Hunley were wrested from their moorings by the Hurricane Gustav surge on the morning of September 1, 2008. There was no damage to any bridges or structures by the Courier, American Explorer or Hunley and, working with the USCG, the company successfully re-moored the vessels and dismantling was continued. —Preceding unsigned comment added by Visavixen (talk • contribs) 15:26, 2 March 2010 (UTC)Reply

Hello, Pdeitiker.

Maybe you will be interested in this issue. In Brazilians of Spanish descent, this paper, by Brazilian geneticist Andrea Rita Marrero, is used as a source for the information that "Gaúchos [...] are mostly descended from Spanish ancestors, and less from Portuguese". As this runs contrary to mainstream knowledge about the region, it would be interesting to understand what exactly are the bases for the paper's conclusions. Another paper by the same scientist (in collaboration with others) gives more details about the subject. Could you please help us with this subject?

Thanks in advance. Ninguém (talk) 12:49, 13 July 2010 (UTC)Reply

There is a discussion about some content you created here. You are welcome to join if you wish. Biophys (talk) 18:54, 27 July 2010 (UTC)Reply

I have granted your account an exemption from IP blocking. This will allow you to edit through full blocks affecting your IP address when you are logged in.

Please read the page Wikipedia:IP block exemption carefully, especially the section on IP block exemption conditions.

Note in particular that you are not permitted to use this newly-granted right to edit Wikipedia via anonymous proxies, or disruptively. If you do, or there is a serious concern of abuse, then the right may be removed by any administrator.

Appropriate usage and compliance with the policy may be checked periodically, due to the nature of block exemption, and block exemption will be removed when no longer needed (for example, when the block it is related to expires).

I hope this will enhance your editing, and allow you to edit successfully and without disruption. - Alison ^❤ 12:11, 25 March 2011 (UTC)Reply

 

I have granted rollback rights to your account; the reason for this is that after a review of some of your contributions, I believe you can be trusted to use rollback correctly, and for its intended usage of reverting vandalism, and that you will not abuse it by reverting good-faith edits or to revert-war. For information on rollback, see Wikipedia:New admin school/Rollback and Wikipedia:Rollback feature. If you do not want rollback, just let me know, and I'll remove it. Good luck and thanks. Alison ^❤ 12:11, 25 March 2011 (UTC) - Alison ^❤ 12:11, 25 March 2011 (UTC)Reply

Talk:Air_France_Flight_447#In-depth_information_regarding_latest_report

• Need for intergration of all available data has been expressed and your ACARS table could be a start; need help.

Patelurology2 (talk) 21:29, 2 June 2011 (UTC)Reply

Please review and comment:
http://en.wikipedia.org/wiki/Haplogroup_J1_(Y-DNA)
http://en.wikipedia.org/wiki/Talk:Haplogroup_J1_(Y-DNA)
JohnLloydScharf (talk) 00:10, 22 August 2011 (UTC)Reply
Thank you for your timely and detailed response. I was surprised, as you seem to be, at the departure from research methodology by using anything less than n=30 for a sample population. Saying a nation is a certain way by sampling students tells me about students rather than the nation, whether it is politics or genetics. I think you need 2000 samples, but at least 600 would be good and 12 will not do. However, what do I know.... I only took three research classes at the 400 level; one for psychology, one for sociology, and one for math classes, but that experience changed my perspectives and expectations about probability and statistics. Even political polls are off with less than 1600. JohnLloydScharf (talk) 23:48, 22 August 2011 (UTC)Reply

http://en.wikipedia.org/wiki/HLA-DQ1#Gluten-sensitive_neuropathy_controversy
Do you know what OTHER three SNPs are associated with this?

Effective Detection of Human Leukocyte Antigen Risk Alleles in Celiac Disease Using Tag Single Nucleotide Polymorphisms http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386975/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685746/ http://www.ncbi.nlm.nih.gov/pubmed/18509540 http://www.snpedia.com/index.php/Gs221

This genoset tags the DQ2.2 haplotype in Europeans, and thus increased risk gluten intolerance and for autoimmune disorders such as celiac disease.[PMID 18509540] http://www.snpedia.com/index.php/Gs221/criteria

I am not able to interpret the above, have data on my own personal SNPs of the three in that reference.

• rs2395182 chromosome 6 nt position 32521295 TG - DQ2.2, DQ4
• rs7775228 chromosome 6 nt position 32766057 TT - DQ2.2, DQ4
• rs4713586 chromosome 6 nt position 32767560 AA - DQ4

John Lloyd Scharf

" At first the sensitivity and specificity for DQ2.2 was high and accurate but the predictive value was low. The SNPs for DQ2.2 (rs2395182, rs7775228) not only tagged DQ2.2 but also included the relatively infrequent DQ4 allele. We therefore decided to tag DQ4 as well (rs4713586) making it possible to call a person DQ2.2 when the alleles were positive for DQ2.2 and negative for DQ4. This led to three tag SNPs being needed for the prediction of DQ2.2, with an overall sensitivity of 0.992, a specificity of 0.998 and a PPV of 0.977. Only four of the 1448 tested chromosomes gave false results (0.28%). "

DQ2.5cis haplotype is tagged by: "The tag SNP selected for prediction of DQ2.5 (rs2187668) showed an overall sensitivity of 1.000, a specificity of 0.999 and a PPV of 0.998. Only one of the 1458 tested chromosomes gave false results (0.07%). This person did indeed carry half of the DQ2.5 haplotype (DQA1*0501)"

And in fact the haplotype DQA1*0501 DQB1*0202 exists in Africa along with *0505 - *0202. There are also evidence of some Linkage Disequilbrium in Norway.

DQ2.5 cis haplotype is tagged by DQ2.2 tags and: "The tag SNP for DQ7 (rs4639334) showed an overall sensitivity of 1.000, a specificity of 0.997 and a PPV of 0.959. Four of the 1470 tested chromosomes gave false results (0.27%), of which three carried a rare haplotype consisting of half of the DQ7 haplotype. Two of these three carried a combination of the DQA1*0505 allele of DQ7 with the DQB1*0302 of DQ8 (see results of DQ8 as well) and were predicted to be both DQ7 and DQ8 (see Table S3b, person nos. 11 and 12). For one of these persons we typed the parents and we could see a transmission of this combined haplotype in the family."

DQ8.1 haplotype is tagged by: "The tag SNP for DQ8 (rs7454108) showed an overall sensitivity of 0.991, a specificity of 0.996 and a PPV of 0.948. Seven of the 1484 tested chromosomes gave false results (0.5%)."

This captures, according to the European study 99.97% of all celiac cases.

The danger of using DQA1* tags for celiac disease is that DQB1* confers most of the risk, and risk remains when DQA1*0501 or *0505 are absent. Consequently one has to use both DQA1* and DQB1* tags to accurately detect DQ2.5cis bearing haplotypes. If you are typing patients in Western Ireland, you are going to get the haplotype right no matter what, but if you are typing in N. or W. Africa, particularly in Cameroon, there is a good chance you will tag it wrong.

If fact, during our recent MG study in Houston we found the following haplotype DQA1*0401:DQB1*0201 (an as yet identified haplotype).

Regarding the GSIN. They claim and have never done high resolution studies that I know of, i have presented their findings but disagree with their conclusions. The associated serotype is DQ1. DQ1 is subdivided into DQ5 and DQ6 based on beta chain immunoreactivity. This represents a dozen haplotypes and multiple variants. PB666 ^yap 22:02, 23 August 2011 (UTC)Reply

• Okay, I just discovered you responded. See if I interpret this correctly. Your examination and interpretation of my SNPs is I am DQ4, which is not associated with Celiac or gluten intolerance. That is consistent with my not having a diagnosis of having those. I had a "Family Finder" test done by FTDNA. I have a file for a batch of autosomal SNPs and X SNPs. I have had over 120 yDNA STRs and a full sequence of my mtDNA done by them as well. I want to learn how to read/understand these SNPs and Chromosome 6 is as good a place to start as any.

• My interest was initially in genealogy for testing, but I have always had an interest in archaeology since my pre-teen years. That is why I am interested in ancient DNA and how haplogroups line up with such things as Pre-Pottery Neolithic. The more I look at how they structured yDNA haplogroups, the more I am reminded of how they base everything in mtDNA, as well as some of HLA, is based on a woman who died the year I was born. At least HLA has a practical use, like ABO.

Thanks for the additional information on my talk. I have had something in the back of my mind for quite some time. How do they determine what an "ancestral" allele or SNP by just molecular rather than historic means? John Lloyd Scharf 18:35, 24 August 2011 (UTC) Also, I posted a response to your message on my talk page. John Lloyd Scharf 20:16, 24 August 2011 (UTC)

Maps are hard, you have to both follow wikis, often silly, rules (And they are, for instance if two papers give to ranges for dates say 85 to 135, and 125 to 235, both studies cannot be correct, but you cant then say the date range is 85 to 235, that is a synthesis, even though the wiki admins cannnot decide which is best or correct to give in the article, IOW they force a concensus to cherry pick rather than actually represent scientific range) and avoid the legal issues. At the same time you can't assume one author did correct research in reading others M and M section of papers included in his graph, so you have to actually read papers and see where these study points represent.

It is the Abilene paradox demonstrated by Wikipedia consensus decision-making. If the ultimate objective is not to "rock the boat", then reality is defined the effort to appease everyone while informing no one. John Lloyd Scharf 23:44, 23 August 2011 (UTC)

• I hope you understand I was not indicting Genie as a sock puppet. To my knowledge, Genie was never in question as being a sock puppet. The IPS making comments without signing in was posting long before Genie. You cannot let Andrew paint the picture on this issue. In fact, I welcomed Genie's additions and complimented that and believe I had invited Genie to the Discussion.
• I challenged Andrew for naming off nations without naming Israel as a part of the Levant. So, he said Levant and Jews. This was right after I had said the Levant is Syria, Lebanon, Israel, and Jordan. He refuses to say Israel anywhere in the J1 article. To my knowledge, Behar's work was based on the Askenazi, so, if anything, they should be either named as Israel or the US, since they were murdered in Germany. They are Jews from Germany with ancient origins in Israel specifically and the Levant in general. If you divide up a subject by geography, you cannot switch up and suddenly go by ethnic group. His perspective makes him a suspect for being the one who makes changes without sign-in. Genie and the sock puppet are in conflict on the Jews, if you look closely at what both have been doing. John Lloyd Scharf 00:54, 25 August 2011 (UTC)

Apart from the Jewish "Cohen" haplotype, Semino et al. (2000) harvtxt error: no target: CITEREFSeminoPassarinoOefnerLin2000 (help) associated this DNA profile with the Arab expansion in the seventh century AD, and noted that it was most frequent amongst J1 men in the Middle East and North Africa, but less frequent in Ethiopia and Europe.

• I noticed this and did a check. Semino does not mention J1, J1c3, P58, or the Arab Expansion. John Lloyd Scharf 04:54, 4 September 2011 (UTC)

Fixed.--Andrew Lancaster (talk) 08:11, 4 September 2011 (UTC)Reply

• Like you fix every article. Saying they all agree with you because you force it in every article is not convincing. This was my comment to P, not you. You are, as usual, a consensus of one. John Lloyd Scharf 04:31, 7 September 2011 (UTC)

These talk pages are provided for conversations related to improving Wikipedia articles. This is not a private website. You made a point (which you should have made on the article talk page) and I was able to remove the source of concern you described. So you should be ok with that? Are you now saying you would preferred the article before my edit? Then what was your point? I get the impression this is like your post about me "tainting" a proposal by being involved in it, even though you agreed with it.--Andrew Lancaster (talk) 15:09, 7 September 2011 (UTC)Reply

• • Nor are these pages for paranoid harassment of other individuals, Andrew. Snooping around on others pages obsessively to see what other might say about you is representative of a disturbed behavioral trait. This talk page is my talk page, and its up to me to criticize or not criticize what is posted here. If you have a problem with what he says on my page, then why don't you take it to your or his talk page.PB666 ^yap 19:58, 7 September 2011 (UTC)Reply

The above one word post "Fixed" is about an article, and I doubt that it should be called paranoid, obsessive, disturbed etc. It is a constructive response to JLS's concern, and was posted here simply because a comment about an article was posted here.--Andrew Lancaster (talk) 19:28, 8 September 2011 (UTC)Reply

• • • I should add deceptive also. I was refering to "what my talk page is for and not for", not what you think is fixing a bad reference. It is for discussing with me problems, not for you snooping around to see what others are saying. I have already concluded that Semino et al. 2000 is an inappropriate reference and should not be quoted. His statement only reiterates the point that you think you can fix 'garbage' science. Just as you tried to fix the Klyosov nonsense from that de-facto manifesto published in your favorite half-refereed journal.PB666 ^yap 20:30, 8 September 2011 (UTC)Reply

Please make your point on the article talk page then, whatever it is. And please WP:AGF.--Andrew Lancaster (talk) 07:38, 9 September 2011 (UTC)Reply

• • • • Get off my talk, you have a PB666 sub page, if you want to cry to mama you can do it on your paranoid/delusional subpage devoted to me.PB666 ^yap 14:26, 9 September 2011 (UTC)Reply

I think you got his number and sized up the situation well. John Lloyd Scharf 04:10, 9 September 2011 (UTC) I just noticed He-Who-Is-A-Consensus-Of-One changed back your edit removing the unscientific speculative crap. He never lets the consensus in the scientific community get in the way of his world view. John Lloyd Scharf 17:36, 14 September 2011 (UTC)

• "rs2421826","11","35187181","GG"

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2421826

This allele is not listed and it is the result I got from Family Finder DNA. Is it possible there has been a malfunction,

http://www.ncbi.nlm.nih.gov/pubmed/19877174

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3020103/

John Lloyd Scharf 04:02, 9 September 2011 (UTC)

ref_assembly - 35187181 G

GG is a phenotype, it means that a state (i.e. individual, risk phenotype, or etc:something representing both strands of chromosome 11) and that both sister chromosomes are in the same state.

The mutation appears not to be part of a CNV

"In fact, half of the reported SNPs are still only candidate SNPs and are not validated in a population. We describe the identification of SNDs (single nucleotide differences) in humans, that may contaminate the dbSNP database. These SNDs, reported as real SNPs in the database, do not exist as such, but are merely artifacts due to the presence of a paralogue (highly similar duplicated) sequence in the genome."

There are several things one has to remember about SNPs.

• Many SNPs are restricted to closely related lineages and are excluded from the population after a few generations, mostly by drift, sometimes by negative selection.
• SNPs in the databases are usually quite common in some populations and are well characterized. Most (if not all) of the SNPs that you and I will ever deal with are sufficiently characterized . . .But:

-The order of the SNPs on different peoples chromosomes may not be characterized, in general the order of SNPs on the chromosome is assumed however I know researchers that have questioned both the order of SNPs and the direction on the chromosome.

-Some SNPs are part of larger variable units (indels) and these insertions are often variable in size.

-Some SNPs that have been characterized have been characterized cells of clonal origin that represent mutations that are not carried in the germ-line DNA. Sometimes the mutations are a found frequently. I can give examples where a somatic mutation is commonly found in cells with cancer, the non-cancerous cells dont carry the mutation, but the cancerous cells often do.

PB666 ^yap 21:47, 13 September 2011 (UTC)Reply

• When you say "restricted to closely related lineages," I think of the so-called CEU population used to represent Europeans. Every time I look at an individual in that group, they are clearly stated to be "Morman." (Example: http://www.ncbi.nlm.nih.gov/SNP/snp_ind.cgi?ind_id=171 )

By the way, when they claim "Caucasian/UTAH/MORMON" I know there is an ignorant bias. It sends up a red flag when they use "Caucasian" and may as well be "Aryan." Unless their genetic/geographic origin from between the Black Sea and Caspian Sea, they are just another Western European type. The British Isles are distinctly different than even mainland Western Europe. I think we need a group other than Northeast Utah LDS to represent "Europeans." John Lloyd Scharf 17:54, 14 September 2011 (UTC)

The CEU sample for the USA comes from the Mormon population of Utah.PB666 ^yap 19:45, 14 September 2011 (UTC)Reply

There is not one genetic background for England. Ireland, Scotland, NW England, Wales can be distinquished from the rest of England by the unusually high level of ancestral haplotypes. The Cornish population is this plus some other (presumbably phonecian) influences. Central England is cosmopolitan, but the core Ethnic Anglo group shows relatively high presence of Latin (French, Italian, Spanish) influences whereas SE England tends to reflect the genetic makeup on the other side of the Channel (Netherlands, Belgium, N France, N. Denmark).

By and large, the genetic makeup of Americans tends to most closely reflect people of NW Ilse region and Scandinavia with a slight tilt toward German. British proper are not very representative of Europe as a whole, I suppose the french are probably the most representative, but there has to be a cost paid because if you are trying to distinguish European descent (e.g. North of the Italian Alps, West of the Carpathian Mts) from Middle Easterners and Meditteraneans, France and Belgium have particularly high levels of fingerprint HLA from NE Mediterranean, Eastern Black Sea region, and the Levant. France is an antinode within the standard repertoire HLA haplotype nodes (A1-B8-DR3-DQ2.5, A3-B7-DR15-DQ6.2, A2-B7-DR15-DQ6.2, and A2-Cw5-B44 haplotypes). That does not help much if you are trying to distinquish a European enriched disease from disease of other parts of the world.

IMO at this stage of the game, with 100 European HapMapped one does not expect a high level of precision. I would be more concerned about founder effects in the Mormon population, but this can be diluted with selected sampling from good geneologies, which they have. There, of course, is no way to do Y-VNTR of long deceased males to confirm paternity, and when monogamy in Utah's rural area is a joke, then we can basically argue that paternity can be called into question. Such patterns of concealment of paternity can lead to unseen rapid drift. Nonetheless the level of precision for the designator CEU, given the rather undefinable nature of the designator is adequate. Once we get 10,000s of European Genomes types by SNP, then it should be possible to look at say Western Irish, Southern Irish, Northern Irish and Eastern Irish. This will reveal SNPs that evolved locally and expanded over prehistoric time, but with a low level of backflow their presence in Europe would be treated as rare to 'nascent mutation'.

Consider other sources of error:

-Faulty assay materials (this was observed and published upon recently, a researcher got a batch of plates that gave unusual results, after testing the plates he found they were not reporting as per manf.

-Mistyped SNPs and somatic mutations.

PB666 ^yap 19:45, 14 September 2011 (UTC)Reply
Because of the famine caused in Ireland by the British and in stealing lands from the Scots, the influx of immigrants from those regions in the beginning in the late 1700s to the late 1800s the genetic make-up of the US is decidedly Scots-Irish. The LDS founders who produced the most offspring are from Anglia where Scandinavian Influence is stronger from prior to 1000 AD. I believe seven generations washes out most alleles, but there is little left after 16 and more. Being an island nation brings a lot of isolation. The is aggravated by a couple dozen founders, some of which were already related, having up to 50 offspring. The deeper the roots in LDS, the higher the probability of red hair and dark eyes.
I doubt we shall see 10,000 Irish genomes anytime soon and there is little standardization in how the haplotypes are being read. At this point, this "science" looks more like astrology than astronomy and the "genetic genealogists" are quick to muddle the interpretations for the results, if not the researchers themselves. They declare no biases, but there is more than financial interests involved. John Lloyd Scharf 02:58, 17 September 2011 (UTC)

• I have been looking at a section of my Chromosome 2 because I match that section with someone else. This mentions A, AA, AG, G, and GG genotypes. I have been tested and the genotype stated is CC. Should that be interpreted as a GG?

Illumina-"rs884460","2","140642488","CC"

Affy-rs884460 2 140642488 CC

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs884460

John Lloyd Scharf 19:19, 10 October 2011 (UTC)

Yeah, that is one of the screwiest looking SNPs I've seen. The sense strand to me looks like T, not A, and therefore what they you CC is right. Why on the page they you A/G versus T/C is simply confusing the issue.PB666 ^yap 21:18, 10 October 2011 (UTC)Reply

Okay, so it is not some magical mystery I just am ignorant of. I ran into "one of those" like the one you have problems with here on SNPedia. He is just a software type. There are many like this listed there. I can see why you recommended NCBI. They are muddy, but this guy just aggravates that. Much of the research seems not to be relevant to my medical issues and the risk alleles are not named more often than not. Today I found SNP listed on SNPedia claiming to be for a Haplogroup on Y and it was listed as Chromosome 2 and actually referred to a SNP for Chromosome 5. It is like Wikipedia in that it is edited with incompetence by Gene Nazis. ;>John Lloyd Scharf 02:49, 11 October 2011 (UTC)

Chromosomal position number more or less arbitrarily choose one 5' to 3' direction off of one end of the chromosome. The sequence that they obtain is from contigs that oriented from the other end. Its easy to 'transform' the contiq sequence to make it a + strand and avoid the confusion. The problem here is that in some cases substitutions are not transitions, but transversions, and the - strand contigs have the same sequence as the minor variant. It gets confusing and you have to dot your i's and cross your t's when working with this stuff. Moreover some SNPs are actually part of insertions and deletions, which means the adjacent variants are not included. Its a headache. Try processing 1000s of these SNPs as I was doing earlier this year. I actually had a macro in microsoft excel VB application that would search out the SNP page for adjacent variants downloaded from the hapmap, and was able to deduce the major and minor variants. I can say that most of the SNPs presented from genome wide association studies are not causal mutations, they are linked to causal mutations. The GWAS do not present a fair representation of linkage disequilibrium or the representation density of haplotype variants already described by HapMap. As a consequence an SNP linked to any given low penetrance causal variant could be a million nucleotides from that causal variant. It was not uncommon to see GWAS associations that were later to be shown as QTL loci 50,000 to 500,000 nucleotides away from the GWAS SNP associated. GWAS are great, BUT they generally do not disclose their weaknesses.PB666 ^yap 21:48, 14 October 2011 (UTC)Reply

1. That they are representative, only about 1 per 100 known SNPs in any given population are used. 2. That they are corrected, and without a highly refined assessment of linkage disequilibrium between representative markers, the correction method is likely to underestimate probability. 3. That because they are representative, regional associations are generally not maximally optimized. 4. That because of 1 - 3 that many associations are missed, marginal associations that exist between the broad band between uncorrected and corrected probability thresholds.

Medical issues are difficult to deduce with random genetics. SNPs, unfortunately generally do not equal genes (as in functional allelic variants at disease-related loci).PB666 ^yap 21:48, 14 October 2011 (UTC)Reply
As a teen I was a pheasant hunter. I had some old ammo. When I pointed directly at a rooster flying away from me dirt flew up all around the bird, but it had no reaction. It fired a lead donut of bird shot. Chromosomes and mitochondria are not all the same in their order for each individual, if my mtDNA is any example. I have no deletions, but I do have extra basepairs at certain points than the Cambridge model. I think the problem, from what you are saying, is that a SNP may or may not affect the function of a gene. I always wonder if that old term "junk DNA," may be a load of redundant genes that either correct what a malfunction does or actually acts as a backup to do that function of the gene. However, I do continue with my personal DNA testing with the hope that it will be useful to my offspring, if not myself. I have hypertriglyceride levels and Type II Diabetes [insulin resistance]. I think the two are connected and I may be thyroid "resistant" as well. John Lloyd Scharf 05:31, 15 October 2011 (UTC)

CRS sequence is not stable, it has changed several times since it was first sequenced. It is known that if you take sequence from different body tissues for CRS bearing individuals you will get different sequence. There are several points in the HVR2 region that account for this instability.

We are not asking the question about Junk, although it is a valid question with many SNPs. The question that the association begs is whether the SNP is involved (either causal or protective) in disease or is simply a representative marker, or in some cases random marker. Since there are a large many diseases that have inherited components, then there is a possibility that some of the SNPs associated with certain disease are causal with other diseases (unlikely but plausible in most instances). This is the way statistics works sometimes. We have to ask simple binary questions, then correct later on with the issue of multiple sampling or analysis.

[Most of post refactored, see history]PB666 ^yap 20:10, 24 October 2011 (UTC)Reply

My point in saying this is that certain foods may not be recommended to the general public, but for some people, those foods may be the best source of protein and fat, and common foods like beef, wheat-containing foods, high starch diet are 'more or less' poisonous. PB666 ^yap 07:09, 15 October 2011 (UTC)Reply

This seems to be what my specialist is telling me. John Lloyd Scharf 23:20, 21 October 2011 (UTC)

This is the model for editing a reverse orientation

• A->T
• T->A
• C->G
• G->C

"rs3819001","1","1128776","TT" -My result-

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3819001

http://mutdb.org/cgi-bin/mutdb.pl?snp=rs3819001&variant=291487&rsid=NM_004195

Wild type nucleotide: A

Variant nucleotide: G

Chromosome strand orientation: reverse

• Given the above, the TT represents the A or "Wild type." Am I correct in this assumption?

John Lloyd Scharf 21:35, 31 October 2011 (UTC)

Hi, I'm translating Anti-mitochondrial_antibody into Chinese. There is one thing I'm not quite sure about because I'm not professional in this field. Would you please tell me that the relationship between

• pyruvate dehydrogenase, E2 subunits
• 2-oxo-glutarate dehydrogenase
• branched chain 2-oxo-acid dehydrogenase

and

• AMA
• PBC

Do you mean that "pyruvate dehydrogenase, E2 subunits", 2-oxo-glutarate dehydrogenase and branched chain 2-oxo-acid dehydrogenase are the "major liver antigens"?

Thank you. Sumtec (talk) 06:36, 27 October 2011 (UTC)Reply

Primary biliary cirrhosis (PBC) is a type of autoimmune liver disease.

The disease is caused by the progressive obstruction of the ductile facilities of the liver resulting in the backup of bile into the liver. Complete obstruction causes endstage liver disease.

Antibodies in PBC react with the ductile cells. There are two major catagories.

1. Reactivity to Nuclear proteins. (e.g. Anti-gp210 antibodies). Reactivity to the nuclear proteins is the best evidence for progressive (toward endstage disease)
2. Reactivity toward anti-mitochondrial antibodies (AMA). The importance of their involvement is not so clear.

While using the "word major liver antigens" could be used, it is probably not appropriate. First, these are not the antigens that typify the most dangerous form of disease, second these cells are liver cells but that are specialized components of the ductile tissue that drain the liver (as opposed to venous tissue or hepatocytes). They are the most common antigen of these tissues. There is autoimmune liver disease that attacks hepatocytes, so . . . . .

http://www.cpmc.org/advanced/liver/patients/topics/hep_autoimmune.html

AMA are, at least, indicators of the occurrence of a destructive anti-ductile tissue immune response. Not sure that they are pathological autoimmune targets. This page is somewhat obsolete and you might try looking up more recent papers on AMA involvement in PBC on Pubmed.PB666 ^yap 16:21, 27 October 2011 (UTC)Reply

The Y chromosome is abstractly described as a highly differentiated variant of the X chromosome. This definition might be considered an oversimplification of the reality because all chromosomes are "highly differentiated variants" of other chromosomes. But in the case of the Y chromosome the analogy has more specific meaning.

1. There is a region of the Y chromosome which is called NRY (non-recombinant portion of Y). This makes up the majority of the y chromosome.

2. The remainder is the recombinant portion of Y which has analogous sites on the X chromosome. The SNPs on Y that are close to recombination hotspots have comparable sites on X. These sites are spread widely across the x chromosome but are packed into a small region of Y.

3. The basic concept of recombination is that you have similar regions on two chromosomes in which the recombination machinary can build a "X" structure that then can resolve itself. Therefore the fact that X and Y can undergo recombination means that there are sites between 20 and 100 nts in length that are nearly identical between X and Y. Statistically we have to think about this. If there are 4 nts used at roughly the same frequency the odds of a match is 1/4 for 1 nucleotide, 1/16 for 2 nucleotides, 1/64 for 3 nucleotides. By the time you get to 17 nucleotides in length the probability of exact match of 2 sequences is less than 50% for the entire genome. Therefore for specific recombination to work the matching needs to be for sequences >16 nts in length. (Otherwise Y would recombine with other chromosomes or other parts of X). To get it down to the point that no recombination site will undergo false recombination you need recognition of approximately 25nts. What Parhan and Ohta found in 1986 is that to achieve gene conversion in the HLA class I, typically lengths of 30nt were resulting in abortive recombination if there was a single or multiple mismatches. So somewhere between 22 residues and 1 mismatch (favoring gene conversion) and 30 nts with no mismatches favors (classic recombination). BTW, if gene conversion occurred between 2 improperly paired but similar sequence, we would not identify these as convertants, they would appear to us as point mutations as a result of some other cause.

4. There are other areas of Y scattered widely and at very low density in the Y chromosome that have undergone some 'recombinative' activity with X, probably some form of abortive recombination. This indicates that an adequate amount of sequence conservation has persisted in parts of the NRY.

5. The NRY of Y evolves in a anomalous manner relative to other chromosomes. Comparison of chimpanzee and human Y chromosome has revealed that vast regions of Y have undergone marked insertion and deletion events. The so-called STRs have a tendancy to expand and contract greatly as new STRs appears and old STRs disappear. Interdispersed in these are stretches of somewhat conserved DNA that mutate at an elevated but autosomal like rate. Our understanding of how Y chromosome evolves is far from complete. I expect that in the next few years as many human Y are fully sequenced and we get more information from the Y chromosomes of archaic homo sapiens aDNA sequence, as well as multiple chimpanzee and gorilla Y chromosomes, we will have a much better picture of how the Y chromosome is evolving. Lets just say right now that there is evidence of spurts of evolution in Y chromosome in anthropoid apes.

To solve your question, you have to do a little homework. Match the positions of the sequence in the X chromosome with those found on the Y. To do this use the sequences of the variants and do seaches. You might be able to reconstruct in your head a diagram of comparative structure of X and Y.PB666 ^yap 17:00, 28 October 2011 (UTC)Reply

Monotrenes, such as platypus have bird like Y chromosomes, this indicates that our version of Y started evolving around 150-250 million years ago, after birds (dinosaurs) and mammals (from therapsids) split.

http://en.wikipedia.org/wiki/Y-chromosome

Genome Res. 2008 Jun;18(6):965-73. Epub 2008 May 7.Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes.Veyrunes F, Waters PD, Miethke P, Rens W, McMillan D, Alsop AE, Grützner F, Deakin JE, Whittington CM, Schatzkamer K, Kremitzki CL, Graves T, Ferguson-Smith MA, Warren W, Marshall Graves JA.

"In therian mammals (placentals and marsupials), sex is determined by an XX female: XY male system, in which a gene (SRY) on the Y affects male determination. There is no equivalent in other amniotes, although some taxa (notably birds and snakes) have differentiated sex chromosomes. Birds have a ZW female: ZZ male system with no homology with mammal sex chromosomes, in which dosage of a Z-borne gene (possibly DMRT1) affects male determination. As the most basal mammal group, the egg-laying monotremes are ideal for determining how the therian XY system evolved. The platypus has an extraordinary sex chromosome complex, in which five X and five Y chromosomes pair in a translocation chain of alternating X and Y chromosomes. We used physical mapping to identify genes on the pairing regions between adjacent X and Y chromosomes. Most significantly, comparative mapping shows that, contrary to earlier reports, there is no homology between the platypus and therian X chromosomes. Orthologs of genes in the conserved region of the human X (including SOX3, the gene from which SRY evolved) all map to platypus chromosome 6, which therefore represents the ancestral autosome from which the therian X and pair derived. Rather, the platypus X chromosomes have substantial homology with the bird Z chromosome (including DMRT1) and to segments syntenic with this region in the human genome. Thus, platypus sex chromosomes have strong homology with bird, but not to therian sex chromosomes, implying that the therian X and Y chromosomes (and the SRY gene) evolved from an autosomal pair after the divergence of monotremes only 166 million years ago. Therefore, the therian X and Y are more than 145 million years younger than previously thought."

Therefore it appears that mammals evolved a male heterogamy system from a female heterogamy system. There is a review that discusses this "Sex-chromosome evolution: recent progress and the influence of male and female heterogamety", Hans Ellegren Nature Reviews: Genetics 12:157, where they outline the evolution. The monotreme chromosome 6 (m6) is the male-quiescent arm of chromosome primates (XY). PB666 ^yap 19:55, 31 October 2011 (UTC)Reply

Thanks for pointing out the above information. It was far afield from what I was looking for, but interesting to me and useful to the head of the science department of a high school who I share with regularly. As usual, I get a broader perspective from you than my original intent, which I am thankful for. John Lloyd Scharf 21:20, 31 October 2011 (UTC)

• This is an example of Family Tree DNA SNP test results for my X Chromosome DNA

"rs28413172","X","154764271","---"

"rs7056623","X","154766435","GG"

"rs967495","X","154784057","AG"

"rs5983819","X","154795179","TC"

"rs11547143","X","154826176","TT"

"rs7053404","X","154829338","GG"

"rs5940636","X","154842128","GG"

"rs5940638","X","154843176","TC"

"rs3093457","X","154880801","TG"

"rs3093463","X","154881766","CC"

• These are those for Chromosome 22

"rs715586","22","49510004","TC"

"rs2301584","22","49518363","GG"

"rs756638","22","49518559","GG"

"rs3810648","22","49522492","AA"

"rs2285395","22","49524956","GG"

"rs13056621","22","49528625","GG"

"rs5771007","22","49542594","TT"

"rs3888396","22","49558258","TC"

• I thought human somatic cell contains 46 chromosomes: 2 complete haploid sets, which make up 23 homologous chromosomes. [5] That is 22 haploid sets and then the 23rd set, which is XX for women and XY for men. How can you have two numbers for X when men are XY?

John Lloyd Scharf 01:31, 28 October 2011 (UTC) The chromosome evolved starting with this m6 which then lost certain activities on the male specific lineage (it may have not been male initially, but was negatively selective in males). Eventually this became such a strong determinant in males that the alternative sex-determination chromosome was no longer a determinant, and somewhere in evolution the sex-differentiation was lost without lossing the sex-acting genes. As time went on the differentially male portion became devoid of most genes. Later autosomal material (XAR - X-added region) was added to XY and this further developed by more Y silencing. By the time one reaches primates there is further loss of transgender expression in the XAR, leaving only a small psuedo-autosomal region at one end. This is the region where most of the recombination has occurred.PB666 ^yap 17:00, 28 October 2011 (UTC)Reply

So, is what you are saying is that the second allele given for the X chromosome is actually derived from the Y chromosome? John Lloyd Scharf 20:39, 29 October 2011 (UTC)

It may be derived from the Y chromosome. In instances where the allele is a heterozygote this seems the likely explanation, in instances where it is marked off as a homozygote it 'might or might not' come from the Y as homozygotes are difficult to discern from monoploidy by PCR.PB666 ^yap 19:55, 31 October 2011 (UTC)Reply

Okay, my uninformed perspective resulted in the same answer, assuming they did not make these up. "rs7891378","X","383983","TG" is an example of a heterozygote.

• These two are also difficult to interpret

1. "rs28413172","X","154764271","---"
2. "rs35378569","X","2711361","--"

Notice that one shows three dashes and the other two dashes. My best guess is the "---" is a deletion at both the X and Y at that position and "--" is a deletion on the X and there is no corresponding spot on the X. Just to be clear, this is from an Illumina test chip that FTDNA uses.

John Lloyd Scharf 21:08, 31 October 2011 (UTC)

You have to do your homework on these, look at the SNP pages on medline, and also do searches of the "rs....." on pubmed, there may be publications in these out there.PB666 ^yap 16:01, 1 November 2011 (UTC)Reply

J is a subclade of IJK, which is a subclade of F. Here is a conundrum for you. If J is a subclade of F, does it have all the SNPs of an F? Is it possible for someone only tested for F SNPs to be a crypto - J1? John Lloyd Scharf 22:20, 31 October 2011 (UTC)

There is always a risk of a reverse mutation, but reverse mutation of single site polymorphisms on Y are incredibly rare. I would say that not enough markers were typed in that example. Frequently in HLA analysis one strategy was to define the group markers first, after defining the group markers select from a shorter list of subgroup markers and then get a refined analysis. HLA analysis is so far ahead of Y that now we can define the overwhelming majority of human major antigen HLA at the refined level in a single step.PB666 ^yap 15:59, 1 November 2011 (UTC)Reply

I am not referring to a reverse mutation. J1 is a subclade of F. You have to qualify to be an F in order to be a J. F>IJK>IJ>J>J1 is the progression from clades to subclades. I am trying to see if the testing assumptions excluded testing for J just because an F SNP was found.

Check these results of mine:

• Haplogroup J1

rs9341313 Y 21151206 G [Indicates a J1 subclade]

• Haplogroup I

i4000186 Y 12994387 C [Indicates an I subclade]

Regarding HLA, I have been thinking about it as a way of establishing ethnic roots for a couple years now and the information in that area has exploded since I first became conscious of it. The Y chromosome is only 70,000 years old. HLA for homo sapiens sapiens began developing before the existence of mitochondrial Eve 200,000 years ago, if not for the past 535 million years. It is a unique survival strategy for a small group where some HLAs survived over others as humans existed in small families and tribes over 5200 years ago. If HLA testing of surviving dental pulp was done from remains, it would go a long ways toward advancing cultural anthropology. Establishing Y chromosome origins will likely come from HLA research.

John Lloyd Scharf 16:23, 7 November 2011 (UTC)

Hello there,

You've put in much dedicated work and are far ahead of me in your Wikipedia savvy, but I want to do what I can to contribute to the Y-haplogroup A page, as I have been intensively (as best I can with a full-time job) studying this clade for much of the past year, and am now helping to coordinate research on it. I have just finally posted the 2012 ISOGG phylogenetic tree for Haplogroup A, and the Wikipedia page needs to be updated to reflect it. I wonder if you can help with this task.

I understand that you are sensitive to the requirement that original research not appear in Wikipedia articles, but once we at ISOGG analyze the new research findings and incorporate them into our tree, which is then published on our website, my impression is that it has been considered a valid source for Wikipedia.

I just stopped by the Haplogroup A article and noticed a small error, that the Yorkshire members of A were entered under A2-T, when in fact they are A1a-M31, as it states in King's original article. I added that material to the A1a section.

Even updating the phylogeny to the ISOGG tree that we have today, won't be a fix for very long, as dozens of new SNPs are being discovered through Walk Through the Y sequencing, which are adding and modifying branches.

So, there is much more that needs to be done -- I don't know the best place to start. Suggestions for what I can do that would be most helpful with the least input of very limited time? Iris-J2 (talk) 19:59, 18 February 2012 (UTC)Reply

06~03~2012~15.32~

Hello, if possible, would you please be so kind to give me the corrisponding meaning of certain genetic markers? I'm searching the internet and having problems, the appointment with the doctor is still far and I'm eager to find out what they mean, thank you in advance for any help.

My 3 y.o. son was tested as follow:

HLA A 01, 11 HLA B 51, 57 HLA C 06, 15 HLA DRB1 07, 14 HLA DQB1 03, 05

DR14-DQ5 = DRB1*1401 - DQA1*0104 - DQB1 *0503 is a DR-DQ (e.g DR14 DQ5) haplotype it is sometimes associated with very rare instances of MuSK antibody positive myasthenia gravis. The risk is very very small DR7-DQ3 = DRB1*0701 DQA1*0201 DQB1*0303 most of the time. This haplotype is not overly common but it is of increased frequency in areas of Europe and Asia with recent African contribution. DQB1*0303 also called DQ9 is associated with a few AID. The HLA mediated risk for type 1 diabetes and celiac disease are neglegible. For Rheumatoid arthritis ther is some unknown level of risk for the 05 locus (*0501 associates with RA, but not known for DQA1*0104 : DQB1*0503)

A*01 Cw*06 B*57 is a haplotype found in western Europe. It is the core component of the A1-B57-Cw6-DR7-DQ9 haplotype. It is my suspicion that this haplotype, specifically, is associated with psoriatic arthritis (PsA). To be clear, this is a very long range haplotype in a region that may contain over 300 genes. We do not know which of these genes causes psoriatic arthritis but we do know that that Cw6 (HLA C 06) is the best marking allele and is elevated in PsA. This haplotype in Poles, Irish, Spanish is likely due to a recent identity-by-common-descent from a single ancestor, probably not more than 10,000 years ago.

Balding J, Kane D, Livingstone W, Mynett-Johnson L, Bresnihan B, Smith O, FitzGerald O. Cytokine gene polymorphisms: association with psoriatic arthritis susceptibility and severity. Arthritis Rheum. 2003;48:1408-1413. González S, Martínez-Borra J, López-Vázquez A, García-Fernández S, Torre-Alonso JC, López-Larrea C. MICA rather than MICB, TNFA, or HLA-DRB1 is associated with susceptibility to psoriatic arthritis. J Rheumatol. 2002;29:973-978. Grubic Z, Peric P, Eeèuk-Jelicic E, Zunec R, Stingl K, Curkovic B, Kerhin-Brkljacic V. The MICA-A4 triplet repeats polymorphism in the transmembrane region confers additional risk for development of psoriatic arthritis in the Croatian population. Eur J Immunogenet. 2004;31:93-98. Ho PY, Barton A, Worthington J, Plant D, Griffiths CE, Young HS, Bradburn P, Thomson W, Silman AJ, Bruce IN. Investigating the role of the HLA-Cw*06 and HLA-DRB1 genes in susceptibility to psoriatic arthritis: comparison with psoriasis and undifferentiated inflammatory arthritis. Ann Rheum Dis. 2008;67:677-682. Deitiker PR, Oshima M, Jankovic J, Duane DD, Aoki KR, Atassi MZ. Association of HLA Class II alleles and haplotypes with cervical dystonia: HLA DR13-DQ6 (DQB1*0604) homozygotes are at greatly increased risk of cervical dystonia in Caucasian Americans. Autoimmunity. 2011;44:167-76.

If my deduction is correct then it means that the other haplotype is: A11 Cw15 B51 DR14 DQ5 (HLA A 11, B 51, C 15 . . . ). Parham believes that A11 evolved from a Neanderthal-like humans (Desanovans/Narmadans) that once lived in eastern Asia (In other words it is not from Africa as recently as %96 of most human genes). The Cw15 B51 is found more commonly in Asia and Middle eastern regions. DR14-DQ5 also spreads across northern Eurasia. The A11 allele may be protective for Asian water borne diseases. The only noted full length haplotype has been found: A*11:02-B*51:02-C*15:02-DRB1*14:01-DQB1*05:02 was an Asian American, noting that when the study was done DQB1 may have been mis-subtyped and the frequency is very low. The frequency mode for A11 Cw15 B51 is between Poland and England. C15-B51-DR14 is found considerable more frequently in Asians than Europeans (mostly poles). The DR14-DQ5 segment is modal in the China Yunnan Province Drung, more than likely this part of the haplotype originated in the surrounding regions of Asia.

In terms of risk associated with this. It is generally at such a low frequency risk is not commonly associated. Risk was found with Muscle Specific Kinase antibody (anti-MuSK) autoimmune myasthenia gravis, and our work here in Houston supports that assertion.

Int J Immunogenet. 2011 Feb;38(1):55-62. doi: 10.1111/j.1744-313X.2010.00979.x. Epub 2010 Nov 25. Association with HLA DQ of early onset myasthenia gravis in Southeast Texas region of the United States. Deitiker PR, Oshima M, Smith RG, Mosier D, Atassi MZ. Strong association of MuSK antibody-positive myasthenia gravis and HLA-DR14-DQ5. Niks EH, Kuks JB, Roep BO, Haasnoot GW, Verduijn W, Ballieux BE, De Baets MH, Vincent A, Verschuuren JJ. Neurology. 2006 Jun 13;66(11):1772-4.

Again the risk is very rare, something like 1 in a million have this form of myasthenia gravis. Even amoung people who have DR14-DQ5 the risk is 1 per 100,000 or so. PB666 ^yap 23:54, 6 March 2012 (UTC)Reply

p.s. you can email me at pinklunamoon@hotmail.com thank you

— Preceding unsigned comment added by 87.20.185.184 (talk) 14:36, 6 March 2012 (UTC)Reply 

Hi, I just came across User:Pdeitiker/Soil Moisture and Ocean Salinity (SMOS) satellite and replaced it with a link to the live article.

Please would you have a look through Special:Prefixindex/User:Pdeitiker and tag any user sub-pages with {{db-author}} if you do not need them any more? WP:STALEDRAFT explains why.

Also, this talk page is rather long. If you would like to archive it, see WP:ARCHIVE for alternative methods, or I'd be happy to do it for you; please drop me a note if I fail to respond here. Best wishes, – Fayenatic London 18:35, 19 December 2012 (UTC)Reply

Your upload of File:A2-peptide.PNG or contribution to its description is noted, and thanks (even if belatedly) for your contribution. In order to help make better use of the media, an attempt has been made by an automated process to identify and add certain information to the media's description page.

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you may wish to check that this is the correct fix to the parameter numbering problem. Frietjes (talk) 23:32, 27 January 2015 (UTC)Reply

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The file File:DR beta 1 SEI.JPG has been proposed for deletion because of the following concern:

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Hi, One of the refs used in quoting HLA frequencies turns out to have been retracted. I've removed the table rows that depended on it. If you happen to know of any other papers that include the same data, it'd be good to restore some of the info. There are also a few parts of the text that I'm unsure of so if you have a minute to go through, that'd be v useful. Thanks! T.Shafee(Evo&Evo)^talk 10:38, 22 February 2019 (UTC)Reply

  Portal:Molecular anthropology, a page which you created or substantially contributed to, has been nominated for deletion. Your opinions on the matter are welcome; you may participate in the discussion by adding your comments at Wikipedia:Miscellany for deletion/Portal:Molecular anthropology and please be sure to sign your comments with four tildes (~~~~). You are free to edit the content of Portal:Molecular anthropology during the discussion but should not remove the miscellany for deletion template from the top of the page; such a removal will not end the deletion discussion. Thank you. BrownHairedGirl (talk) • (contribs) 23:16, 10 May 2019 (UTC)Reply

 

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The file File:BreadWheatEvolution.JPG has been proposed for deletion because of the following concern:

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This bot DID NOT nominate any file(s) for deletion; please refer to the page history of each individual file for details. Thanks, FastilyBot (talk) 01:01, 10 March 2020 (UTC)Reply

 

Thanks for uploading File:Apolipoprotein-H.png. I noticed that while you provided a valid copyright licensing tag, there is no proof that the creator of the file has agreed to release it under the given license.

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 Template:HLA database link has been nominated for deletion. You are invited to comment on the discussion at the entry on the Templates for discussion page. Primefac (talk) 16:44, 24 May 2024 (UTC)Reply
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