tag:blogger.com,1999:blog-4123559132014627431.post3175042725724493747..comments2024-03-18T18:30:48.719-07:00Comments on Eurogenes Blog: The Basal-rich K7Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger369125tag:blogger.com,1999:blog-4123559132014627431.post-45410716995136189302017-08-13T14:48:00.847-07:002017-08-13T14:48:00.847-07:00The instructions for ordering the Basal-rich K7 ar...The instructions for ordering the Basal-rich K7 are here...<br /><br />http://eurogenes.blogspot.com.au/2016/11/fund-raising-offer-basal-rich-k7-andor.htmlDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-68791599041849367932017-08-13T13:05:08.187-07:002017-08-13T13:05:08.187-07:00This comment has been removed by the author.Nezih Sevenhttps://www.blogger.com/profile/02774883142650286421noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-49391765429739364372017-01-31T01:50:02.667-08:002017-01-31T01:50:02.667-08:00It ought to be fairly accurate, within some confid...It ought to be fairly accurate, within some confidence interval, as long as all populations can be modelled as wholly ANE-WHG-Basal-rich. Since the distance between these three may be accurately visualized as a triangle.<br /><br />I realize of course that this is not the case. Simonhttps://www.blogger.com/profile/13145168404928155148noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-64560761847542245922017-01-31T01:42:51.942-08:002017-01-31T01:42:51.942-08:00I don't know.
It's very difficult as a ru...I don't know.<br /><br />It's very difficult as a rule to show true genetic distances on two dimensional graphs or plots, because genetic structure is multi-dimensional.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-37603106616754716132017-01-31T01:12:21.328-08:002017-01-31T01:12:21.328-08:00Thanks, I've seen it. Would you say that the &...Thanks, I've seen it. Would you say that the 'true genetic distances version' could be faithfully superimposed on a grid representing FST distance between any of the data points? Simonhttps://www.blogger.com/profile/13145168404928155148noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-70805456150913114222017-01-10T15:28:02.704-08:002017-01-10T15:28:02.704-08:00You might find this version of the plot more infor...You might find this version of the plot more informative in terms of true genetic distances.<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQSFVnTDZkT0RURjQ/view?usp=sharing<br /><br />This is the datasheet I use for plotting the K7 results.<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQMXIxc2Q1cjYybWc/view?usp=sharing<br /><br />You can plot it with the freely available Past3 Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-24638774012936941772017-01-10T07:13:36.293-08:002017-01-10T07:13:36.293-08:00The skewed projection is very intuitive for illust...The skewed projection is very intuitive for illustrating population shifts. But as you say, the x axis is disproportionately longer, therefore a vector between two given sample points in the chart will not proportionally reflect genetic distance. For example, Yamnaya appears to be equally distant from Sintashta and Iran_Neolithic if you don't understand the diagram, while if the length of PC2Simonhttps://www.blogger.com/profile/13145168404928155148noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-85370303635344186772017-01-08T14:43:06.884-08:002017-01-08T14:43:06.884-08:00If you mean the triangle plot, that's rotated ...If you mean the triangle plot, that's rotated to fit geography. That's why it's skewed, with PC2 longer than PC1, and ANE looking so dominant.<br /><br />The reason I rotated it to fit geography, is because this makes it easier to grasp the key population shifts, like the migrations from the steppe.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-2197234735080873622017-01-08T13:43:17.429-08:002017-01-08T13:43:17.429-08:00ANE influence appears inflated in the graph from a...ANE influence appears inflated in the graph from an FST point of view. Am I right if I say that the PCA would more accurately describe the FST genetic differance between samples and clusters if the sides of the triangle were adjusted to correspond to the FST differences between ANE, Basal-rich and Villabruna-related?Simonhttps://www.blogger.com/profile/13145168404928155148noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-16971644760071047842016-11-19T14:15:36.089-08:002016-11-19T14:15:36.089-08:00There's absolutely no evidence of any admixtur...There's absolutely no evidence of any admixture from Iran on the Bronze Age steppe.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-55979528224586767172016-11-19T08:04:29.791-08:002016-11-19T08:04:29.791-08:00My concern with some of the related studies, is th...My concern with some of the related studies, is that the sampling for "Neolithic Anatolian" is restricted to samples from the far west of Turkey; at one extreme of an interaction zone that stretched eastwards to it's polar end in Iran. In contrast to some assertions, the data does not support that West Anatolians were a unique ancestral source (as is more clearly the case with blogmasterhttps://www.blogger.com/profile/11834163614642737338noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-74958579612935068922016-09-28T09:00:42.176-07:002016-09-28T09:00:42.176-07:00@Davidski
Can you please add Native-Australians t...@Davidski<br /><br />Can you please add Native-Australians to your K7 spreadsheet?<br /><br />MaxThttps://www.blogger.com/profile/12920295419805648337noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-24894173632834725742016-09-14T04:43:42.510-07:002016-09-14T04:43:42.510-07:00Thank you for explaining, I thought Samara_HG and ...Thank you for explaining, I thought Samara_HG and Samara_Eneolithic were alike when i came across them. <br /><br />"So the first dilution of ANE on the steppe occurred with the migration of southern people to the Samara region, and admixture between Samara_HG people and these newcomers from the south. The result of this mixture was Samara_Eneolithic, with less ANE than Samara_HG."<br /MaxThttps://www.blogger.com/profile/12920295419805648337noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-19864762608227737452016-09-14T04:27:11.968-07:002016-09-14T04:27:11.968-07:00Samara_Eneolithic refers to Copper Age Khvalynsk s...Samara_Eneolithic refers to Copper Age Khvalynsk samples, not the Samara Hunter-Gatherer.<br /><br />Samara_HG and Karelia_HG form the Eastern_HG clade in respect to all other ancient samples, which means that their ancestry proportions are basically the same. This is what all papers to date show and it's what my new K7 shows (apart from some minor noise in Samara_HG due to low quality DNA).<Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-42210582774617495352016-09-14T04:08:00.946-07:002016-09-14T04:08:00.946-07:00Thank you, Davidski. It is under "Extended Da...Thank you, Davidski. It is under "Extended Data Table 2". <br /><br />He notes regrading Samara_Eneolithic & Yamnaya_Samara. <br /><br />"First dilution of Ancient North Eurasian ancestry (prior to the Bronze Age Yamnaya culture)"<br /><br />In same "Extended Data Table 2" he notes regrading late Yamnaya_Samara & Yamnaya_Kalmykia<br /><br />"ContributionMaxThttps://www.blogger.com/profile/12920295419805648337noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-64629348436726042462016-09-14T03:35:48.151-07:002016-09-14T03:35:48.151-07:00Nope, they're the same, with around 55% ANE in...Nope, they're the same, with around 55% ANE in the K7, which means 70% ANE overall, because the Villabruna cluster is about 15% ANE.<br /><br />They form a very tight clade in formal stats in all papers published to date, including Mathieson et al.<br /><br />So maybe you're confusing Samara_HG with Samara_Eneolithic? But as per the quote you posted, Samara_Eneolithic has less ANE than Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-10765664191830949592016-09-14T03:17:57.392-07:002016-09-14T03:17:57.392-07:00Davidski, it would still be helpful as Samara_HG h...Davidski, it would still be helpful as Samara_HG has higher ANE (around 70s%) than Karelia_HG's ANE (around 50s%). They do seem different on that aspect. <br /><br />Mathieson et al (2015) notes that "First dilution of Ancient North Eurasian ancestry" occurred in Samara_Eneolithic. study link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918750/#SD3<br /><br />It's an important MaxThttps://www.blogger.com/profile/12920295419805648337noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-309661320291927972016-09-13T15:27:31.687-07:002016-09-13T15:27:31.687-07:00Samara_HG is almost identical to Karelia_HG, just ...Samara_HG is almost identical to Karelia_HG, just a little more noisy, with minor <1% Sub-Saharan admix due to its lower quality (that's why it's not in the datasheet).Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-21390647568566425372016-09-13T07:56:32.914-07:002016-09-13T07:56:32.914-07:00Davidski, can you please include Samara_HG as well...Davidski, can you please include Samara_HG as well? I could not find it on spreadsheet.MaxThttps://www.blogger.com/profile/12920295419805648337noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-1127557583621380372016-09-11T08:51:02.038-07:002016-09-11T08:51:02.038-07:00Hi Davidski,
I see you don't have any Coptic r...Hi Davidski,<br />I see you don't have any Coptic reference population. I believe it should be interesting to include and test Coptic raw data as well in your new calculator. If interested I can provide you with the Coptic genome of the Coptic/Ethnic Egyptian Christian in the R1a project here https://www.familytreedna.com/public/R1a?iframe=yresults And here https://www.yfull.com/tree/R-YP1272Theramsterhttps://www.blogger.com/profile/01300691374555389102noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-13431001149716670392016-08-25T20:17:01.798-07:002016-08-25T20:17:01.798-07:00I updated the post above and the K7 spreadsheet.
...I updated the post above and the K7 spreadsheet.<br /><br />I'll be doing this regularly.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-22876924335466592912016-08-17T05:22:43.961-07:002016-08-17T05:22:43.961-07:00This blog has everything covered pretty well, espe...This blog has everything covered pretty well, especially for beginners. You just have to take a bit of time to check out the posts and comments.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-39237041569940311462016-08-17T05:15:31.617-07:002016-08-17T05:15:31.617-07:00Can you tell me what Basal means in regards to dna...Can you tell me what Basal means in regards to dna and the genome? Where do I need to go to learn this stuff as a primer.duge_buwembohttps://www.blogger.com/profile/15671078175031481458noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-20777312209836550222016-08-08T21:23:50.803-07:002016-08-08T21:23:50.803-07:00None of the Chalcolithic Iberians that I have show...None of the Chalcolithic Iberians that I have show any steppe admixture. I don't have ATP3. It's too low quality to run in any of my analyses.<br /><br />ATP9 is from the Late Bronze Age, so it post dates the main expansions from the steppe, and it was obvious for a while now from formal stats that it was showing an eastern shift, probably caused by steppe admixture.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-62499370908606185132016-08-08T21:02:51.033-07:002016-08-08T21:02:51.033-07:00It's interesting how the Bronze Age Iberian, A...It's interesting how the Bronze Age Iberian, ATP9, is now showing some evidence of ANE admixture, which had escaped previous calculators. From some time now, Genetiker's K13 runs, too, have been showing steppe admixture in 7 of the 8 El Portalón samples, especially in ATP9 and the supposedly R1b-M269-carrying ATP3. I wonder if you can you confirm if ATP3 has ANE admixture?<br />Rafshttps://www.blogger.com/profile/01746094202823415912noreply@blogger.com