tag:blogger.com,1999:blog-37148773.post2078087899189544536..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: My DNA ancestryLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger44125tag:blogger.com,1999:blog-37148773.post-46432047103316183682016-04-20T19:22:42.908-04:002016-04-20T19:22:42.908-04:00Ace - except you don't simply extrapolate acro...Ace - except you don't simply extrapolate across your whole genome: you base it only on the 42 SNPs that have been concluded to be extant in neandertals at the time these calculators were created. Since SNPedia still lists (updated Jan 2016) these 42, I assume that base number has not changed.<br /><br />Here is how you would do the extrapolation if we accept that the range of neandertal in modern Europeans is 1 - 4 %. (see http://ww2.kqed.org/quest/2011/08/29/how-neanderthal-are-you/ ) If you have a low number of these alleles (say 5-7 of 84) you should tend toward the 1%, and if you have a high number (say 20-25) you should tend toward the 4%... NOT 21%. Interpretome no where claims that they are giving you a percentage.<br /> Anonymoushttps://www.blogger.com/profile/02188099389785224345noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4971006216234001702016-04-20T15:59:41.187-04:002016-04-20T15:59:41.187-04:00Most certainly have ancestries with slaves, slaver...Most certainly have ancestries with slaves, slavers, cannibals, and horse thieves.W. Bensonhttps://www.blogger.com/profile/11019350102074238654noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24968570911324378772016-04-20T04:22:27.855-04:002016-04-20T04:22:27.855-04:00> which is run by a fundie xian computer progra...> which is run by a fundie xian computer programmer<br /><br />I didn't know that. I'm not sure why it makes a difference though so long as he understands the concepts. The point I'm making though is that it seems to be the case that there are different ways of coming up with different numbers depending on how you set parameters.<br /><br />I had tried interpretome before and it told me I matched 18 out of 84 positions. If this could be extrapolated to the rest of my genome it would make me 21% Neanderthal which would be ridiculous. 23andme tell me I am 3% Neanderthal. My concern with interpretome is that they only use 42 SNPs to draw their conclusion.Aceofspadeshttps://www.blogger.com/profile/09534611408824723712noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8343239864656740642016-04-18T21:59:52.688-04:002016-04-18T21:59:52.688-04:00Here are the SNPs and relevant alleles listed in S...Here are the SNPs and relevant alleles listed in SNPedia: https://www.snpedia.com/index.php/Neanderthal<br />Took me some time to find, but with a little bit of work, anyone with their genome data should be able to do some calculations. Sorry for the several posts.<br />Anonymoushttps://www.blogger.com/profile/02188099389785224345noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-3962672639869187712016-04-18T21:40:13.835-04:002016-04-18T21:40:13.835-04:00I should have also referenced a little known onlin...I should have also referenced a little known online neandertal calculator from Interpretome at http://www.interpretome.com/<br /><br />They only accept 23andme files (and 1 other company I don't know).<br />Benefit is that they list the 42 SNPs (84 alleles) they use for calculation, so I would guess any one who has their SNP data and this list of SNPs might be able to make a rough calculation. For example, according to 23andme calc. I am 3.1% which is 97th-98th percentile for Europeans. At Interpretome this shows me having the neandertal allele in 15 of 84 positions.<br />If Larry approves I will post the 42 SNP table... I suspect they can be found online, e.g at ISOGG.<br /><br /><br />The "grain of salt" admonition applies here: Most of these tests are "tentative" and just for fun. They might improve as we get more neadertal genomes sequenced. Anonymoushttps://www.blogger.com/profile/02188099389785224345noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35198752884324683892016-04-18T20:34:21.696-04:002016-04-18T20:34:21.696-04:00I don't know how opaque 23andme's analysis...I don't know how opaque 23andme's analysis is. The estimator program was created by Eric Durand who has a good background in genome analysis. His white paper on the genome estimator can be found at 23and me site as well as online, e.g. http://stanford.edu/class/gene210/files/readings/23andme_Neanderthal_Ancestry.pdf<br /><br />I trust its results infinitely more than I would trust the y-str.org results which is run by a fundie xian computer programmer.Anonymoushttps://www.blogger.com/profile/02188099389785224345noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49724322300788236692016-04-18T11:17:46.019-04:002016-04-18T11:17:46.019-04:00I have some idea why the two results are different...I have some idea why the two results are different and that has to do with the parameters used.<br /><br />23andme tell me that I am 3% Neanderthal which is above average for their European members. How they come up with that number though is completely opaque.<br /><br />When I run the app I linked to however I am able to tweak the parameters.<br /><br />Here is the result of my comparison with <a href="https://genome.ucsc.edu/Neandertal/" rel="nofollow">Vi33.26</a><br /><br />http://i.imgur.com/7SAQUkX.png<br /><br />If I increase the allowed errors per segment to 2 my percentage match rises to 2.86%<br /><br />http://i.imgur.com/fiV99Zh.png<br /><br />If I decrease the "total SNPs per DNA segment" from 60 to 50, my amount of shared DNA rises to 2.17%<br /><br />http://i.imgur.com/nHnCzYj.pngAceofspadeshttps://www.blogger.com/profile/09534611408824723712noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84767373779794662142016-04-17T05:53:04.638-04:002016-04-17T05:53:04.638-04:00I think he's onto something. I do find that al...I think he's onto something. I do find that all the animals in a region are exactly the same, apart from the differences. It's like dogs that look like their owners. Only DNA. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7397154581207229452016-04-16T20:05:27.012-04:002016-04-16T20:05:27.012-04:00"Polar bears are scared to the point of white..."Polar bears are scared to the point of white hair."<br />It's to Byers what the Banana is the Ray Comfort. Or fishing hooks to Adnan Oktar. Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62835919227453809562016-04-16T17:27:42.331-04:002016-04-16T17:27:42.331-04:00I have to say I'm disappointed that he mention...<i>I have to say I'm disappointed that he mentions polar bears, yet fails to deliver his classic catchphrase.</i><br /><br />Its just a line of reasoning?<br /><br />Well, I can attest to his reasoning as I have observed that I am much whiter in the winter and more browner in the summer. Who can tell what I would look like if I spent winters in Florida. Surely that would confound the ancestory services.SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13966922264408215632016-04-16T15:04:23.363-04:002016-04-16T15:04:23.363-04:00I have to say I'm disappointed that he mention...I have to say I'm disappointed that he mentions polar bears, yet fails to deliver his classic catchphrase.Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71639519047124136992016-04-16T12:52:32.446-04:002016-04-16T12:52:32.446-04:00This is why I like having Robert Byers comments. ...This is why I like having Robert Byers comments. I learn things I'd never have thought anyone thought. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-3754579721723135422016-04-15T18:58:02.703-04:002016-04-15T18:58:02.703-04:00I don't think this has been looked at yet, exc...I don't think this has been looked at yet, except of course for the fact that Neanderthal admixture is not much into Africans. We do expect to see "selective sweeps" of Neanderthal or non-Neanderthal sequences through regions of the human sequence, where there is selection favoring one or the other.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-78232217684805267452016-04-15T13:32:56.722-04:002016-04-15T13:32:56.722-04:00Hey, if, as hypothesized, some of that neandertal ...Hey, if, as hypothesized, some of that neandertal DNA is under selection, shouldn't we expect a bit of a north-south frequency cline?John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21848983688449930722016-04-15T11:22:32.924-04:002016-04-15T11:22:32.924-04:00The contribution of Neanderthal DNA to European ge...<i>The contribution of Neanderthal DNA to European genomes is almost fixed. There isn't much variation segregating in this population as far as I know.</i><br /><br />I'm not so sure. My colleagues Josh Akey and Ben Vernot <a href="http://science.sciencemag.org/content/343/6174/1017" rel="nofollow">conclude otherwise</a>.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30365690191051158142016-04-15T07:40:53.028-04:002016-04-15T07:40:53.028-04:00You have eight great-grandparents. Each one contri...You have eight great-grandparents. Each one contributed, on average, 12.5% of your genome. The contribution from each of your great-grandparents makes up 6.25% of your genome. That's about as far back as you can go and still have a reliable estimate of where your ancestors came from. <br /><br />The contribution of Neanderthal DNA to European genomes is almost fixed. There isn't much variation segregating in this population as far as I know. Everyone has the same Neanderthal markers. It's unlikely that two people with mostly European ancestors will differ in the amount of Neanderthal DNA. I would be very skeptical of any company that reported a differenceLarry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86475575488570300762016-04-15T00:15:22.954-04:002016-04-15T00:15:22.954-04:00Aceofspades: any ideas which is the most accurate ...Aceofspades: any ideas which is the most accurate assessment and why two different methods would yield different results? How different were your results? Kind of intrigued with trying this after this post, but on other hand there is no value in inaccurate information.SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30258316782746320312016-04-14T17:17:28.372-04:002016-04-14T17:17:28.372-04:00My wife was born in Ireland and her 23&me resu...My wife was born in Ireland and her 23&me results showed a bit of Middle-Eastern. We got the results coincident with media reports last year about the earliest Irish settlers being from that area. Presumably some of her Irish roots go very deep.<br /><br />I was also pleased to note that she has a bit more Neanderthal than I do.Capt Stormfieldhttps://www.blogger.com/profile/06406739898230505330noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25356433223437291102016-04-14T14:00:35.810-04:002016-04-14T14:00:35.810-04:00Thanks! Thanks! Duane Waitehttps://www.blogger.com/profile/01821680994817609850noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61965141565638468282016-04-13T10:31:47.812-04:002016-04-13T10:31:47.812-04:0023andme offers this service. Alternatively, you co...23andme offers this service. Alternatively, you could take your results from ancestry.com and use this tool:<br /><br />http://www.y-str.org/2014/12/ancient-calculator.html<br /><br />Warning: I get 2 very different results from these two different tools so we can't be sure what parameters 23andme use to come up with their results.Aceofspadeshttps://www.blogger.com/profile/09534611408824723712noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15098776135158515852016-04-13T05:57:22.633-04:002016-04-13T05:57:22.633-04:00*recent ancestry :P*recent ancestry :PAceofspadeshttps://www.blogger.com/profile/09534611408824723712noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8253230229162936962016-04-13T02:56:42.298-04:002016-04-13T02:56:42.298-04:00Robert Byers said:I just question speculate the de...<strong>Robert Byers said:</strong><i>I just question speculate the details in the gene ancestry stuff.</i><br />With little brains, speculation is all you can do. Scientists are stupid, you know better, science is useless, science is for morons, isn't it? How come they can trace ancestry simply by checking DNA samples? Is it just an irrelevant coincidence that you are stuffed with the DNA of your parents - and not by the DNA of people not in a close relationship with you?Rolf Aalberghttps://www.blogger.com/profile/12878337054438652463noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89516104995993815162016-04-12T23:32:20.973-04:002016-04-12T23:32:20.973-04:00I'm thinking of doing this myself to see if th...I'm thinking of doing this myself to see if they can find any Neanderthal and/or Denisovan DNA in my genome. Is this something that Ancestry is able to do?Duane Waitehttps://www.blogger.com/profile/01821680994817609850noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1015085213012964732016-04-12T23:07:55.346-04:002016-04-12T23:07:55.346-04:00I understand this and watch it on youtube.
its not...I understand this and watch it on youtube.<br />its not about close modern relationships.<br />i'm questioning the more past ones based on these things.<br />They admit its all about Celts and Germans in these areas. THEN they say they can track it further. Right down to Danes, Swedes, etc<br />I question the deeper conclusions.<br />this because I find the whole thing of DNA tracking to be speculative. Even though true at recent relationships.<br />Further i question that dNMA is a good track because i see it can be influenced by like conditions to unlike population groups.<br />This is a big subject.<br />Yet a example is that all white europeans were already segregated in tribes, speaking different languages, before coming to Europe and getting white.<br />So whiteness was not from biological breeding relationship but just a envirormental trigger. <br />Like with White, rabbits, wolves, bears up north.<br />So the WHITE skin genes would be in everyone but not becaise of bio breeding.<br />I am sure marsupial wolves are just placental wolves despite having genes like the other "marsupials". SO its easy to see the adaptive triggers bring a like genetic "score" but not from a common descent concept.<br /><br />They do cool stuff with gebne tracking. They say they can find the Vikings in the North English gene pool. Hmmm. Maybe but they are all the same.<br />I just question speculate the details in the gene ancestry stuff.<br />Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84233145952506724222016-04-12T22:36:57.376-04:002016-04-12T22:36:57.376-04:00I stabd corrected. I understood almost all were Sc...I stabd corrected. I understood almost all were Scots. Then the small number of english, Welsh, Dutch etc would of been assimulated by marriage because the whole group over the centuries would of taken on a Protestant Irish identity. no longer just breeding in their original identities. possibly because people moved around so little the english identity would endure. <br />I did think you might of not known the settlers were mostly Scots because its common to say it was a English settlement.<br /><br />same as in cAnada. americans think Ontario was settled by english yet it was settled by a Yankee northern migration that also settled the states this side of the Mississippi. <br />Then after the 1830's(possibly due to the revolts here) it was a protestant Irish, scottish, migration from Great britain that settled ontario. very few English until the late 1800's and that around the lake in towns/cities.<br />I never said yanks settled ontario but rather they were 80% of those who settled from the revolution until the 1830's. then heavy migration from Britain.<br />Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.com