tag:blogger.com,1999:blog-4123559132014627431.post6732808374400329154..comments2024-03-18T18:30:48.719-07:00Comments on Eurogenes Blog: Population genomics of Early Bronze Age Europe in three simple graphsDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger95125tag:blogger.com,1999:blog-4123559132014627431.post-47304343976389820912015-07-21T12:34:41.869-07:002015-07-21T12:34:41.869-07:00Interesting stats. Despite Lithuanians rather than...Interesting stats. Despite Lithuanians rather than Georgian sharing more drift with Pathan on the Pathan-Mbuti axis, Georgians rather than Pathans are much closer to Lithuanians on the Lithuanian-Mbuti.<br /><br />Or put another way, the Georgians have a bit more non-Pathan relatedness than Lithuanians, while the Pathans have a quite a bit more non-Lithuanian relatedness than Georgians.<br /><br Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-46469604366261353452015-07-20T14:43:53.173-07:002015-07-20T14:43:53.173-07:00I agree. The South Asian cluster, no matter if it ...I agree. The South Asian cluster, no matter if it is 74% or 88%, always comes out just over 60% ENA. I've checked three unsupervised tests. Paniyas were at 74,84, and 88% of this cluster. Depending on the amount, dictates how much excess shows up in Onge, Papuan, and Atayal. I used Kharias (76% ENA on Admixture and qpAdm) to gauge the amount, in all three tests, and all three are about as Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-28930869769099440242015-07-20T02:38:09.029-07:002015-07-20T02:38:09.029-07:00Thanks Chad for providing these statistics. They s...Thanks Chad for providing these statistics. They suggest that Pathans must have significantly more ENA than the 9% in Davidski's qpAdm modeling of them.Balajihttps://www.blogger.com/profile/09561110603904765636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-57429027752099396602015-07-19T12:00:07.601-07:002015-07-19T12:00:07.601-07:00But, then there's this...
result: Mbuti ...But, then there's this...<br /><br />result: Mbuti Lithuanian Georgian Pathan -0.0181 -14.882 16997 17622 354212 <br />result: Mbuti Lithuanian Armenian Pathan -0.0155 -12.174 17066 17605 354212<br />result: Mbuti Kharia Georgian Pathan 0.0251 20.835 17366 16515 354212 <br />result: Mbuti Kharia Armenian Pathan Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-71021768387221926512015-07-19T02:05:33.342-07:002015-07-19T02:05:33.342-07:00Alberto,
Thanks for bringing up some interesting ...Alberto,<br /><br />Thanks for bringing up some interesting discussion. Davidski had calculated some months ago some of the same statistics that you requested but with Chimp instead of Mbuti. I compare them below<br /><br />D(WHG,LBK_EN;Pathan,Mbuti) = 0.0069 z = 1.71<br />D(WHG,LBK_EN;GujaratiA,Mbuti) = 0.0107 z = 2.409<br />D(WHG,LBK_EN;GujaratiD,Mbuti) = 0.0136 z = 2.961<br /><br />D(WHG,Balajihttps://www.blogger.com/profile/09561110603904765636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-75341905245312288562015-07-18T05:08:01.719-07:002015-07-18T05:08:01.719-07:00Here it is...
http://polishgenes.blogspot.com.au/...Here it is...<br /><br />http://polishgenes.blogspot.com.au/2015/07/around-65-lneba-european-ancestry-in.htmlDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-51673805983604400562015-07-18T03:27:36.730-07:002015-07-18T03:27:36.730-07:00@Matt
Yes, I agree with all what you said, and it...@Matt<br /><br />Yes, I agree with all what you said, and it seems difficult to really grab the whole picture without spending hours doing/analysing tons of stats. They seems to be very sensitive to certain events (early branching, small amount of "exotic" admixture,...)<br /><br />Since I don't have that possibility for now, from the stats above:<br /><br />Mbuti Kharia GujaratiD Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-49180061444823286312015-07-18T02:37:02.141-07:002015-07-18T02:37:02.141-07:00Alberto: Ok, so the explanation could be that ASI ...Alberto: <i>Ok, so the explanation could be that ASI and Basal Eurasian are extremely distant from each other and have a huge effect on the stats?</i><br /><br />Could be (and the effect of even low level African admixture in the recent Near East for that involve those via IBD, etc).<br /><br />I think David has noted before that D-stats place huge weight on how early populations branch from one Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-69173049602558230702015-07-18T01:03:42.075-07:002015-07-18T01:03:42.075-07:00Ok, so the explanation could be that ASI and Basal...Ok, so the explanation could be that ASI and Basal Eurasian are extremely distant from each other and have a huge effect on the stats?<br /><br />So the stat:<br /><br />D(WHG,LBK_EN;Pathan, Mbuti) D=0.0069, Z=1.71<br /><br />could be explained by this other one:<br /><br />LBK_EN WHG Dai Mbuti<br /><br />being extremely negative?Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-88312997446333277002015-07-17T22:35:30.761-07:002015-07-17T22:35:30.761-07:00That sounds very interesting.That sounds very interesting.Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-31190804384878880712015-07-17T22:06:26.750-07:002015-07-17T22:06:26.750-07:00I have solid evidence that the qpAdm estimates of ...I have solid evidence that the qpAdm estimates of 60-70% steppe ancestry in the Hindu Kush might well be correct. I'll post it later today.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-70668414366625363842015-07-17T21:56:06.330-07:002015-07-17T21:56:06.330-07:00Very interesting stuff. And yes, I am definitely p...Very interesting stuff. And yes, I am definitely pleased to see these stats (hat tip to Matt):<br /><br />D(Lithuanian, Georgian; Pathan, Mbuti) D= 0.0051<br />D(RISE_baAfan, Georgian; Pathan, Mbuti) D= 0.0079<br />D(Lithuanian, Iranian; Pathan, Mbuti) D= 0.0128<br /><br />Not to mention these stats, from Chad:<br /><br />D(Mbuti, Corded_Ware_LN; Kharia, Pathan) D= 0.0541 <br />D(Mbuti, Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-75978189957177762322015-07-17T16:14:39.029-07:002015-07-17T16:14:39.029-07:00More examples here. It doesn't matter the dire...More examples here. It doesn't matter the direction of flow. Loschbour like admixture in the Bedouins is stronger than any signal for a few pops. Either into, or from Bedouins. Look at the Caucasus pops! Even Yamnaya is further from Bedouins than Loschbour. Add a little Bedouin, Onge, and Atayal, then you have Pathans. That is why they are further. Not because they lack Near Eastern, but Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-8485380140801391772015-07-17T15:48:41.080-07:002015-07-17T15:48:41.080-07:00For instance, Loschbour can go into Bedouins at 35...For instance, Loschbour can go into Bedouins at 35-40%, maybe. Whereas it would be less than that for Pathans, and probably a little less Bedouin into Pathans than that figure for Loschbour. Dstats don't differentiate between direction of flow. Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-48507873292191936172015-07-17T15:38:45.068-07:002015-07-17T15:38:45.068-07:00Because of the ASI, would be my guess. Look at the...Because of the ASI, would be my guess. Look at them compared to ASI heavy folks. Much closer to Bedouins. Plus, it's Loschbour admixture into Bedouins, not Pathan admixture.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-56412000916576802742015-07-17T15:37:13.503-07:002015-07-17T15:37:13.503-07:00result: Mbuti Lithuanian GujaratiD Patha...result: Mbuti Lithuanian GujaratiD Pathan 0.0211 14.578 17631 16904 354212 <br />result: Mbuti Georgian GujaratiD Pathan 0.0208 14.848 17559 16845 354212 <br />result: Mbuti LBK_EN GujaratiD Pathan 0.0240 15.670 17578 16754 353603 <br />result: Mbuti Kharia GujaratiD Pathan -0.0213 -15.485 16742 17471 354212 <br /Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-61016398412117527422015-07-17T15:26:29.009-07:002015-07-17T15:26:29.009-07:00Thanks Chad.
But I think those results rather ins...Thanks Chad.<br /><br />But I think those results rather insist in Pathans having little ENF (and they are at the top of S-C Asians, as you get into India it's less). For example:<br /><br />Mbuti BedouinB Loschbour Pathan -0.0161 -5.365 16675 17222 351075<br /><br />How can Pathans have much BedouinB, when Loschbour has 0% Bedouin admixture and it's still closer to Bedouin than Pathan?Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-70571196276615415692015-07-17T15:19:06.120-07:002015-07-17T15:19:06.120-07:00Sorry, for the repeats. I'm multi-tasking a li...Sorry, for the repeats. I'm multi-tasking a little too much.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-84163970328970880202015-07-17T15:15:56.604-07:002015-07-17T15:15:56.604-07:00Gujaratis have a good amount of ENA. You need to c...Gujaratis have a good amount of ENA. You need to compare to other mixed pops. See here:<br /><br />result: Mbuti Lithuanian Tajik_Pomiri Pathan -0.0129 -10.321 17050 17496 354212 <br />result: Mbuti Georgian Tajik_Pomiri Pathan -0.0088 -7.393 17045 17347 354212 <br />result: Mbuti LBK_EN Tajik_Pomiri Pathan -0.0125 -9.122 16963 17394 353603 Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-33627795349632387192015-07-17T15:01:44.173-07:002015-07-17T15:01:44.173-07:00@Chad
SC Asians have a good amount of Bedouin lik...@Chad<br /><br /><em>SC Asians have a good amount of Bedouin like admixture.</em><br /><br />But see this:<br /><br />GujaratiD LBK_EN Palestinian Mbuti -0.0519 -18.272<br />Pathan LBK_EN Syrian Mbuti -0.0299 -11.908<br />WHG Syrian GujaratiD Mbuti 0.0244 6.87<br /><br />While the Sub-Saharan and ASI might be influencing these stats, it still doesn't look to me like S-C Asians have much ENF (Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-69258415193764410222015-07-17T14:52:02.180-07:002015-07-17T14:52:02.180-07:00@Matt
Yes, indeed some weird results there. I thi...@Matt<br /><br />Yes, indeed some weird results there. I think a good part of the weirdness of the ones with Syrian and Palestinian are because of the small amount of Sub-Saharan, especially when those population are in positions A or B and Mbuti is on D. I didn't think about it, but probably Mbuti is not a neutral outgroup for Near Eastern populations.<br /><br />The Pathan-Lithuanian Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-57055485892969562382015-07-17T14:35:53.192-07:002015-07-17T14:35:53.192-07:00Gujarati are less Near Eastern than Pathans, and P...Gujarati are less Near Eastern than Pathans, and Pathans are less Near Eastern than Georgians. Not a real surprise. Tajiks may be significantly closer to Lithuanians than Pathans.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-39132959635813942032015-07-17T14:25:10.385-07:002015-07-17T14:25:10.385-07:00SC Asians have a good amount of Bedouin like admix...SC Asians have a good amount of Bedouin like admixture. Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-3578296344863651792015-07-17T14:04:47.422-07:002015-07-17T14:04:47.422-07:00@ Alberto:
Very weird bunch of stats, huh?
D( Li...@ Alberto:<br /><br />Very weird bunch of stats, huh?<br /><br />D( Lithuanian, Georgian; LBK_EN, Mbuti) D= 0.009, D= 4.16<br />D (WHG, Georgian; LBK_EN, Mbuti) D= 0.0082,Z = 1.984<br />D( Lithuanian, Palestinian; LBK_EN, Mbuti) D= 0.0328, D= 16.39<br />D (WHG, Palestinian; LBK_EN, Mbuti) D= 0.0317,Z = 7.909<br /><br />Implies Lithuanian essentially no closer to LBK than WHG (although you could Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-909702782578720872015-07-17T13:54:01.535-07:002015-07-17T13:54:01.535-07:00@ Grey - "This may be a dumb question but cou...@ Grey - "This may be a dumb question but could some of this be archaic rather than specifically African?<br />(so it survived in the Caucasus rather than moved there)"<br /><br />If the haplotype arrived in the Caucasus, say, 40kya it would be highly equilibrated. That is not the case, in fact it is in strong disequilbrium. Suggesting more recent asymmetric migration, probably in the Anonymoushttps://www.blogger.com/profile/13013399855770625556noreply@blogger.com