tag:blogger.com,1999:blog-4123559132014627431.post8731774133471594362..comments2024-03-19T06:09:36.134-07:00Comments on Eurogenes Blog: Modeling Steppe_EMBADavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger42125tag:blogger.com,1999:blog-4123559132014627431.post-89963850963479651372016-07-12T17:22:54.957-07:002016-07-12T17:22:54.957-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-33188238009819275882016-07-12T16:11:16.160-07:002016-07-12T16:11:16.160-07:00And with Wong et al's D-stats using high cover...And with Wong et al's D-stats using high coverage genomes French are not closer to San, Dinka or Mbuti than East Asians are so we can't say there is significant French-like mixture around Sub-Saharan Africa.Shaikorthhttps://www.blogger.com/profile/04468485423355664299noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-65204803468272042662016-07-12T13:16:08.834-07:002016-07-12T13:16:08.834-07:00But there are too many problems there. If this:
C...But there are too many problems there. If this:<br /><br />Chimp Ju_hoan_North Mota French 0.0127 3.889 28311 27604 593430<br /><br />Is because Ju_hoan_North have a significant amount of Eurasian admixture, and closer to French admixture than to Han admixture, because:<br /><br />Chimp Ju_hoan_North Mota Han 0.0070 2.095 28213 27822 593430<br /><br />Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-48116701450392667942016-07-12T09:18:14.868-07:002016-07-12T09:18:14.868-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-57898485088662758652016-07-12T01:59:19.742-07:002016-07-12T01:59:19.742-07:00I don't think that anyone can make much sense ...I don't think that anyone can make much sense of those stats. I kind of expected those kind of results, and I think that adding more populations will only make things worse.<br /><br />In any case, this is why I'm a bit sceptic about the Basal Eurasian not being closer to Africans as part of the definition of Basal Eurasian. Being "closer to Africans" is a very vague concept in Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-185456943268130772016-07-11T11:51:39.037-07:002016-07-11T11:51:39.037-07:00Thanks David. Chimo, what a fail...
So, these vio...Thanks David. Chimo, what a fail...<br /><br />So, these violate my expectations in numerous ways:<br /><br />----<br />D (Chimp Ju_hoan_North Yoruba Han) = 0.019 Z= 9.023<br />D (Chimp Ju_hoan_North Mota Han) = 0.007 Z= 2.095<br />D (Chimp Ju_hoan_North Mbuti.DG Han) = 0.0192 Z= 6.646<br />D (Chimp Ju_hoan_North Biaka Han) = 0.0258 Z= 10.992<br />D (Chimp Ju_hoan_North Somali Han) = -0.0047 Z= Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-82976262265225985662016-07-11T02:10:37.436-07:002016-07-11T02:10:37.436-07:00Matt, you wrote Chimo instead of Chimp. Haha.
htt...Matt, you wrote Chimo instead of Chimp. Haha.<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQNkowbTd5Zl9EV3M/view?usp=sharing<br /><br />Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-16355863463427276782016-07-11T01:33:34.527-07:002016-07-11T01:33:34.527-07:00@Alberto
Those differences don't seem to be ...@Alberto <br /><br />Those differences don't seem to be so significant, actually. For instance, Orcadian-Chinese ASD to Mbuti is comparable to Chinese-Palestinian ASD to Mbuti.Shaikorthhttps://www.blogger.com/profile/04468485423355664299noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-35521501310404900172016-07-11T00:26:41.901-07:002016-07-11T00:26:41.901-07:00@ Alberto: Thanks for that explanation. It all sou...@ Alberto: <i>Thanks for that explanation. It all sounds reasonable, but did the D-stats confirm those patterns? From the 4 run by Chad above 3 would be consistent with them, but this one doesn't seem to be:<br /><br />Chimp Mbuti Loschbour Masai 0.0111 3.888 27704 27095 596893<br /><br />And when you introduce related populations it works? Like Gambian forming a clade with Yoruba to everyoneMatthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-60520095786103771232016-07-11T00:02:36.034-07:002016-07-11T00:02:36.034-07:00@Shaikorth
Yes, there are some small differences,...@Shaikorth<br /><br />Yes, there are some small differences, but the populations that have some SSA admixture are clearly more significant. So with that data at least I see more consistency and could buy the Basal Eurasian hypothesis. Though I would have been nice to see some East African population included to see how those ones behave.<br /><br />@Ryu<br /><br />Yes, would be great to check Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-63502682472231720292016-07-10T22:23:08.196-07:002016-07-10T22:23:08.196-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-55709951541013529322016-07-10T20:28:48.788-07:002016-07-10T20:28:48.788-07:00Tons. 41 from the non-public set, plus another 40 ...Tons. 41 from the non-public set, plus another 40 or so from a low coverage set with Sudanese, Fulani, and Ethiopian groups. Of my 4000 samples, probably half are Africans, but some are very admixed of course.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-86376546803098247352016-07-10T16:21:07.485-07:002016-07-10T16:21:07.485-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-50021495995394195682016-07-10T16:04:36.385-07:002016-07-10T16:04:36.385-07:00Alberto, may not be that simple as Europeans are m...Alberto, may not be that simple as Europeans are more distant from Africans than Armenians and Han in that table. <br /><br />Occasionally we see African edges to East Asians in TreeMix too...Shaikorthhttps://www.blogger.com/profile/04468485423355664299noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-11463577557219301202016-07-10T15:45:05.158-07:002016-07-10T15:45:05.158-07:00@Shaikorth
Thanks. So those numbers do seem to su...@Shaikorth<br /><br />Thanks. So those numbers do seem to support a Basal Eurasian population that is not closer to Africans, since Armenians and Han are equidistant to Africans. And also it shows that populations with African admixture are closer to Africans (Jordan, Yemen, Bedouin). Also it does show that Africans are significantly closer to each other than to Eurasians. So all that looks Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-46995423605153906682016-07-10T14:35:21.730-07:002016-07-10T14:35:21.730-07:00@ Alberto again, just to visually describe the cla...@ Alberto again, just to visually describe the clade pattern I described from my previous post:<br /><br />http://i.imgur.com/7p02v6o.png<br /><br />This contrasts the kind of models that fall out of software like treemix, where there is a differential clading of different Africans with Eurasians, with a model that would have all Africans form a clade together against Eurasians.<br /><br />(note Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-78804617692041990612016-07-10T13:27:23.312-07:002016-07-10T13:27:23.312-07:00@ Alberto:
Another thing that puzzles me is the be...@ Alberto:<br /><i>Another thing that puzzles me is the behaviour of D-stats with Africans. Has someone ever attempted to run more stats with them to build some tree or see which clades they form or whatever?</i><br /><br />My understanding is, besides the East Africans whose admixture we know about (from both West Africa and West Eurasia), African patterns go like this:<br /><br />Ju_Hoan_North:Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-44549023828720521532016-07-10T13:14:41.342-07:002016-07-10T13:14:41.342-07:00
Lower diagonal is standard errors I think.
...<br /><br /> Lower diagonal is standard errors I think.<br /> So Armenian-Yoruba is 0.28569 and Jordanian-Yoruba 0.27960.<br /><br /> Subtract those from 1 and the number should be the IBS they get with Yoruba using that set.Shaikorthhttps://www.blogger.com/profile/04468485423355664299noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-52680225525855671272016-07-10T11:53:28.659-07:002016-07-10T11:53:28.659-07:00@Shaikorth
Thanks! Though I'm not sure I'...@Shaikorth<br /><br />Thanks! Though I'm not sure I'm understanding those numbers correctly. For example, Georgians, Armenians or Adyghe are about 0.0004 distance from Africans, but Jordanians are 0.0015. That means that Jordanians are very significantly further away from Africans than Caucasus populations?Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-57755889608871789262016-07-10T11:52:16.374-07:002016-07-10T11:52:16.374-07:00I'm with Ryukendo and Alberto on this one. I t...I'm with Ryukendo and Alberto on this one. I think the figures for basal are too high, and the split too recent. <br /><br />If you imagine a stat in the form<br />Mbuti test K14 Ust_Ishim<br />A test population with 100% basal, ENA, or any extra crown Eurasian branch should get a value of 0.<br />If we use Vestonice16 as our upper bound in K14 relatedness, we get a D value of -.914. <br /><Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-70770019334888824522016-07-10T10:23:05.275-07:002016-07-10T10:23:05.275-07:00Alberto, supplementary table 2 here has a large se...Alberto, supplementary table 2 here has a large set of pairwise allele sharing distance comparisons between Eurasians and Africans. That method should correspond to IBS. Lower distance = closer.<br /><br />http://www.nature.com/nature/journal/v466/n7303/extref/nature09103-s1.pdfShaikorthhttps://www.blogger.com/profile/04468485423355664299noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-49666497459008998002016-07-10T10:09:45.153-07:002016-07-10T10:09:45.153-07:00Looking at the f3 of shared drift with Ust-Ishim, ...Looking at the f3 of shared drift with Ust-Ishim, the difference between WHG and LBK_EN is slightly bigger than between LBK_EN and Jordanians and Palestinians, but about half as much as between LBK_EN and Tunisians and Algerians. Since Levant_Neolithic is already quite more Basal than LBK_EN, it would probably require a similar amount of admixture from a similarly divergent African branch as Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-61044061962215889402016-07-10T08:03:41.752-07:002016-07-10T08:03:41.752-07:00In the sense that no BE carrying pops are closer t...In the sense that no BE carrying pops are closer to Africans, but share more drift with each other than with hunters, and less with East Asians it makes sense.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-78757003374421295162016-07-10T08:02:34.762-07:002016-07-10T08:02:34.762-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-40596663449040337092016-07-10T07:28:52.361-07:002016-07-10T07:28:52.361-07:00@RK
Yes, exactly. According to D-stats the term A...@RK<br /><br />Yes, exactly. According to D-stats the term African does not seem to define one specific clade. So whatever African branch that might have admixed with Eurasians to create this decrease in affinity to other Eurasians might no longer exist in its pure form. So D-stats with modern Africans are not going to be informative about it.<br /><br />As for the amount it doesn't have to Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.com