tag:blogger.com,1999:blog-4123559132014627431.post4073097486984013965..comments2024-03-18T22:01:02.498-07:00Comments on Eurogenes Blog: D-stats/4mix tour of ancient EurasiaDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger130125tag:blogger.com,1999:blog-4123559132014627431.post-75177107585540090142016-03-15T06:32:00.166-07:002016-03-15T06:32:00.166-07:00This comment has been removed by the author.batmanhttps://www.blogger.com/profile/00810638398479713844noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-67214090220972824532016-03-15T06:31:41.193-07:002016-03-15T06:31:41.193-07:00@Davidski
What happened to your original post on ...@Davidski<br /><br />What happened to your original post on the 4-way stat, as of March 1st? Have your blog been hacked?batmanhttps://www.blogger.com/profile/00810638398479713844noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-88601534691357590552016-03-11T17:13:36.879-08:002016-03-11T17:13:36.879-08:00@FrankN
No problem, I didn't suppose you mean...@FrankN<br /><br />No problem, I didn't suppose you meant any offence by it, having come across stronger than intended many times myself.<br /><br />I hope we do have African results to discuss soon, there have been some good recent papers on South Africa, but West and Central Africa are certainly due for more work (a truckload of Y chromosome full sequences would be a good start).capra internetensishttps://www.blogger.com/profile/15951755327460295070noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-73634514604943160012016-03-11T11:21:59.466-08:002016-03-11T11:21:59.466-08:00@capra: In my previous reply to you, I gave in to ...@capra: In my previous reply to you, I gave in to my sarcastic mood. Hope you didn't misunderstand that. You asked thought-provoking, and as such valuable and legitimate questions. I appreciate that, but probably didn't signal such appreciation particularly well (if at all). <br /><br />I also still owe you thanks for earlier correcting me on the issue of African rice (a discussion to be FrankNhttps://www.blogger.com/profile/01292462554916779884noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-72656372585941342062016-03-11T11:21:57.790-08:002016-03-11T11:21:57.790-08:00For completeness after seeing David's post, I ...For completeness after seeing David's post, I tried with Anatolia Neolithic instead of Lebanese, but adding Esan too:<br /><br /> Kalash<br />"Caucasus_HG" 35.3<br />"Selkup" 31.3<br />"Anatolia_Neolithic" 18.9<br />"Karelia_HG" 11.3<br />"Esan_Nigeria" 3.2<br />distance = 0.001404<br /><br />So that works quite Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-77303413064715194222016-03-11T09:40:14.081-08:002016-03-11T09:40:14.081-08:00I have the Onge. I'll see about joining in on ...I have the Onge. I'll see about joining in on this soon.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-23929254036119716162016-03-11T08:58:17.278-08:002016-03-11T08:58:17.278-08:00@FrankN
Thanks for the info!@FrankN<br /><br />Thanks for the info!capra internetensishttps://www.blogger.com/profile/15951755327460295070noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-21355256960606696852016-03-11T07:11:57.093-08:002016-03-11T07:11:57.093-08:00Yes, we need some ancient Near Eastern that is mor...Yes, we need some ancient Near Eastern that is more basal than Anatolia Neolithic. For Asian populations it's not possible to model them well without using a modern Near Eastern.<br /><br />Looking at the Kalash, the behaviour is interesting. Starting from David's model above:<br /><br /> Kalash<br />"Dravidian_India" 39.1<br />"Andronovo_full" 29.7Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-52006819869694156632016-03-10T19:00:22.723-08:002016-03-10T19:00:22.723-08:00You can work it out with 4mix/nMonte by finding a ...You can work it out with 4mix/nMonte by finding a good three- or four-way fit for BedouinB including Anatolia Neolithic, Caucasus HG and one or two African populations.<br /><br />Then use the Anatolia Neolithic/Caucasus HG proportions to guide you.<br /><br />Whoever lived in the Middle East before the Sub-Saharan admixture happened here, they were very similar to Anatolia Neolithic, Caucasus HGDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-57846153505666107832016-03-10T18:48:54.719-08:002016-03-10T18:48:54.719-08:00I'm just looking for trends. If we didn't ...I'm just looking for trends. If we didn't have EEF genomes and did the same experiment for Europe, we'd find an EEF-trend via Sardinians, North Italians, and Iberians. ADMIXTURE did this before ancient DNA. I think D-stats of the form D(Chimp, West Asian)(Mbuti, West Asian), where West Asian=Bedouin, Lezgin, Cypriot, etc(not asking for you to do a test yet) can do this. <br /><br />Krefterhttps://www.blogger.com/profile/01055804913528477710noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-27025470143208048412016-03-10T18:23:53.059-08:002016-03-10T18:23:53.059-08:00Can't think of one.
You can try and make a pr...Can't think of one.<br /><br />You can try and make a proxy, until we get some ancient genomes from the Middle East.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-437133402612150762016-03-10T18:20:07.798-08:002016-03-10T18:20:07.798-08:00@Davidski,
What Middle Eastern outgroups do you t...@Davidski,<br /><br />What Middle Eastern outgroups do you think would be best, to express Middle Eastern diversity? Making all Middle Easterners 80%+ Cypriot isn't realistic. We know Middle Easterners have non-EEF and non-CHG, but heavily Basal Eurasian, ancestry, and so I'm asking what outgroups do you think are best to deceiver what this ancestry is. <br /><br />@Matt,<br /><br />Krefterhttps://www.blogger.com/profile/01055804913528477710noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-75151425024483254682016-03-10T17:30:33.987-08:002016-03-10T17:30:33.987-08:00huijbregts,
Thanks, that's very useful.
Matt...huijbregts,<br /><br />Thanks, that's very useful.<br /><br />Matt,<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQaFBZb0tqb0paSWc/view?usp=sharingDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-72211419143261307032016-03-10T13:02:10.907-08:002016-03-10T13:02:10.907-08:00@ Davidski, would it be possible to do a version o...@ Davidski, would it be possible to do a version of the "EHG as row not column datasheet" with BedouinB as a column stat, and not a row (or ideally, splitting the BedouinB into two subsets so you can have one of both)?<br /><br />I'd be interested to see if this model can handle the recent Near Eastern / Middle Eastern admixture, and I think that's best tested with an explicit Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-77790976531009497452016-03-10T12:36:58.712-08:002016-03-10T12:36:58.712-08:00FrankN
The changing arid / ameriolate cycles are ...FrankN<br /><br />The changing arid / ameriolate cycles are well described in the steppe & Balkans between 5000-2000 BC<br /><br />Have you come across anything for central and Northern Europe ?Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-87721113369423800902016-03-10T12:08:04.422-08:002016-03-10T12:08:04.422-08:00@David
I have saved a script temp_nMonte.R in my d...@David<br />I have saved a script temp_nMonte.R in my dropbox<br />https://www.dropbox.com/sh/1iaggxyc2alafow/AACIjLtnkuaNNsJ5oKME_3XHa?dl=0<br />Is this what you need? If so, I will will rename temp_nMOnte.R to nMonte.Rhuijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-86089742685373584922016-03-10T11:13:08.409-08:002016-03-10T11:13:08.409-08:00@Capra: "If you had a scenario where a new gr...@Capra: <i>"If you had a scenario where a new group .."</i><br />You mean, like Afanasevo, with their package of sheep, wheat and arsenic bronze, who were instrumental to the emergence of the North Chinese Longshan culture after the preceding Yangshao culture's demographic collapse? Yup, they clearly made Chinese speaking IE! Whether they were also behind the appearance of FrankNhttps://www.blogger.com/profile/01292462554916779884noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-9697147589620795662016-03-10T06:29:08.663-08:002016-03-10T06:29:08.663-08:00Actually, scratch that idea with the 10000 cycles;...Actually, scratch that idea with the 10000 cycles; it doesn't improve the runs.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-78999806124001376352016-03-10T06:19:30.036-08:002016-03-10T06:19:30.036-08:00Basically I'd like to get the output like this...Basically I'd like to get the output like this, or horizontally, but in the same way, if possible.<br /><br />Afanasievo<br />Anatolia_Neolithic 0.00 <br />Caucasus_HG 8.60<br />Dai 0.00 <br />Esan_Nigeria 0.05<br />Loschbour_WHG 0.00 <br />Masai_Kinyawa 0.00<br />Ulchi 2.95<br />Yamnaya_Samara 88.40Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-16869313254491343392016-03-10T06:07:20.380-08:002016-03-10T06:07:20.380-08:00@Davidski
You mean setting a field separator to &#...@Davidski<br />You mean setting a field separator to '\t'?<br />I will do it, but you know that reformatting an output is often more complicated than you expect.<br />As to the 10000 cycles, this indicates that the simulation has not sufficiently converged. So the runtime is not as ample as I thought. nMonte needs to burn a lot of computer cycles.huijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-84523680739246059442016-03-10T05:46:58.438-08:002016-03-10T05:46:58.438-08:00By the way, those of you running nMonte, try 10000...By the way, those of you running nMonte, try 10000 cycles. You can do this by opening the R file as a text file and changing the 1000 to 10000.<br /><br />It produces much cleaner results for me now, and it's still pretty fast.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-68522911247319434202016-03-10T01:50:45.383-08:002016-03-10T01:50:45.383-08:00@huijbregts
Is there a way to modify the nMonte s...@huijbregts<br /><br />Is there a way to modify the nMonte script so that the results are arranged so that they can be copy pasted quickly into a spreadsheet directly from the screen?<br />Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-51178240830939183472016-03-09T22:05:33.075-08:002016-03-09T22:05:33.075-08:00@Frank
If you had a scenario where a new group wi...@Frank<br /><br />If you had a scenario where a new group with a common origin and shared language and a compelling ritual/religious system settled over a wide area among Balkanized, quarreling previous groups*,even if a minority, it might be to the advantage of all concerned to assimilate to the newcomers rather than the other way around. Mere conjecture, I know little of the actual cultures capra internetensishttps://www.blogger.com/profile/15951755327460295070noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-45934406142671552662016-03-09T20:06:05.849-08:002016-03-09T20:06:05.849-08:00Frank
Nice summary (as always)
What about the su...Frank<br /><br />Nice summary (as always)<br /><br />What about the subsequent period - the BA proper. Unetice, the Carpathian metallurgical centres, etc. Ie the rise of true chiefdoms, inequality and power relations ? Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-74424527524644531652016-03-09T20:05:47.299-08:002016-03-09T20:05:47.299-08:00FrankN
"I had been thinking about a CWC->...FrankN<br /><br />"I had been thinking about a CWC->Hittite->Anatolian->Greek/Illyrian/Italic scenario"<br /><br />Unless it has changed since IIRC Davidski's stats linked Yamnaya with Afanevso (sp?) and Corded Ware with Sintashta which implied (to me anyway) there was an initial Yamnaya stage which was the catalyst for and eventually got over run on by the later Corded Greyhttps://www.blogger.com/profile/13398462488549380796noreply@blogger.com