tag:blogger.com,1999:blog-4123559132014627431.post7067139600149696834..comments2024-03-28T17:16:03.042-07:00Comments on Eurogenes Blog: The IberomaurusiansDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger177125tag:blogger.com,1999:blog-4123559132014627431.post-5420599377268314272019-08-09T05:55:29.841-07:002019-08-09T05:55:29.841-07:00
From Western Andalusia in South of Spain. Ne...<br /><br /><br /><br /><br /><br />From Western Andalusia in South of Spain. Next is my G25. <br /><br />Anatolia_Epipaleolithic,54.6<br />Caspian_steppe_Eneolithic,28.4<br />Western_Hunter-Gatherer,8.2<br />Levant_Natufian,7.6<br />MAR_Iberomaurusian,0.6<br />Yoruba,0.6Juan R.https://www.blogger.com/profile/17393850956169393757noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-27067963765730151582018-03-28T09:59:41.737-07:002018-03-28T09:59:41.737-07:00>"But I can tell you that on such global p...<br />>"But I can tell you that on such global plots Denisovans and Neanderthals cluster with Sub-Saharan Africans in dimensions 1 & 2."<br /><br /><br />It's possible to make Neanderthals and Denisovans plot pretty far from Africans.<br /><br /><br />https://imgur.com/a/DJthK<br /><br />Unknownhttps://www.blogger.com/profile/10595025984675876037noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-46020206925168178812018-03-25T12:49:39.082-07:002018-03-25T12:49:39.082-07:00@Arza
Your issues are all about the question wheth...@Arza<br />Your issues are all about the question whether the samples are penalized in the correct way.<br />I wonder whether you understand the idea behind the nMonte algorithm.<br />There are no bad samples that should be penalized. It is the mixture that can have bad frequencies. And it is the mixture that should be optimized and penalized. That is quite different from 'sample in the mix huijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-49173195431689236722018-03-25T12:06:00.665-07:002018-03-25T12:06:00.665-07:00Little correction: EEF had ~10% BE, not earlier An...Little correction: EEF had ~10% BE, not earlier Anatolians.Unknownhttps://www.blogger.com/profile/10595025984675876037noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-33770785257440941802018-03-25T11:53:18.171-07:002018-03-25T11:53:18.171-07:00New study came out that says Basal Eurasians diver...New study came out that says Basal Eurasians diverged 80,000 years ago and Neolithic Anatolians only had 10% BE. They also released a new tool that is supposed to be more accurate than simple tree-like models such as D and F stats.<br /><br />https://www.biorxiv.org/content/early/2018/03/23/287268<br /><br />https://github.com/popgenmethods/momi2Unknownhttps://www.blogger.com/profile/10595025984675876037noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-12812762622436746182018-03-25T10:57:10.009-07:002018-03-25T10:57:10.009-07:00@Arza
I will study #2 and #3.
#1 is not true. The ...@Arza<br />I will study #2 and #3.<br />#1 is not true. The order of sampling is completely random. The penalty changes over time as the temporary estimation converges to the final estimation. This is how it should be. huijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-82939283975397432462018-03-25T03:25:50.125-07:002018-03-25T03:25:50.125-07:00@Ryukendo, can you expand on that a little? (What ...@Ryukendo, can you expand on that a little? (What is "like fst"?)Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-77426596799818854332018-03-25T01:31:09.646-07:002018-03-25T01:31:09.646-07:00@Josep
Ah, I see. Yeah, I recall reading somethin...@Josep<br /><br />Ah, I see. Yeah, I recall reading something about extensive re-population of Valencia region once. Nice to see your expertise in the matter corroborate it. <br />How about settlers from further north(Languedoc, etc.)? Not as significant? I recall looking at a surname map of Spain once and some rather Occitan-specific surnames popped up in Valencia. I'll try to remember and/Anthro Surveyhttps://www.blogger.com/profile/07686104871694563174noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-77868014787634715812018-03-24T15:07:56.119-07:002018-03-24T15:07:56.119-07:00@ Matt
Don't you think this is because its PC...@ Matt<br /><br />Don't you think this is because its PCA, so you may get fst-like effects, i.e. drift is represented in a nonlinear way and cannot be summed?Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-3606585468519694842018-03-24T12:11:13.682-07:002018-03-24T12:11:13.682-07:00
Natufian
Yemenite_Mahra 74.00
Iberomaurusian 17....<br />Natufian<br /><br />Yemenite_Mahra 74.00<br />Iberomaurusian 17.75<br />Iberia_EN 8.25<br /><br />Based on this it looks like Soqotris and Mehris are mostly Natufian and most basal modern populations?<br /><br />Could you test if Mahra takes any South Asian or prehistoric and modern East African?Unknownhttps://www.blogger.com/profile/10595025984675876037noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-21144284711772708842018-03-24T12:01:21.080-07:002018-03-24T12:01:21.080-07:00>Did you include "KHOISAN" as a possi...<br />>Did you include "KHOISAN" as a possible source population for North Africans? Please try that if you haven't... I bet the fits improve<br /><br />BBayA sample should be used for that, instead of modern Khoisan with Eurasian and Bantu admixtures.Unknownhttps://www.blogger.com/profile/10595025984675876037noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-26515276732526516172018-03-24T08:08:15.737-07:002018-03-24T08:08:15.737-07:00@Anthro Survey
For Balears almost all the settler...@Anthro Survey <br />For Balears almost all the settlers came from Catalonia and in València there were catalans, aragonese and castilians, in this order from the most numerous to the least. Foreigners were present but very minor everywhere.<br /><br />Repopulations after the reconquista is another matter worth discussing about because according to the last paper the genetics going north to southJosep Coderchhttps://www.blogger.com/profile/11818389718589201753noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-36742004996656681302018-03-24T08:02:10.724-07:002018-03-24T08:02:10.724-07:00Test case as in the comments above:
[1] "pena...Test case as in the comments above:<br />[1] "penalty= 0.001"<br />[1] "Ncycles= 1000"<br />[1] "distance%=0"<br />A<br />B,50<br />C,25<br />D,25<br /><br />Capra's model:<br /><br />Ethiopia_4500BP _____Dinka _Iberomaurusian __Levant_N <br />_______23.81712 __29.86112 _______30.65544 __41.96868 <br /><br />[1] "penalty= 0.001"<br />[1] "Ncycles= Arzahttps://www.blogger.com/profile/10459843383682766479noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-60537682300589186052018-03-24T08:01:35.616-07:002018-03-24T08:01:35.616-07:00Had a chance to pick up Global25 data, focusing on...Had a chance to pick up Global25 data, focusing on visualization and distances rather than fits.<br /><br />A few plots of raw distance from the Natufian average vs the Iberomaurasian average: https://imgur.com/a/lYAm0<br /><br />African populations are deciedly closer to Iberomaurasian and West Eurasians to Natufians. But I was surprised to see that in the dimensions defined by G25 (scaled), Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-42792923263880802962018-03-24T07:52:55.644-07:002018-03-24T07:52:55.644-07:00bugfix pull request
# iniatialize objective funct...bugfix pull request<br /><br /># iniatialize objective function<br />colM1 <- colMeans(matAdmix)<br />sumcolM1 <- sum(colM1^2)<br />#eval1 <- (1+pen) * sum(colM1^2) <br /># Ncycles iterations<br />for (c in 1:Ncycles) {<br />__# fill batch data<br />__dumPop <- sample(1:Ndata, Nbatch, replace=T)<br />__dumAdmix <- dif2targ[dumPop,]<br />__# loop thru batch<br />__# penalty is Arzahttps://www.blogger.com/profile/10459843383682766479noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-78862463157593161672018-03-24T07:51:48.437-07:002018-03-24T07:51:48.437-07:00@ huijbregts
You made 3 errors.
1. You're app...@ huijbregts<br />You made 3 errors.<br /><br />1. You're applying penalty in unfair conditions that depend on the order of sampling (ratio of penalty/distance changes over time).<br /><br />2. You're not applying penalty belonging to the sample that is already in the mix when you compare the old one with the new one. Applying it would create equal conditions for both samples and it wouldArzahttps://www.blogger.com/profile/10459843383682766479noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-18501903751597650122018-03-24T02:11:27.944-07:002018-03-24T02:11:27.944-07:00@Josep
Oh, for Catalonia proper, yeah, but does t...@Josep<br /><br />Oh, for Catalonia proper, yeah, but does this hold for the southern Catalo-sphere, though?---Valencia and Baleares.<br /><br />@Alogo<br /><br />Good stuff. Your models confirm what I've been getting. England_Roman:Iberia_BA ratios are clearly highest in former Celtic zones(Galicia, Portugal, Castilla and Extremadura) and lowest in Basques, suggesting a higher degree of 'Anthro Surveyhttps://www.blogger.com/profile/07686104871694563174noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-87971879886446731312018-03-24T00:53:06.402-07:002018-03-24T00:53:06.402-07:00@Arza
nMonte performs a successive approximation. ...@Arza<br />nMonte performs a successive approximation. <br />After the first few cycles both the temporary result and the penalty are way off, but after a few hundred cycles both should be good approximations.<br />It is important that there are no systematic differences in the random samples during the random walk. this is guaranteed by sampling with replacement.huijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-64241008564266157942018-03-23T21:02:31.259-07:002018-03-23T21:02:31.259-07:00@Arza,
Thanks, nice find.
From a quick look, ther...@Arza,<br />Thanks, nice find.<br /><br />From a quick look, there they appear as a mix of IAM, Anatolian Neolithic and a little something steppe-related (later "European" ancestry, something Beaker-related to go along with the non V88 R1b the Guanche Y-DNA study found?). From what I recall from the recent Guanche study, they seem to have had slightly less "SSA proper" Alogohttps://www.blogger.com/profile/12311735856824330486noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-34386733159919275712018-03-23T14:27:15.531-07:002018-03-23T14:27:15.531-07:00Repopulation in Catalonia was not very strong beca...Repopulation in Catalonia was not very strong because the muslim/converts population was little so few were expelled. What did happen was that during the muslim invasion people fled to the Pyrenees to take refuge in the mountains and after christians reconquered they returned to the south, so basically the lands were resettled with the same people who inhabited the lands before the muslim Josep Coderchhttps://www.blogger.com/profile/11818389718589201753noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-32190074526998068132018-03-23T13:16:03.442-07:002018-03-23T13:16:03.442-07:00Wasn't the Catalonian portion of the Reconquis...Wasn't the Catalonian portion of the Reconquista rather aggressive and entailed far greater degree of resettlement of people from north Catalonia and even Languedoc in many cases?Anthro Surveyhttps://www.blogger.com/profile/07686104871694563174noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-19845703555078133322018-03-23T12:57:42.423-07:002018-03-23T12:57:42.423-07:00@Josep
"What reduced the indo-european ances...@Josep<br /><br />"What reduced the indo-european ancestry in the former is a greater admixture with west asian and north african peoples that came later....<br /><br />Precisely what I'm thinking right now.<br /><br />"...dominated by males and over a longer period of time, thus having a strong impact in the Y-DNA of the population but without changing their language."<br /><Anthro Surveyhttps://www.blogger.com/profile/07686104871694563174noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-17836441062671813332018-03-23T12:18:42.623-07:002018-03-23T12:18:42.623-07:00@Anthro Survey
Yes, in these times (https://upload...@Anthro Survey<br />Yes, in these times (https://upload.wikimedia.org/wikipedia/commons/thumb/3/3a/Iberia_300BC-fr.svg/1242px-Iberia_300BC-fr.svg.png) indo-european ancestry was higher where indo-european tribes lived, and lower where iberian tribes were present. What reduced the indo-european ancestry in the former is a greater admixture with west asian and north african peoples that came later.Josep Coderchhttps://www.blogger.com/profile/11818389718589201753noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-59303111041685969232018-03-23T12:06:11.879-07:002018-03-23T12:06:11.879-07:00@André de Vasconcelos
What I meant about the Pyren...@André de Vasconcelos<br />What I meant about the Pyrenees is that since mountainous regions are harder to conquer the later invading waves such as indo-europeans and middle eastern-like peoples left there a lesser genetic impact. The same is true for the french side, regions closer to the french Pyrenees being known for higher neolithic ancestry and also higher Y-DNA R1b.<br /><br />@Cossue<br /Josep Coderchhttps://www.blogger.com/profile/11818389718589201753noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-20913215932657726552018-03-23T11:38:08.027-07:002018-03-23T11:38:08.027-07:00@Andre
The qp run is legit, but:
Let me emphasize...@Andre<br /><br />The qp run is legit, but:<br />Let me emphasize again that I don't mean overall steppe vs overall EEF signal in Galicia. In this regard, it doesn't differ much from the rest. <br /><br />I'm talking specifically about ratio of Europe_MLBA(Bronze and Iron age extra-Iberian migrants) vs native EEF. So, places like Portugal and Galicia were potentially more French-like Anthro Surveyhttps://www.blogger.com/profile/07686104871694563174noreply@blogger.com