tag:blogger.com,1999:blog-7785493.post420794022574868824..comments2024-01-04T04:11:55.717+02:00Comments on Dienekes’ Anthropology Blog: New papers on human Y-chromosome phylogeny (Poznik et al. and Francalacci et al.)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger44125tag:blogger.com,1999:blog-7785493.post-58460978624257555912013-08-21T07:41:43.567+03:002013-08-21T07:41:43.567+03:00Dienekes wrote:
"Another interesting finding...Dienekes wrote: <br />"Another interesting finding of Poznik et al. is the discover of deep substructure within Y-haplogroup A-L419 (bottom of the picture)."<br /><br />Actually it just shows what were once called A2 and A3, now A1b1a and A1b1b, which were just in the past year or so discovered by Thomas Krahn to be united by the L419 mutation. <br /><br />When you consider that these are the most recent major downstream clades of A, with A1a and especially A0 being much deeper, yet widespread in some parts of Africa, it give you a clue how much their choice to use only those two subclades limits their TMRCA to a more recent timeframe than would have been the case with a more complete set of A haplogroups represented.BEShttps://www.blogger.com/profile/06078272595547867802noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-38039751253691051502013-08-18T08:36:22.175+03:002013-08-18T08:36:22.175+03:00@Nenos Birko
I know they were deported from Euro...@Nenos Birko <br /><br />I know they were deported from Europe but than since R2a is almost extinct among Europe Sinti and Roma but common among Central Asians, I assume that they got it somewhere there or it was a founder effect. The only Europeans with significant frequency of R2a are the Jews.Kurtihttps://www.blogger.com/profile/00818803833239507313noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-40603746378657950782013-08-11T21:05:51.838+03:002013-08-11T21:05:51.838+03:00Just to answer a suggestion made by Nirjhar007:
G...Just to answer a suggestion made by Nirjhar007:<br /><br /><i>Giving a hint isn't the Gedrosian/baloch component present in Sardinians?</i><br /><br />The answer is no; although the Gedrosia component is present throughout western Europe, Sardinia is one of the places where this component reaches 0%. In my opinion European Gedrosia is associated with R1b, and apparently most R1b reached Sardinia late and didn't get as common as in western/central Europe.Simon_Whttps://www.blogger.com/profile/04454497745874406294noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-79986676164618059552013-08-10T23:29:57.570+03:002013-08-10T23:29:57.570+03:00"Thank you, and this Sinti from Spencer Wells..."Thank you, and this Sinti from Spencer Wells study were Sintis from Tajikistan, which itself has significant frequency of this Haplogroup. So I assume it was more a local thing. At least other studies on Roma show no presence of R2 but H and quite significant number of other local Haplogroups (depending on the country the tested individuals are from."<br /><br />While the Sinti sample was taken from Central Asia. They were originally deported from Europe by the Nazis during the second world war.NBhttps://www.blogger.com/profile/17676616345913295352noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-6365686142920995282013-08-09T06:04:45.766+03:002013-08-09T06:04:45.766+03:00@Nenos Birko
"Whether it's from a Roma b...@Nenos Birko<br /><br />"Whether it's from a Roma background or not I cannot say since we have yet to receive a Roma sample in the project. The only R2 among the Roma I'm aware of goes back to the Spencer Wells study where a small number of Sinti tested high for this haplogroup. But this is an old study so we're unsure if the lineage they carried was R2a1 or not."<br /><br />Thank you, and this Sinti from Spencer Wells study were Sintis from Tajikistan, which itself has significant frequency of this Haplogroup. So I assume it was more a local thing. At least other studies on Roma show no presence of R2 but H and quite significant number of other local Haplogroups (depending on the country the tested individuals are from.Kurtihttps://www.blogger.com/profile/15370578131814705759noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-11257147415471425032013-08-08T21:01:44.717+03:002013-08-08T21:01:44.717+03:00@Aaron
I got it. Thanks!
Seems to be a good matc...@Aaron<br /><br />I got it. Thanks!<br /><br />Seems to be a good match to Amerindian admixture in Europeans seen in the autosomes.<br /><br />http://anthropogenesis.kinshipstudies.org/2012/09/how-europeans-got-to-be-10-american-indians/<br /><br />I'll post something meaningful on my blog in the next day or so.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-77296299570843054802013-08-08T14:58:15.234+03:002013-08-08T14:58:15.234+03:00534 SNPs obtained for CT. Apparently he meant hapl...<i>534 SNPs obtained for CT. Apparently he meant haplogroup CT, as It is connected with the output from Africa.</i><br /><br />Vladimir,<br /><br />The paper cannot say much about CT, because it does not have any C nor D or T samples. The 535 SNPs is indeed for the FR / DE split, measured on the FR side. For comparison, E is a quite similar 542. Apparently, E split from DE right at ooA, while F (including all descendants - so better FR or FT, in general) is the only survivor of likely many groups on that side.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-32538853184656373352013-08-08T06:55:40.890+03:002013-08-08T06:55:40.890+03:00@German Dziebel
The chart in the Francalacci et a...@German Dziebel<br /><br />The chart in the Francalacci et al. paper is a little misaligned, and I can see why you thought the 13.8 is associated with the Q haplogroup, but if you look at the color coding, you can see that the 13.8 is the diversity in the R1a samples they had. The Q individual is a purple branch that is only 7 SNPs off from the Q-R split.Aaronhttps://www.blogger.com/profile/01270554253475715322noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-33050596620621881452013-08-08T06:21:17.442+03:002013-08-08T06:21:17.442+03:00"the diversity of Qs in America is much large..."the diversity of Qs in America is much larger than in South Siberia suggesting a back-migration". <br /><br />Not necessarily so at all. The diversity in Siberia may have been greatly reduced by the reduction in habitat available during periods of intense cold whereas diversity in America is a product of the haplogroup's huge expansion there. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-28812180691974116212013-08-08T06:04:57.497+03:002013-08-08T06:04:57.497+03:00@Aaron
"On the Phylogeny Tree in the Francal...@Aaron<br /><br />"On the Phylogeny Tree in the Francalacci et al. paper you can see that the Q lineage has a very short branch length. It only varies from the R-Q split by 7 SNPs. I still think this might be due to their filtering methods. The authors stated that they only considered SNPs valid if there were 2 instances of that SNP appearing. Since there was only 1 Q haplotype individual in their Sardinian sample, their filtering may have shortened the branch length."<br /><br />In Fig.1 of Francalacci, the average no. of SNPs in Q is given as 13.8. Where did you get 7? R2a1 is 8.5. There are fewer SNPs between Q and the QR node than between R1 and the QR node, but it seems that R2 has even fewer. The whole picture is unusual in the sense that Q looks sandwiched between two Rs - R1 and R2.<br /><br />I agree with you, though, that the diversity of Qs in America is much larger than in South Siberia suggesting a back-migration.German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-66443817526444646212013-08-08T03:12:00.069+03:002013-08-08T03:12:00.069+03:00To support Birko's comment, it is worth highli...To support Birko's comment, it is worth highlighting the insignificance of R2a-M124 in the Roma of Europe. Of several studies concerning their Y-DNA, I've only ever seen one confirmed sample (1/39 (2.6%), Tokaj Vlax Roma of Hungary).<br /><br />The Sinti Roma of Central Asia do have an excess of R2a. Given the higher frequency of R2a in Central Asia, it's more likely in my opinion that the high frequency is nothing more than genetic drift on account of either an aboriginal Central Asian line or one from the Indian Subcontinent.DMXXhttps://www.blogger.com/profile/16689998564656086919noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-64616335589484936162013-08-08T02:31:37.709+03:002013-08-08T02:31:37.709+03:00In the blog Dienekis is a typo. I quote: "The...In the blog Dienekis is a typo. I quote: "The main non-African super-haplogroup FR shows an average variation of 534.8 (± 28.7) SNPs, corresponding to a MRCA of ~ 110,000 years ago, in agreement with fossil remains of archaic Homo sapiens out of Africa". 534 SNPs obtained for CT. Apparently he meant haplogroup CT, as It is connected with the output from Africa.Anonymoushttps://www.blogger.com/profile/01875770439873638337noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-67379076328852915872013-08-07T17:21:14.543+03:002013-08-07T17:21:14.543+03:00@Aaron
WRT to Q diversity, you might be correct, ...@Aaron<br /><br />WRT to Q diversity, you might be correct, but even in the presence of significant extant diversity, the picture 15kya might have been quite different. <br /><br />But i think you have misread the relation of Q to R. They are collateral to each other, R is not derived from Q<br /><br /><br />Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-276730062925720992013-08-07T14:38:47.499+03:002013-08-07T14:38:47.499+03:00"FR 535 SNPs = 107,000 y
G/H/IJK split 389 SN...<i>"FR 535 SNPs = 107,000 y<br />G/H/IJK split 389 SNPs = 78,000"</i><br /><br />I should also note that these two dates roughly align with the two MIS 5c (100 kya) and MIS 5a (80 kya) wet phases. So, AMHs outside the D and C male lineages may indeed have been stuck in some still decently wet area of the NE subcontinent before being able to move on.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-32107886965603537022013-08-07T10:05:05.185+03:002013-08-07T10:05:05.185+03:00How can I get a pdf copy of this work? A silly que...How can I get a pdf copy of this work? A silly question but I have a PhD in Business Economics and I am old (54 less tax = 32)?<br /><br /><br /><br />Lord Ladehttps://www.blogger.com/profile/01672513896680945375noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-82755900397670967102013-08-07T08:27:47.219+03:002013-08-07T08:27:47.219+03:00Thanks for the info Nenos Good to Know.
I overl...Thanks for the info Nenos Good to Know. <br /><br />I overlooked the fact that r2 has significant presence in middle east central Asia. European details are new to me.Nathan Paulhttps://www.blogger.com/profile/18392998104066477963noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-27669029586973246822013-08-06T23:25:55.400+03:002013-08-06T23:25:55.400+03:00@Dr Rob
Check out Figure 5 from the Regueiro et a...@Dr Rob<br /><br />Check out Figure 5 from the Regueiro et al. paper in J. Am. Phys. Anthropology (2103)<br /><br />I agree with you that Y-STR diversity is not perfect, but the difference between Central Americans and Siberians is not slight, it is massive, the Asians are clearly branches off of the much larger diversity seen in the Americans.<br /><br />@German Dziebel<br /><br />On the Phylogeny Tree in the Francalacci et al. paper you can see that the Q lineage has a very short branch length. It only varies from the R-Q split by 7 SNPs. I still think this might be due to their filtering methods. The authors stated that they only considered SNPs valid if there were 2 instances of that SNP appearing. Since there was only 1 Q haplotype individual in their Sardinian sample, their filtering may have shortened the branch length.Aaronhttps://www.blogger.com/profile/01270554253475715322noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-73059501393295122622013-08-06T19:30:10.396+03:002013-08-06T19:30:10.396+03:00Just to be clear about the R2 found in Sardinia, i...Just to be clear about the R2 found in Sardinia, it's the form of R2a1 (L295+). This is the most common R2a subclade found in India today. In the R2-WTY project this specific clade is also found in Arabia and a very small number in Europe (Britian, Italy, and Iberia).<br /><br />Whether it's from a Roma background or not I cannot say since we have yet to receive a Roma sample in the project. The only R2 among the Roma I'm aware of goes back to the Spencer Wells study where a small number of Sinti tested high for this haplogroup. But this is an old study so we're unsure if the lineage they carried was R2a1 or not.<br /><br />Also another important note to mention about R2a in Europe is that it's mostly present among Ashkenazi Jews, but it has been established that the European Jewish R2a is L295-.NBhttps://www.blogger.com/profile/17676616345913295352noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-32701484787016853482013-08-06T17:13:26.985+03:002013-08-06T17:13:26.985+03:00@Aaron
"I find it interesting that the Q lin...@Aaron<br /><br />"I find it interesting that the Q lineage is basal to the R lineages. This may be due to how they filtered their SNPs rather than a true relation.<br /><br />What irritates me though is the assumption that Haplogroup Q came from Siberia. There is more Y-STR diversity in America than there is in Siberia indicating that the Q's in Siberia were actually a back migration from America, not the other way around."<br /><br />Absolutely agree with your critique of the assumption that Q is derived from Siberia. In fact it's a clear sign of a back migration. (Just like hg E is a clear sign of a back migration to Africa).<br /><br />But where do you see that Q is basal to R?German Dziebelhttps://www.blogger.com/profile/10703679732205862495noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-50330610226286010222013-08-06T15:35:23.911+03:002013-08-06T15:35:23.911+03:00Grognard:
"It might be bad dating (which app...Grognard:<br /><br /><i>"It might be bad dating (which applies to all dating) but there's now quite a few sites that put things back a lot further than this."</i><br /><br />"Clovis First" has joined the ranks of the undead and, like other zombie hypotheses, will likely be with us for at least another generation. Among the laity and in disciplines outside of North-American anthropology, it will persist even longer.Va_Highlanderhttps://www.blogger.com/profile/04671547664669092756noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-67723660684964915052013-08-06T11:12:12.762+03:002013-08-06T11:12:12.762+03:00"But even if it were not present there, given..."But even if it were not present there, given the harsh environment of Beringia, clearly it would be easy for a haplogroup to just vanish (compared to the expansion in the Americas). Theoretically, it could have been present 30,000 ya - doubling the time estimate the same way the true ooA date likely doubles that estimate". <br /><br />Quite. <br /><br />"I find it interesting that the Q lineage is basal to the R lineages". <br /><br />That's not really the case. Both R and Q derive independently from P. <br /><br />"What irritates me though is the assumption that Haplogroup Q came from Siberia. There is more Y-STR diversity in America than there is in Siberia indicating that the Q's in Siberia were actually a back migration from America, not the other way around". <br /><br />Q's phylogeny strongly suggests an origin west of the Altai/Hindu Kush mountain ranges. Same goes for R. Just the derived versions Q1a2-L56 (America and Ket/Selkup)and Q1a1a1-F1096 (northern China)are found further east, although Q1a-MEH2 is listed in Koryaks and Eskimos but downstream mutations may not have been checked. <br /><br />"I consider that Q and R are sister clades and emanated out from West Asia, R went to Europe and Q went to America". <br /><br />Basically correct. terrythttps://www.blogger.com/profile/17327062321100035888noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-41369956906943093072013-08-06T07:55:37.163+03:002013-08-06T07:55:37.163+03:00One thing that hasn't been discussed here is t...One thing that hasn't been discussed here is the dating of the R lineage in the Francalacci et al. paper. From Table 1 and Fig. 1, using their 200 years / SNP:<br /><br />FR 535 SNPs = 107,000 y<br />G/H/IJK split 389 SNPs = 78,000<br />P 359 SNPs = 72,000 y<br />R 241 SNPs = 48,000 y<br /><br />R1a / R1b split: 160 SNPs = 32,000 y<br /><br />Thus, the P/Q split could correspond to a post-Toba differentiation. Although a more conservative timing could point to the G/H/IJK split to represent a post-Toba expansion, I see no reason why the lines shouldn't have split soon after they first entered the Subcontinent, and I prefer to think that as pre-Toba. It is crazy enough that there were 30,000 years between that and ooA, as is (although this ignores the DE (D) and C lineages, which may have blocked F-spread until an opportune moment).<br /><br />Moving on, R started with the UP, and the R1a/ R1b split conforms with the beginning of the Gravettian. That could indicate the source of the (proto-) E Siberian admixture in Europeans, and would leave sufficient time to make these haplogroups pre-LGM in Europe. Also, compare to the first main I split (230 SNPs = 46,000 y), which conveniently coincides with the first populating of Europe.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-39907106062025812872013-08-06T05:51:02.662+03:002013-08-06T05:51:02.662+03:00Before I learned of the dates used for “calibratio...Before I learned of the dates used for “calibration” in this study (thank you once again Barthélémy ) I thought that there would be much to criticize about the date of entry into the Americas but now I find the 50kya date for OoA the much more dubious assumption. I am continually amazed at the malleability of this date amongst OoA supporters. I have heard everything from 250kya up to 50kya and everything in between. The date always varies and is usually “calibrated” so as to include whatever fossil that particular proponent thinks makes the best case for OoA. As for the date of entry into the Americas I am glad to see the researchers acknowledge the Monte Verde dates but question their use for calibration purposes. In my opinion it is unlikely that the humans responsible for Monte Verde traveled straight to that site from Beringia but since there is currently no evidence to indicate that they did not I cannot rule it out. I think the date of Monte Verde should be considered a bare minimum for entry into the Americas.CleverPrimatehttps://www.blogger.com/profile/07348182461045006012noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-23919330544036091582013-08-06T00:44:08.483+03:002013-08-06T00:44:08.483+03:00@ Aaron
"What irritates me though is the ass...@ Aaron <br />"What irritates me though is the assumption that Haplogroup Q came from Siberia. There is more Y-STR diversity in America than there is in Siberia indicating that the Q's in Siberia were actually a back migration from America, not the other way around."<br /><br />Well you clearly have missed the past 2 years of discussion as to how it is almost pointless to speculate where a haplogroup 'originates' from based on miniscule differences in STR variationRobhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-20852875408356016212013-08-05T23:50:11.574+03:002013-08-05T23:50:11.574+03:00I find it interesting that the Q lineage is basal ...I find it interesting that the Q lineage is basal to the R lineages. This may be due to how they filtered their SNPs rather than a true relation.<br /><br />What irritates me though is the assumption that Haplogroup Q came from Siberia. There is more Y-STR diversity in America than there is in Siberia indicating that the Q's in Siberia were actually a back migration from America, not the other way around.<br /><br />Perhaps we need to look for another source of Haplogroup Q to America. It would be interesting to see the Y-STR variability of Q in West Asia. I consider that Q and R are sister clades and emanated out from West Asia, R went to Europe and Q went to America.Aaronhttps://www.blogger.com/profile/01270554253475715322noreply@blogger.com