tag:blogger.com,1999:blog-3023805782808412230.post8666787334224423195..comments2024-03-09T15:46:44.638+01:00Comments on For what they were... we are: Caucasus and Swiss hunter-gatherer genomesMajuhttp://www.blogger.com/profile/12369840391933337204noreply@blogger.comBlogger43125tag:blogger.com,1999:blog-3023805782808412230.post-18028208173010337832018-12-07T18:34:07.018+01:002018-12-07T18:34:07.018+01:00Yes, that's it: ideally we'd have a comple...Yes, that's it: ideally we'd have a complete chronological and geographic genetic record, in reality we only have a limited number of samples, although growing...Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-54623196011928219122018-12-02T15:17:15.487+01:002018-12-02T15:17:15.487+01:00For the record, I did contact the author Eppie Jon...For the record, I did contact the author Eppie Jones regarding the CHG samples, (specifically relating for her study, The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers, published in Current Biology Volume 27, Issue 4, 20 February 2017, Pages 576-582) and she acknowledged by criticism: <br /><br /><br />Dr. Jones, <br /><br />I did notice however that the CHG groups sampled were considerably older, including a 13,300 year old and 9,700 year old male from western Georgia, in the Caucasus. This is compared to the sample of Iranian Neolithics/Chalolithics, which combined (as you have done in your study) are, at least, 4000 years later than those samples. Without similarly dated samples from Iran, how would can we be sure about the direction of genetic influence? I know the geographic distance between the two sites between the Zagros and the Caucaus Mountains is very small, so do you think it's even possible, to accurately determine this, or should these groups be considered the same, for practical purposes?<br /><br />Thank You!<br /><br /><br /><br /><br /><br />Dear Jeremy,<br /><br />We would need older samples from the Zagros to know for sure.<br />Hopefully more ancient DNA will come out of this region in the coming years.<br /><br />All the best,<br /><br />Eppie<br /><br />Tminushttps://www.blogger.com/profile/14670330637347557641noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-23187262147523926362018-11-19T09:11:45.102+01:002018-11-19T09:11:45.102+01:00Anyhow, is there any sample at all from Southern A...Anyhow, is there any sample at all from Southern Anatolia? In the past it used to be the only productive area in terms of prehistory, yet I see that the oldest sample (Pinarbasi) is from NW Turkey. Not too Western but definitely not Southern Anatolian. <br /><br />This adds to perplexity even more.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-12614787349594735152018-11-19T09:06:03.395+01:002018-11-19T09:06:03.395+01:00As a thought experiment you could get a modern Iri...As a thought experiment you could get a modern Irish and a modern Russian (or Hungarian or whatever within the big Northern European geneteic homogeneity blob) and find them genetically very close, but they are not the same culture and genetically they have remained pretty much isolate from each other since the late Chalcolithic for all we know. Just as word of caution, not saying it's the same thing but that I'm perplex that Anatolian Neolithic seems to have such a well defined personality since day one.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-40983931804557487902018-11-19T09:01:24.118+01:002018-11-19T09:01:24.118+01:00This comment has been removed by the author.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-29470877012706713262018-11-19T08:58:41.218+01:002018-11-19T08:58:41.218+01:00I meant that the South Anatolian Neolithic of Çata...I meant that the South Anatolian Neolithic of Çatalhöyuk and such is clearly not the same culture as the one we see in the Aegean, even if they may be related somehow. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-51651494975927995792018-11-19T08:53:01.435+01:002018-11-19T08:53:01.435+01:00Interesting what you say about WHG yellow. It'...Interesting what you say about WHG yellow. It's probably just some "noise" for all those populations having a common origin but then of course we can't disregard migrations and backmigrations that would be very hard to detect if not hegemonic. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-74178212522200790932018-11-17T22:22:28.043+01:002018-11-17T22:22:28.043+01:00Observe the limited point of sampling (extreme wes...Observe the limited point of sampling (extreme western fringe) for the "Anatolian" population. The same dubious type of conclusion came from an earlier study which I mentioned here on Maju's blog. However, a small sampling just a couple hundred miles East, and indeed, the Iranian Neolithic component shows. Of course, even further East in Anatolia, there will be more of any Iran_N component. Selective sampling is a convenient way of de-Easternizing the genetic influence from the East, but that's really just bad science. Tminushttps://www.blogger.com/profile/14670330637347557641noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-67520006398202830482018-11-17T16:34:07.510+01:002018-11-17T16:34:07.510+01:00Actually, I just noticed that WHG also carries tha...Actually, I just noticed that WHG also carries that 'yellow' in some small but conspicuous quantity. So it's probably more likely that whatever of that specific yellow that is shared between Mala and Iranians and WHG, should technically not be assigned to "Mala". The same phenomena is also evident in WHG with a tinge of the 'Anatolian_N Orange' (see extended analysis). That specific orange in WHG, can probably be better explained as vestigal genes that are remnant of a very deep common ancester between anatolians and WHG, as the earliest populations moved into Europe through the Mediterranean route. <br /><br /><br />Tminushttps://www.blogger.com/profile/14670330637347557641noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-2551767048011917482018-11-17T14:26:18.376+01:002018-11-17T14:26:18.376+01:00Excellent. Thank You so much for bringing that to...Excellent. Thank You so much for bringing that to my attention. Yes, interestingly, it appears that Iranians possess some component that is common to South Indians. I wonder if that would be, is it actual admixture from India, or does it represent some ancestral trace which was shared between Iranians and ancient Indians before they split in the paleolithic? <br /><br />Also, in K22, in the extended analysis, it does actually reveal Iranian_NeolithicSG as bearing the 'green/teal' component, followed by Iran_Ganj_Dareh_Neolithic Iran_HotuIIIb Iran_HotuIIIb and CHG about equal amounts. Tminushttps://www.blogger.com/profile/14670330637347557641noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-68725549837852766402018-11-17T14:24:17.140+01:002018-11-17T14:24:17.140+01:00"Is not "one" but at least two.&quo..."Is not "one" but at least two."<br /><br />Interesting,I have reviewed all Neolithic Anatolian data published so far.They were all exactly the same as the first Neolithic settlers in central Anatolia.<br /><br />If by "second community" you mean proto or early Neolithic societies like gobeklitepe in southeastern proviences of Turkey, they are already considered in PPNA/B culture,not Anatolian.<br /><br />Also Anatolian Neolithic was not more recent than Zagros or levant.PPNA and zagros began circa 9500BC Anatolian circa 8500 BC only 1000 years between than,not a long time for archeology and archeogenetic.<br />Memhttps://www.blogger.com/profile/18187296722668110917noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-64280579709910523532018-11-17T13:31:55.032+01:002018-11-17T13:31:55.032+01:00First quick read: it's suggestive of populatio...First quick read: it's suggestive of population continuity but I miss more clear data, like an Admixture analysis. Still interesting.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-24152467038703964882018-11-17T13:09:35.775+01:002018-11-17T13:09:35.775+01:00Will read it right away. However the Anatolian Neo...Will read it right away. However the Anatolian Neolithic:<br /><br />1. Is not "one" but at least two.<br /><br />2. Is more recent than the one from Levant (PPNA/B) and the NE Zagros (several groups). There is very limited pre-Neolithic inhabitation known in Asia Minor.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-36142865337883426662018-11-17T12:28:44.092+01:002018-11-17T12:28:44.092+01:00Kaixo Maju
"And even then it can be confusin...Kaixo Maju<br /><br />"And even then it can be confusing because the Proto-Vasconic or Anatolian Neolithic population was found in previous studies to be mostly a mix of Iran/Zagros Neolithic and Palestine/Levant Neolithic, with a very slight touch of Paleoeuropean. But here, for lack of Levant Neolithic, samples we see a different picture somehow."<br /><br />Nope.The most recent studies at Neolithic Anatolian samples show that they were largely descended from Paleolithic Anatolian.<br /><br />"Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000 year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity between the hunter-gatherer and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago that extends to central Europe during the post-last-glacial maximum period. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia."<br /><br />https://www.biorxiv.org/content/early/2018/09/20/422295Memhttps://www.blogger.com/profile/18187296722668110917noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-33608386909988853542018-11-17T04:34:59.186+01:002018-11-17T04:34:59.186+01:00Actually, see supp. fig. 1 (extended Admixture ana...Actually, see supp. fig. 1 (extended Admixture analysis): https://www.biorxiv.org/content/biorxiv/suppl/2018/05/16/322347.DC1/322347-3.pdf ... the yellow component is consistently dominant among the Mala, which is an Indian tribe, i.e. should be akin to ASI or pre-Neolithic Indian (Paleoindian but do not confuse with Paleoamerind).<br /><br />So I can see more favorably their stand in favor of using CHG as reference instead of Iran-Neolithic, now that I have looked at the extended Admixture analysis, because the yellow component might indicate Paleoindian admixture among Zagros Neolithic peoples, that is effectively absent in CHG and proto-Indoeuropeans. <br /><br />More research is needed and I would not heavily lean in favor of either population being the source of proto-IE "green" admixture, probably there were other unsampled related populations involved as direct source instead. <br /><br />BTW Iran-Neolithic is not from "the Iranian plateau" but from the Zagros mountains, what we usually call Kurdistan. We don't know anything about the ancient genetics of Iran proper, which AFAIk appears in the archaeological record only after the Neolithic (proto-Elamites and their Eastern cousins of Jiroft, both in the southern regions and surely somehow intermediate with Baloch-Indian Neolithic). <br /><br />I'm not sure why you get the idea of anybody suggesting "a complete replacement of the people of the Iranian plateau by CHG groups". All we can say is that CHG and Iran-Neolithic (Zagros Neolithic, East Kurdistan Neolithic) were close relatives, as they still are relative to modern Iranians, Kurds and even Turks, although there seems to have been an increase of the orange component since Late Neolithic or Chalcolithic. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-56533114231688719342018-11-17T02:55:39.851+01:002018-11-17T02:55:39.851+01:00Thanks Maju. As far as I can tell, the 'yello...Thanks Maju. As far as I can tell, the 'yellow' is also an Iranian N component. I don't believe it is Iran_N noise, as other groups share the same color. Similarly, you can also see a small unique component among AG3 (light green), which is sparsely distrbuted in across the Caucasus region. <br /><br />But what I was trying to suggest is that the small 'yellow' component, which is clearly centered around Iranians Neolithics, should actually be regrouped with the 'green' component as Iran_N. The CHG group and others carry minute amounts of it, but given it's sparcity among Iranian_N, that still makes it significant. Lazaridis 2016, rejected CHG as a founder population, but rather a later product of, predominately, Iranian Neolithics, but given the significantly higher Haplogroup diversities around Iran and Turkey (in particular J), I am more likely to uphold his view, and view CHG as a slightly later population which resulted from expansions from the Near East, sometime between the late LGM and the earliest phases of the Neolithic. Because nothing in genetics, archeology,or anthropology is otherwise suggesting there is a complete replacement of the people of the Iranian plateau by CHG groups. Tminushttps://www.blogger.com/profile/14670330637347557641noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-33691896156328636002018-11-16T16:51:06.835+01:002018-11-16T16:51:06.835+01:00Yes, the more I look at it that graph is probably ...Yes, the more I look at it that graph is probably best understood at K=3, with three components: Paleoeuropean dark blue, Proto-Vasconic or Neoeuropean orange, and Zagros-Caucasus Green. <br /><br />And even then it can be confusing because the Proto-Vasconic or Anatolian Neolithic population was found in previous studies to be mostly a mix of Iran/Zagros Neolithic and Palestine/Levant Neolithic, with a very slight touch of Paleoeuropean. But here, for lack of Levant Neolithic, samples we see a different picture somehow.<br /><br />It's not like you will get final answers with any single autosomal analysis, you have to look at the questions from various angles, considering different complementary analyses with different sampling strategies, etc. and then maybe, if you can, try to build a synthesis that makes sense.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-21751434404211864382018-11-16T16:43:41.099+01:002018-11-16T16:43:41.099+01:00Anyhow, in fig. 2, from which you take your detail...Anyhow, in fig. 2, from which you take your detail image, we see that neither the yellow, nor the purple nor the light blue components have any reference population. To my eyes they look just some sort of "noise". I would take a look to the supp. materials to see if there is a more extended Admixture analysis, because those three components seem suspect of being artifacts, minor deviations of each of the populations because of their own genetic isolation or something like that, not really significant probably.Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-72850917200907317352018-11-16T16:36:35.035+01:002018-11-16T16:36:35.035+01:00But the issue of having, apparently, more load of ...But the issue of having, apparently, more load of a ghost component that has been called "Basal Eurasian" (or I sometimes call quasi-African, because it's something betwen Yoruba and mainstream Eurasian but we don't really know for sure if it is African, Asian or both) makes it not "older" but DIFFERENT. And it seems for what I've seen here and there that the population that influenced genetically the early Indoeuropeans was not that much loaded with "Basal Eurasian". <br /><br />If I said "CHG is older" it'd be indeed as you say a tautology, but it's not just older it's different in that detail, which could be indicative of Iran-Neolithic and not Caucasus Hunter-Gatherers the partial source population at the Indoeuropean genesis (the other part is EHG, i.e. WHG+ANE, "Siberianized Paleoeuropeans" from the Eastern and Northern fringes of the continent). <br /><br />I fully agree with Y-DNA J being restricted to West Asia (and maybe Northeast Africa?) until at least the Neolithic. But we should consider the Caucasus region as part of West Asia, as it is today per its genetics, even the parts technically in Europe.<br /><br />As for the yellow element in ancient Iranian samples, it's clear that it indicates some admixture not present in the Eurasian steppe but that can just suggest a third unstudied population that had not that admixture but was otherwise closer to Iran-Neolithic than to CHG in that lower load of "Basal Eurasian". We can't expect to be lucky enough to have sampled all the key populations, there's always blanks and lacunes in our knowledge. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-19102073283371563502018-11-16T14:55:03.519+01:002018-11-16T14:55:03.519+01:00It seems as with a few of these recent studies, CH...It seems as with a few of these recent studies, CHG being 'older' than Iranian Neolithic is merely a tautological point; Simply taking an 11Kbp Caucaus sample and calling it 'CHG', and taking a 9kbp Iranian sample and calling 'Iranian Neolithic'. But the fact that the two groups share a significant amount of genetic data, does not prove your older sample contributed to the genome of your later sample. Unless you have Iranian samples from the same period time period, it doesn't make sense to draw any such conclusion about the direction of genetic influence. And it would certainly be nice to have more than 2 samples for CHG. <br /><br />That being said, we can take a clue from the prescence of Haplogroups in the two 'CHG' samples, both which were J bearers. It has regularly been considered, for some time now, that Haplogroup JM410 is a near eastern haplogroup. This is in line with the fact that IJ Linker has been found around Iranians - not any CHG group of any time period. And J* only to the South of the Caucaus. J2-m172 is frequent in Iran, and the oldest J2a-410, to date has been assigned to an individual who live in Hotu Cave in northern Iran, dating from 9100-8600 BCE (Lazaridis et al. 2016). This is compared to the earliest J2a assigned to the Caucaus sample; Kotias Klde in Georgia, dating from 7940-7600 BCE (Jones et al. (2015)). J2 diversity, in general, is certainly greater in Iran over the Caucaus. <br /><br /><br />Perhaps, a more interesting observation comes from a new study with Caucaus samples. Wang et al 2018 https://www.biorxiv.org/content/biorxiv/early/2018/05/16/322347.full.pdf <br />If one observes the admixture proportions https://ibb.co/b7Z29f, it can be seen the Iranians have a small, but significant, secondary 'yellow' component, 'purple' and a 'maroon' component, which apparently the CHG samples are both bearing, in some proportion, as well. (And although the amount is minute, it is highly significant, considering the low amount which is, otherwise, exclusive to Iranians). This very well may be taken as evidence of the hypothesis that CHG was a product of Iranians sometime in the upper paleolithic to early neolithic period. <br /><br /><br />The Iranian archaeological record is impeccable. There has been a gradual transition in the agricultural phase from the upper paleolithic to the neolithic agriculturist. To say obscure hunter gatherer settled and replaced the genotype of an already highly populated Iranian plateau, is more specious than viable. Tminushttps://www.blogger.com/profile/14670330637347557641noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-69156869733224662562018-11-16T14:54:29.762+01:002018-11-16T14:54:29.762+01:00This comment has been removed by the author.Tminushttps://www.blogger.com/profile/14670330637347557641noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-64322359058723469322018-11-15T03:21:54.929+01:002018-11-15T03:21:54.929+01:00This comment has been removed by the author.Unknownhttps://www.blogger.com/profile/11566494589399073241noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-84994389862991707562018-11-14T06:37:45.298+01:002018-11-14T06:37:45.298+01:00Wasn't there an issue with the CHG sample bein...Wasn't there an issue with the CHG sample being extreme in its "Basal Eurasianness" tendency? I think that's why it's treated separately and Iran-Neolithic preferred as likely source instead. But the same overall idea anyhow: it's the "Caucasus" component that has come once and again since Admixture-like analysis became a thing and that is closely related to the "Baloch" (sometimes "Gedrosia", "ANI") component further East, representing the "Eastern branch" of West Asian Neolithic quite clearly. Majuhttps://www.blogger.com/profile/12369840391933337204noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-78864817224529620542018-11-14T05:03:44.372+01:002018-11-14T05:03:44.372+01:00Its backwards. People are plainly suggesting that...Its backwards. People are plainly suggesting that chg was<br />a distinct group? That is bad even for 2016 standards. It's obvious that iranians are ancestral to the vast majority of chg samples represented in ancient DNA studies. They are nearly autosomal equivalent, with chg with a slightly higher ehg influence....even there haplogrouos come from iranian plateau. blogmasterhttps://www.blogger.com/profile/11834163614642737338noreply@blogger.comtag:blogger.com,1999:blog-3023805782808412230.post-14246760290773778102018-11-13T23:46:13.211+01:002018-11-13T23:46:13.211+01:00Today we know CHG is essentially Iranian Neolithic...Today we know CHG is essentially Iranian Neolithic with a smaller amount of EHG. Yet, many authors still treat CHG as it is genetically unique. Unknownhttps://www.blogger.com/profile/11566494589399073241noreply@blogger.com