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Thread: GoyetQ 2 - a new component in European ancestry composition

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    Quote Originally Posted by Aspar View Post
    But the problem is we do have one Paleolithic sample from the Balkans, more specifically Romania(Oase1 dated to 40000-35000 BC) belonging to y-dna F and mt-dna N which again doesn't resemble the profile of the WHG.

    From the study:

    Plus:


    So in short, Oase1 belonged to a cluster of samples such as Ust'-Ishim man dated to 43000 BC. This cluster had different profile from the WHG and as quoted above this profile was somehow ancestral for both Europeans and East Asians as Oase1 shared equal alleles with Mesolithic Europeans and East Eurasians suggesting non pre LGM-European admixture in modern Europeans.

    As I want things visualized I've made a West Euroasian PCA based off G25 and including some Paleolithic and Mesolithic European and Asian samples:



    Group_1 is the cluster Oase1 belonged and samples with such a profile a found across Euroasia up to 28700-27300 BC as per the youngest of the samples of this cluster Vestonice16.

    We find somehow transitional samples between the cluster Group_1 to the cluster of WHG in El Miron dated to 16800-16600 BC, Iberian_Southeast_Meso_I10899 and BAL051 dated to the end of Paleolithic, all samples from Iberia.
    G25 model for El Miron:

    Target: Iberia_ElMiron:ElMiron
    Distance: 4.5470% / 0.04546959
    58.8 WHG_Rochedane
    41.2 RUS_Kostenki14

    We can see that the model fits very well with the PCA and it shows exactly that El Miron is a transitional sample from Group_1 to WHG, but the issue is that the model is anachronistic because Rochedane is a younger sample than El Miron. In other words we are missing a crucial component which shifted El Miron in the direction of the WHG and which ultimately gave rise to the WHG.

    Interestingly, it is believed by some finds that the Neanderthals survived the longest in Iberia. Older carbon dating indicated that Neanderthals may have lived as recently as 24,000 years ago while new ones suggest that Neanderthals disappeared around 40,000 years ago including in refugia on the south coast of the Iberian peninsula such as Gorham's Cave.

    The oldest samples of a WHG profile appear in the face of Villabruna and Rochedane at the end of the Paleolithic which are younger than El Miron and probably what this means is that this profile steams from a small surviving population somewhere in Western Europe that ultimately spread eastward and mixed with EHG incoming from the east as shown per cline 3 in the PCA. By that time the profile of Group_1 disappeared completely and the Mesolithic samples in Europe are fitting entirely in the WHG + EHG cline.

    However, even if the extreme profile of the WHG was ultimately produced by mixing with the Neanderthals, that doesn't mean that the modern humans up to that point didn't have any Neanderthal dna in them. In Oase1 from Romania dated to 40000-35000 BC about 6-9% of the genome is Neanderthal in origin. This is the highest percentage of archaic introgression found in an anatomically modern human and together with the linkage disequilibrium patterns indicates that Oase 1 had a relatively-recent Neanderthal ancestor – about four to six generations earlier. That said, most probably the Neanderthals indeed survived up to 24000 years ago in Iberia as per the old radio carbon analysis if during the time of Oase1 there were Neanderthals in Romania. That being said, as the modern humans pushed deeper in Europe, they probably had more contacts and even mixed with Neanderthals. Ultimately all what I have shown here somehow suggests me that profile of the WHG emerged and started spreading from Western Europe instead of the Balkans.
    It´s correct what you stated about Oase1 per se. But Oase1 has not made any notably contribution to today Europeans, see https://www.nature.com/articles/nature17993

    Rather likely it was wiped out (or heavily reduced and then totally outnumbered) together with most Neanderthals by the Campanian Ignimbrit (the eruption of the Phlegraian fields) at at 39,280±110 years BP, see for the eruption https://en.wikipedia.org/wiki/Campan...brite_eruption

    There is no detectable genetic contribution by any Europeans before that Ignimbrit. But there is a clear contribution from Kostenki14 from short after. Likely Europe was repopulated at that time by humans with an average Neanderthal DNA proportion that did not anymore meet any notable numbers Neanderthals in Europe. This would also explain the otherwise strange thing, that Europeans, that are in the home land of Neanderthals, do not have any elevated Neanderthal DNA proportion compared to other extra-African populations.
    The answer is the first Europeans (like Oase1) actually had this to be expected elevation. But they were terminated by the Ignimbrit.

    These late Gibraltar Neanderthal datings are completely unreliebale und likey not applicable.
    Last edited by rothaer; 07-31-2020 at 04:50 PM.

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    Quote Originally Posted by Milkyway View Post
    That is interesting, however I think that the WHG-Neanderthal connection is a bit unlikely (mainly because WHG specimens do not show higher Neanderthal levels than other Upper Paleolithic remains). I think that some of the youngest sites occupied by Neanderthals in Iberia were recently redated and are actually older than 40,000 years. In Fu et al., they found that Villabruna and most of the <14 kya samples from Europe already showed some affinity for populations from the Near East (older Paleolithic samples remained relatively isolated from other populations). Maybe that's why WHG looks relatively diverged from all other Paleolithic components?
    Fully agreed to the first part.

    But as for that Middle Eastern affinity, that might have come by a WHG-like expansion to the Middle East from Europe. Here

    https://www.nature.com/articles/s41467-019-09209-7

    they do calculate somewhat on that topic and do conclude an immigration from the Middle East as the *only* explanation for this affinity can be discarded.
    Last edited by rothaer; 07-31-2020 at 04:57 PM.

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    Quote Originally Posted by rothaer View Post
    It´s correct what you stated about Oase1 per se. But Oase1 has not made any notably contribution to today Europeans, see https://www.nature.com/articles/nature17993

    Rather likely it was wiped out (or heavily reduced and then totally outnumbered) together with most Neanderthals by the Campanian Ignimbrit (the eruption of the Phlegraian fields) at at 39,280±110 years BP, see for the eruption https://en.wikipedia.org/wiki/Campan...brite_eruption

    There is no detectable genetic contribution by any Europeans before that Ignimbrit. But there is a clear contribution from Kostenki14 from short after. Likely Europe was repopulated at that time by humans with an average Neanderthal DNA proportion that did not anymore meet any notable numbers Neanderthals in Europe. This would also explain the otherwise strange thing, that Europeans, that are in the home land of Neanderthals, do not have any elevated Neanderthal DNA proportion compared to other extra-African populations.
    The answer is the first Europeans (like Oase1) actually had this to be expected elevation. But they were terminated by the Ignimbrit.

    These late Gibraltar Neanderthal datings are completely unreliebale und likey not applicable.
    It seems that the Campanian Ignimbrite eruption alone is unlikely to have wiped out Neanderthals (see here). Besides, these were also found in the Middle East and Central Asia. Oase 1 had a recent Neanderthal ancestor and it's just one individual, so I think that he might not be representative of the human population(s) that lived >40 kya in the Balkans.

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    Quote Originally Posted by etrusco View Post
    Interesting stuff thank you.
    There is quite of a debate around Upper paleolithic genetic clusters. For example
    Which west eurasian cluster is the western side of the Yana sample (Kostenki ,Sungir or Goyet or maybe a yet not sampled population ?) as Yana can be modeled as 75% West Eurasian and 25% East Eurasian.
    What is the exact relation between Yana and Ancient North Eurasian ( Malta- Afontonova Gora) are they different or Yana is ancestral to ANE?
    I am not going to pretend that I know a lot about this stuff, I am someone who uses the available online amateurish tools and logic and has passion to learn about this stuff. To me it looks like that none of the Kostenki, Sunghir or Goyet samples are related to Yana. On the other hand both AfontovaGora3,(15000-14500 BC) and MA-1, Mal'ta-Buret' culture,(22000 BC) are in great part related to Yana but as is the case with the WHG who are in great part related to Kostenki14, we are missing a crucial component other than Yana to model them effectively. So I would say that it looks like Yana is definitely ancestral to ANE!

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    Quote Originally Posted by Milkyway View Post
    That is interesting, however I think that the WHG-Neanderthal connection is a bit unlikely (mainly because WHG specimens do not show higher Neanderthal levels than other Upper Paleolithic remains). I think that some of the youngest sites occupied by Neanderthals in Iberia were recently redated and are actually older than 40,000 years. In Fu et al., they found that Villabruna and most of the <14 kya samples from Europe already showed some affinity for populations from the Near East (older Paleolithic samples remained relatively isolated from other populations). Maybe that's why WHG looks relatively diverged from all other Paleolithic components?
    You are probably right about the Neanderthals however these divergence of the WHG is difficult to explain with affinity from the Near East. Especially because we do have some Epipaleolithic samples from North Africa(Taforalt) and Levant(Natufians) and they are diametrically different than the WHG. In other words, you can't model the WHG between Kostenki14 and Near Eastern elements. There is something we are missing that ultimately is included in the ancestral makeup of the WHG. Plus uniparentals wise the WHG show continuity in Europe since 30000 BC having most often than not y-dna haplogroups such as I2 and I1 which are descendants of IJK found in Vestonice16 and having most often than not the same mt-dna as Vestonice16, U5. So most probably what we are missing is quite old. Villabruna looks like it has contribution from EHG which is also visible in his y-dna R1b1 which probably means there was some EHG introgression deeper in Europe:

    Target: ITA_Villabruna
    Distance: 3.2114% / 0.03211378
    99.2 WHG_Rochedane
    0.8 RUS_AfontovaGora3

    POPs in use:
    Code:
    RUS_Kostenki14,0.035285,0.015233,-0.010182,0.063954,0.017849,-0.00251,-0.004465,-0.007846,0.032519,0.007654,0.006658,-0.005545,0.004014,-0.016239,0.013436,0.024794,0.01004,-0.003421,-0.00729,0.015132,0.020713,0.000371,-0.005916,-0.051212,-0.004071
    RUS_Ust_Ishim,-0.050082,-0.11577,-0.090886,0.073644,0.027082,-0.018128,-0.00376,-0.004384,0.0452,0.010387,0.006008,-0.001798,0.000149,-0.003991,0.004614,-0.001724,-0.004955,0.004687,-0.005154,0.015382,0.006613,0.008532,-0.007641,-0.014942,0.007784
    RUS_Sunghir,0.0401228,0.01244,0.0022628,0.0713022,0.030467,-0.0033465,0.0028788,-0.0045,0.0404445,0.0083828,0.011895,-0.0098913,0.0084365,-0.0130397,0.0114685,0.016607,0.0167218,0.0019637,-0.005782,0.029639,0.0263908,0.0058428,-0.0130335,-0.0473262,0.004281
    RUS_Yana_UP,0.0278865,-0.0705795,-0.0173475,0.092378,0.0110785,-0.0001395,-0.013396,-0.0119995,0.0341555,-0.000547,0.012829,-0.0025475,0.0051285,-0.015345,0.0118075,0.00305,0.0008475,0.002217,-0.00264,0.0168205,0.0082355,0.008903,-0.0120165,-0.024702,-0.0020955
    CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
    RUS_MA1,0.078538,-0.025388,0.039598,0.186049,-0.068936,0.04518,-0.048412,-0.056998,-0.019839,-0.069432,0.029879,-0.009591,0.015312,-0.045553,0.014251,0.021082,-0.007693,0,-0.003645,0.000625,-0.027327,0.002844,0.011339,-0.008314,-0.001437
    RUS_AfontovaGora3,0.093335,-0.01828,0.083344,0.231592,-0.091402,0.042949,-0.063688,-0.078228,-0.035383,-0.096221,0.047417,-0.010491,0.023637,-0.074454,0.020358,0.02254,-0.012908,0.003801,-0.003394,0.000625,-0.03706,0.015209,0.013927,0.009278,-0.005149
    KEN_Early_Pastoral_N,-0.234476,0.102061,-0.036015,-0.081073,0.0018465,-0.0430885,-0.004465,-0.0116535,0.121078,-0.0727125,0,-0.0143875,0.008176,0.001376,0.0259225,-0.016839,0.0203395,0.004941,-0.001697,0.001063,-0.000998,0.004575,0.0042525,-0.0001205,0.005269
    BEL_GoyetQ116-1,0.043253,-0.005078,0.003017,0.093993,0.045547,0.001952,-0.00517,-0.000692,0.065857,0.024055,0.00341,0.000899,0.009366,-0.022983,0.019137,0.017634,0.011865,0.004561,-0.006034,0.034767,0.026079,0.002473,-0.023664,-0.061695,0.003712
    CZE_Vestonice16,0.045529,0.024373,0.032809,0.084303,0.0397,-0.001116,-0.004465,0.001154,0.056653,0.023144,0.007795,-0.01169,0.006392,-0.008533,0.008686,0.012066,-0.005737,0.008488,-0.010684,0.022886,0.036436,0.009027,-0.015159,-0.065672,0.000479
    Iberia_ElMiron,0.0774,0.044683,0.105217,0.129201,0.11079,0.031236,0.00188,0.006231,0.088559,0.02442,-0.005359,-0.002847,0.008622,-0.013487,0.037459,0.041633,0.002217,0.006968,-0.015209,0.045772,0.063638,0.007914,-0.036481,-0.129054,0.013053
    MAR_Taforalt,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
    Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
    WHG_Rochedane,0.118376,0.111708,0.178001,0.184111,0.150182,0.044623,0.010575,0.034383,0.090809,0.028064,-0.014615,-0.016186,0.013974,-0.002752,0.058767,0.069344,0.002738,0.014189,-0.015335,0.054151,0.101446,0.013231,-0.050778,-0.178579,0.019519
    Without Rochedane which is a younger sample we get:

    Target: ITA_Villabruna
    Distance: 15.7356% / 0.15735621
    100.0 Iberia_ElMiron

    As demonstrated already El Miron is in great part related to Kostenki14 plus something else we are still missing.

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    Quote Originally Posted by rothaer View Post
    It´s correct what you stated about Oase1 per se. But Oase1 has not made any notably contribution to today Europeans, see https://www.nature.com/articles/nature17993

    Rather likely it was wiped out (or heavily reduced and then totally outnumbered) together with most Neanderthals by the Campanian Ignimbrit (the eruption of the Phlegraian fields) at at 39,280±110 years BP, see for the eruption https://en.wikipedia.org/wiki/Campan...brite_eruption

    There is no detectable genetic contribution by any Europeans before that Ignimbrit. But there is a clear contribution from Kostenki14 from short after. Likely Europe was repopulated at that time by humans with an average Neanderthal DNA proportion that did not anymore meet any notable numbers Neanderthals in Europe. This would also explain the otherwise strange thing, that Europeans, that are in the home land of Neanderthals, do not have any elevated Neanderthal DNA proportion compared to other extra-African populations.
    The answer is the first Europeans (like Oase1) actually had this to be expected elevation. But they were terminated by the Ignimbrit.

    These late Gibraltar Neanderthal datings are completely unreliebale und likey not applicable.
    I agree with you that Europe was likely repopulated from modern humans coming from further east that were likely related to Kostenki14. And most probably they didn't met any Neanderthals on their way. However, what do you think of the possibility of them meeting some older surviving human groups such as Oase1 that had elevated Neanderthal and mixing with them? It certainly would have been precious to have Oase1 in the spreadsheet which unfortunately we don't. Could that explain this shift of the WHG away from Kostenki14? Of course having small amounts of DNA related to those early groups wouldn't show significantly elevated Neanderthal in them as it showed with Oase1 and overtime would have been even more diluted.
    Last edited by Aspar; 08-01-2020 at 10:01 AM.

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    I suspect that there are still many ancient Paleolithic groups that haven't been sampled yet. Europe is the most well-represented (sub)continent when it comes to aDNA, but we still have few >30 kya high-quality genomes. The Aurignacians, for example, are represented by just one 35 kya specimen from Belgium that (unexpectedly) shows an affinity with an early East Asian.

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    Quote Originally Posted by Milkyway View Post
    I suspect that there are still many ancient Paleolithic groups that haven't been sampled yet. Europe is the most well-represented (sub)continent when it comes to aDNA, but we still have few >30 kya high-quality genomes. The Aurignacians, for example, are represented by just one 35 kya specimen from Belgium that (unexpectedly) shows an affinity with an early East Asian.
    Isn't Kostenki considered an aurignacian site?

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    Quote Originally Posted by etrusco View Post
    Isn't Kostenki considered an aurignacian site?
    From what I've read, the oldest human remains of that site (Kostenki 14) aren't assigned to any industry. Genetically speaking, K14 and more recent ones like K12 are (relatively) closely related to early Gravettians but not to GoyetQ116-1.

    The origin of the Gravettians: genomic evidence from a 36,000-year-old Eastern European

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    Distance to: WHG_Rochedane
    0.06680038 ITA_Grotta_Continenza_Meso:RMPR15
    0.15169091 Iberia_ElMiron
    0.29483019 CZE_Vestonice16
    0.31509058 BEL_GoyetQ116-1
    0.33499493 RUS_Sunghir
    0.35203857 RUS_Kostenki14
    0.39991638 RUS_Yana_UP
    0.42730645 RUS_MA1
    0.46052778 RUS_AfontovaGora3
    0.48597855 RUS_Ust_Ishim
    0.50166983 Levant_Natufian
    0.55641299 CHN_Tianyuan
    0.58451637 KEN_Early_Pastoral_N
    0.60745928 MAR_Taforalt
    0.84779554 Yoruba

    Distance to: ITA_Grotta_Continenza_Meso:RMPR7
    0.19690772 Iberia_ElMiron
    0.34454740 CZE_Vestonice16
    0.36190794 BEL_GoyetQ116-1
    0.38427833 RUS_Sunghir
    0.40186753 RUS_Kostenki14
    0.44592789 RUS_Yana_UP
    0.47031530 RUS_MA1
    0.49917879 RUS_AfontovaGora3
    0.52966729 RUS_Ust_Ishim
    0.54681458 Levant_Natufian
    0.59465844 CHN_Tianyuan
    0.62552675 KEN_Early_Pastoral_N
    0.64523529 MAR_Taforalt
    0.87928163 Yoruba

    Distance to: ITA_Grotta_Continenza_Meso:RMPR11
    0.19091870 Iberia_ElMiron
    0.33831480 CZE_Vestonice16
    0.35507422 BEL_GoyetQ116-1
    0.37792803 RUS_Sunghir
    0.39544352 RUS_Kostenki14
    0.43891077 RUS_Yana_UP
    0.46474805 RUS_MA1
    0.49454959 RUS_AfontovaGora3
    0.52164216 RUS_Ust_Ishim
    0.54465365 Levant_Natufian
    0.58704307 CHN_Tianyuan
    0.61790804 KEN_Early_Pastoral_N
    0.63822023 MAR_Taforalt
    0.86734872 Yoruba

    Distance to: ITA_Grotta_Continenza_Meso:RMPR15
    0.20633944 Iberia_ElMiron
    0.35300699 CZE_Vestonice16
    0.37075573 BEL_GoyetQ116-1
    0.39341822 RUS_Sunghir
    0.41120162 RUS_Kostenki14
    0.45388107 RUS_Yana_UP
    0.47827332 RUS_MA1
    0.50689136 RUS_AfontovaGora3
    0.53686863 RUS_Ust_Ishim
    0.55534000 Levant_Natufian
    0.60098521 CHN_Tianyuan
    0.63297981 KEN_Early_Pastoral_N
    0.65272462 MAR_Taforalt
    0.88393292 Yoruba


    I have a question, those "purer" WHGs from Grotta Continenza are all further away from any other human populations including Yoruba compared to Rochedane. Could it be that is just lower quality sampling? But if that's the problem than all three show the same effect.

    Then this:
    Distance to: BEL_GoyetQ116-1
    0.31736546 Levant_Natufian
    0.37075573 ITA_Grotta_Continenza_Meso:RMPR15

    The fact that Goyet is closer to Natufian than WHG makes me think that G25 is pretty much completely broken when it comes to older samples (like 10k years or older).

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