Page 1 of 23 12311 ... LastLast
Results 1 to 10 of 230

Thread: Is Basal Eurasian real or an fstats artifact?

  1. #1
    Registered Users
    Posts
    255
    Sex
    Location
    Canada
    Ethnicity
    Somali
    Y-DNA (P)
    T-L208
    mtDNA (M)
    N1b2

    Canada Somaliland

    Is Basal Eurasian real or an fstats artifact?

    The idea of a Basal Eurasian population which split off main OOA population before they admixed with Neanderthals has been a pretty popular explanation for the depleted Neanderthal alleles present in various ancient Near Eastern populations (Natufians, Iran_N etc).

    The existence of Basal Eurasian population was proposed in order to explain why the Natufians seemed to lack any affinity to SSA populations in the fstats despite having significantly lower Neanderthal admixture.

    Here are some fstats demonstrating that lack of affinity using Yoruba

    Code:
    result:      Chimp     Yoruba        WHG   Natufian     -0.000278      0.000342    -0.811   23075  23215 506375 
    result:      Chimp     Yoruba        EHG   Natufian      0.000221      0.000342     0.647   23353  23242 501620 
    result:      Chimp     Yoruba        CHG   Natufian     -0.000181      0.000359    -0.505   23428  23519 506383 
    result:      Chimp     Yoruba       PPNB   Natufian     -0.000358      0.000310    -1.156   19286  19449 456717 
    result:      Chimp     Yoruba Anatolia_N   Natufian     -0.000510      0.000269    -1.895   22210  22468 506205
    At first glance these stats may seem to support the idea that the Natufians lack any affinity to Sub-saharan populations, however I had previously noted that African admixed populations give very strange Z-scores in simple 4 pop fstat tests due to a weird quirk wherein an aversion to African populations occurs that essentially causes the tested population to prefer Eurasians strongly. This effect is particularly strong on heavily admixed East Africans.

    Knowing about that quirk led me to try out some of the East African samples using the same 4 pop test to verify if these results can be taken seriously.


    Code:
    result:      Chimp     Yoruba        WHG     Somali      0.000197      0.000307     0.641   24713  24631 414978 
    result:      Chimp     Yoruba        EHG     Somali      0.000225      0.000303     0.742   24337  24246 407073 
    result:      Chimp     Yoruba        CHG     Somali      0.000166      0.000316     0.524   24686  24617 414962 
    result:      Chimp     Yoruba   Natufian     Somali      0.000272      0.000418     0.652   11490  11436 196976 
    result:      Chimp     Yoruba       PPNB     Somali      0.000418      0.000312     1.339   18705  18572 318429 
    result:      Chimp     Yoruba Anatolia_N     Somali     -0.000376      0.000197    -1.907   24002  24156 410156 
    
    result:      Chimp     Yoruba        WHG      Oromo     -0.000656      0.000298    -2.201   24343  24616 415042 
    result:      Chimp     Yoruba        EHG      Oromo     -0.000623      0.000293    -2.128   23953  24207 407137 
    result:      Chimp     Yoruba        CHG      Oromo     -0.000688      0.000307    -2.242   24288  24574 415026 
    result:      Chimp     Yoruba   Natufian      Oromo     -0.000624      0.000408    -1.532   11293  11416 197023 
    result:      Chimp     Yoruba       PPNB      Oromo     -0.000541      0.000298    -1.815   18392  18564 318495 
    result:      Chimp     Yoruba Anatolia_N      Oromo     -0.001247      0.000178    -7.002   23595  24106 410219 
    
    result:      Chimp     Yoruba        WHG     Amhara     -0.000178      0.000298    -0.597   24218  24292 415032 
    result:      Chimp     Yoruba        EHG     Amhara     -0.000137      0.000286    -0.478   23861  23916 407122 
    result:      Chimp     Yoruba        CHG     Amhara     -0.000207      0.000301    -0.689   24174  24260 415016 
    result:      Chimp     Yoruba   Natufian     Amhara     -0.000036      0.000404    -0.090   11252  11259 197020 
    result:      Chimp     Yoruba       PPNB     Amhara      0.000003      0.000289     0.011   18271  18270 318487 
    result:      Chimp     Yoruba Anatolia_N     Amhara     -0.000745      0.000174    -4.286   23450  23756 410210 
    
    result:      Chimp     Yoruba        WHG Kenya_PastoralN      0.000113      0.000272     0.416   50097  49985 985968 
    result:      Chimp     Yoruba        EHG Kenya_PastoralN      0.000413      0.000265     1.558   49743  49341 973250 
    result:      Chimp     Yoruba        CHG Kenya_PastoralN      0.000182      0.000270     0.674   50173  49994 985952 
    result:      Chimp     Yoruba   Natufian Kenya_PastoralN      0.000341      0.000322     1.059   24353  24184 494955 
    result:      Chimp     Yoruba       PPNB Kenya_PastoralN     -0.000072      0.000241    -0.298   39593  39650 801132 
    result:      Chimp     Yoruba Anatolia_N Kenya_PastoralN     -0.000158      0.000199    -0.796   49030  49186 984156 
    
    result:      Chimp     Yoruba        WHG Tanzania_PastoralN      0.000000      0.000289     0.000   42293  42293 839641 
    result:      Chimp     Yoruba        EHG Tanzania_PastoralN      0.000267      0.000293     0.911   42102  41880 831236 
    result:      Chimp     Yoruba        CHG Tanzania_PastoralN      0.000055      0.000296     0.185   42290  42244 839607 
    result:      Chimp     Yoruba   Natufian Tanzania_PastoralN      0.000424      0.000346     1.225   22275  22080 457609 
    result:      Chimp     Yoruba       PPNB Tanzania_PastoralN     -0.000304      0.000266    -1.143   35502  35723 726963 
    result:      Chimp     Yoruba Anatolia_N Tanzania_PastoralN     -0.000237      0.000228    -1.041   41447  41646 839376
    Looking at the results for the East Africans we see a similar lack of affinity to a SSA population. If we were to operate on the same assumptions that lead to the statement that the Natufians lacked any SSA affinity we would then have to say that these populations also lack SSA affinity, which is clearly nonsensical and is likely a result of the strange aversion to African populations I noticed earlier.


    Without this lack of affinity to SSA populations is there actually any reason for us to assume the existence of some unsampled "Basal Eurasian" admixture in Ancient Near Easterners when admixture from a North and/or Northeast African population could account for the disparity in Neanderthal admixture in a more parsimonious manner.
    Last edited by Mnemonics; 09-12-2021 at 02:57 PM.

  2. The Following 16 Users Say Thank You to Mnemonics For This Useful Post:

     Angoliga (09-12-2021),  Archetype0ne (09-13-2021),  beyoku (09-12-2021),  blackflash16 (09-12-2021),  Brandon S. Pilcher (09-12-2021),  Dehlisandwich (09-18-2021),  drobbah (09-12-2021),  gihanga.rwanda (09-12-2021),  Keneki20 (09-13-2021),  Lenny Nero (09-12-2021),  Mansamusa (09-19-2021),  Megalophias (09-12-2021),  NetNomad (09-15-2021),  pegasus (09-13-2021),  taharqa (09-14-2021),  Tsakhur (09-13-2021)

  3. #2
    Registered Users
    Posts
    59
    Sex

    I'm fairly sure though the concept of BE was first invoked rather to explain the differential relationship of west and east Eurasians pre-neolithic to Ust Ishim, and how for some weird reason modern Europeans but not pre-neolithic Europeans seemed to have diluted affinity to Ust-Ishim when compared to a broad pool of various east Eurasians. The Natufian samples hadn't been published yet.

  4. The Following 7 Users Say Thank You to mauors For This Useful Post:

     blackflash16 (09-12-2021),  Gadzooks (09-15-2021),  K33 (09-15-2021),  Megalophias (09-12-2021),  Mnemonics (09-12-2021),  Psynome (09-13-2021),  Tsakhur (09-13-2021)

  5. #3
    Registered Users
    Posts
    266

    IMO its probably African genetic substructure specific to North or North East Africa.
    Research has been beating around the bush for years.

  6. The Following 8 Users Say Thank You to beyoku For This Useful Post:

     blackflash16 (09-12-2021),  Brandon S. Pilcher (09-12-2021),  Dehlisandwich (09-18-2021),  egyptian_eediat (09-15-2021),  Lenny Nero (09-12-2021),  Mansamusa (09-13-2021),  Mnemonics (09-12-2021),  taharqa (09-14-2021)

  7. #4
    Registered Users
    Posts
    502
    Sex
    Location
    Rome
    Ethnicity
    Veneto\Toscano
    Nationality
    Italian
    Y-DNA (P)
    R1b-U152-L2-Z367
    mtDNA (M)
    T1a1

    Republic of Venice Italy Veneto Italy Tuscany Italy 1861-1946 European Union Italy
    Quote Originally Posted by Mnemonics View Post
    The idea of a Basal Eurasian population which split off main OOA population before they admixed with Neanderthals has been a pretty popular explanation for the depleted Neanderthal alleles present in various ancient Near Eastern populations (Natufians, Iran_N etc).

    The existence of Basal Eurasian population was proposed in order to explain why the Natufians seemed to lack any affinity to SSA populations in the fstats despite having significantly lower Neanderthal admixture.

    Here are some fstats demonstrating that lack of affinity using Yoruba

    Code:
    result:      Chimp     Yoruba        WHG   Natufian     -0.000278      0.000342    -0.811   23075  23215 506375 
    result:      Chimp     Yoruba        EHG   Natufian      0.000221      0.000342     0.647   23353  23242 501620 
    result:      Chimp     Yoruba        CHG   Natufian     -0.000181      0.000359    -0.505   23428  23519 506383 
    result:      Chimp     Yoruba       PPNB   Natufian     -0.000358      0.000310    -1.156   19286  19449 456717 
    result:      Chimp     Yoruba Anatolia_N   Natufian     -0.000510      0.000269    -1.895   22210  22468 506205
    At first glance these stats may seem to support the idea that the Natufians lack any affinity to Sub-saharan populations, however I had previously noted that African admixed populations give very strange Z-scores in simple 4 pop fstat tests due to a weird quirk wherein an aversion to African populations occurs that essentially causes the tested population to prefer Eurasians strongly. This effect is particularly strong on heavily admixed East Africans.

    Knowing about that quirk led me to try out some of the East African samples using the same 4 pop test to verify if these results can be taken seriously.


    Code:
    result:      Chimp     Yoruba        WHG     Somali      0.000197      0.000307     0.641   24713  24631 414978 
    result:      Chimp     Yoruba        EHG     Somali      0.000225      0.000303     0.742   24337  24246 407073 
    result:      Chimp     Yoruba        CHG     Somali      0.000166      0.000316     0.524   24686  24617 414962 
    result:      Chimp     Yoruba   Natufian     Somali      0.000272      0.000418     0.652   11490  11436 196976 
    result:      Chimp     Yoruba       PPNB     Somali      0.000418      0.000312     1.339   18705  18572 318429 
    result:      Chimp     Yoruba Anatolia_N     Somali     -0.000376      0.000197    -1.907   24002  24156 410156 
    
    result:      Chimp     Yoruba        WHG      Oromo     -0.000656      0.000298    -2.201   24343  24616 415042 
    result:      Chimp     Yoruba        EHG      Oromo     -0.000623      0.000293    -2.128   23953  24207 407137 
    result:      Chimp     Yoruba        CHG      Oromo     -0.000688      0.000307    -2.242   24288  24574 415026 
    result:      Chimp     Yoruba   Natufian      Oromo     -0.000624      0.000408    -1.532   11293  11416 197023 
    result:      Chimp     Yoruba       PPNB      Oromo     -0.000541      0.000298    -1.815   18392  18564 318495 
    result:      Chimp     Yoruba Anatolia_N      Oromo     -0.001247      0.000178    -7.002   23595  24106 410219 
    
    result:      Chimp     Yoruba        WHG     Amhara     -0.000178      0.000298    -0.597   24218  24292 415032 
    result:      Chimp     Yoruba        EHG     Amhara     -0.000137      0.000286    -0.478   23861  23916 407122 
    result:      Chimp     Yoruba        CHG     Amhara     -0.000207      0.000301    -0.689   24174  24260 415016 
    result:      Chimp     Yoruba   Natufian     Amhara     -0.000036      0.000404    -0.090   11252  11259 197020 
    result:      Chimp     Yoruba       PPNB     Amhara      0.000003      0.000289     0.011   18271  18270 318487 
    result:      Chimp     Yoruba Anatolia_N     Amhara     -0.000745      0.000174    -4.286   23450  23756 410210 
    
    result:      Chimp     Yoruba        WHG Kenya_PastoralN      0.000113      0.000272     0.416   50097  49985 985968 
    result:      Chimp     Yoruba        EHG Kenya_PastoralN      0.000413      0.000265     1.558   49743  49341 973250 
    result:      Chimp     Yoruba        CHG Kenya_PastoralN      0.000182      0.000270     0.674   50173  49994 985952 
    result:      Chimp     Yoruba   Natufian Kenya_PastoralN      0.000341      0.000322     1.059   24353  24184 494955 
    result:      Chimp     Yoruba       PPNB Kenya_PastoralN     -0.000072      0.000241    -0.298   39593  39650 801132 
    result:      Chimp     Yoruba Anatolia_N Kenya_PastoralN     -0.000158      0.000199    -0.796   49030  49186 984156 
    
    result:      Chimp     Yoruba        WHG Tanzania_PastoralN      0.000000      0.000289     0.000   42293  42293 839641 
    result:      Chimp     Yoruba        EHG Tanzania_PastoralN      0.000267      0.000293     0.911   42102  41880 831236 
    result:      Chimp     Yoruba        CHG Tanzania_PastoralN      0.000055      0.000296     0.185   42290  42244 839607 
    result:      Chimp     Yoruba   Natufian Tanzania_PastoralN      0.000424      0.000346     1.225   22275  22080 457609 
    result:      Chimp     Yoruba       PPNB Tanzania_PastoralN     -0.000304      0.000266    -1.143   35502  35723 726963 
    result:      Chimp     Yoruba Anatolia_N Tanzania_PastoralN     -0.000237      0.000228    -1.041   41447  41646 839376
    Looking at the results for the East Africans we see a similar lack of affinity to a SSA population. If we were to operate on the same assumptions that lead to the statement that the Natufians lacked any SSA affinity we would then have to say that these populations also lack SSA affinity, which is clearly nonsensical and is likely a result of the strange aversion to African populations I noticed earlier.


    Without this lack of affinity to SSA populations is there actually any reason for us to assume the existence of some unsampled "Basal Eurasian" admixture in Ancient Near Easterners when admixture from a North and/or Northeast African population could account for the disparity in Neanderthal admixture in a more parsimonious manner.
    Wait, you are using Eurasians for East Africans, why would it give you a decent result? It's really a null result. Didn't we talk about this with Mota?

  8. #5
    Registered Users
    Posts
    255
    Sex
    Location
    Canada
    Ethnicity
    Somali
    Y-DNA (P)
    T-L208
    mtDNA (M)
    N1b2

    Canada Somaliland
    Quote Originally Posted by Ariel90 View Post
    Wait, you are using Eurasians for East Africans, why would it give you a decent result? It's really a null result. Didn't we talk about this with Mota?
    The fstat ( Chimp African Eurasian Target ) is what was used to claim a lack of affinity between Natufians and SSA populations, due to the lack of a significant Z-score. I am demonstrating that the Z-score is insignificant even for East African populations with large amounts of SSA admixture... which means we cannot rule out similar admixture in the Natufians.
    Last edited by Mnemonics; 09-12-2021 at 06:25 PM.

  9. The Following User Says Thank You to Mnemonics For This Useful Post:

     drobbah (09-12-2021)

  10. #6
    Registered Users
    Posts
    111
    Sex

    The basal Eurasians continue to be defended. Paper from the 4th of this month:

    https://academic.oup.com/gbe/advance...vab194/6364187

    I don't know if it's right, but since I've known the Basal Eurasians I've thought about this location. On February 28th I published:

    Basal Eurasians have been in the glacier refuge of the Persian Gulf for over 100,000 years, surrounded by deserts. At the time of coastal migration at approx. 60,000 years ago the coast was south of the Strait of Hormuz, possibly also desert and as the migration was mainly of navigators (fishing for hooks and nets only appears later) they may have passed away avoiding conflicts with this area already inhabited. When the gulf is submerged the basal eurasians may have been reduced to slavery when they sought refuge in Iran and Levant (archaic agriculture and grinding require a lot of labor and are very painful especially before using animal traction), and their y chromosomes replaced (or almost replaced) by those of the already settled populations there, as is normally the case for disadvantaged populations.

    https://anthrogenica.com/showthread....655#post753655

  11. The Following User Says Thank You to jose luis For This Useful Post:

     MiranZai (09-21-2021)

  12. #7
    Registered Users
    Posts
    2,075
    Sex
    Omitted

    Hmmm I think you may have hit on something unexpected here... For every African population I've seen Chimp African1 Eurasian African2 is always negative (even when African2 is Mota) because of multiple deep layers of ancestry in Africa presumably. Why doesn't PastoralN show this?

    The only one I've found that's the opposite is Dinka.
    1 Chimp~ Mbuti.DG Mongolia_N_East Dinka.DG 4.32955
    2 Chimp~ Yoruba.DG Mongol~ Dink~ 3.71215
    3 Chimp~ South_Africa_2000BP.SG Mongol~ Dink~ 0.221423
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

  13. The Following 3 Users Say Thank You to Kale For This Useful Post:

     blackflash16 (09-19-2021),  Mnemonics (09-13-2021),  tipirneni (09-13-2021)

  14. #8
    Registered Users
    Posts
    502
    Sex
    Location
    Rome
    Ethnicity
    Veneto\Toscano
    Nationality
    Italian
    Y-DNA (P)
    R1b-U152-L2-Z367
    mtDNA (M)
    T1a1

    Republic of Venice Italy Veneto Italy Tuscany Italy 1861-1946 European Union Italy
    1) How related is "crown" East African to other SSA? (If it's distant enough it could too deep for f-stats, right?)
    2) Could archaic admixture or some extra "basal-human" admixture in SSA screw the model?

  15. #9
    I have noticed that Basal Eurasian components, which were described in the Dzudzuana paper, are too deep and African-related as compared to other varieties from other papers. Therefore, it is useless for Europeans to pretend to be 'Basal Eurasian' in any form, unless Europeans have strong proof that their ancestors came to Africa, mixed with some inhabitants there, and then returned back to Near East to participate in the creation of the Dzudzuana component in the Paleolithic.

  16. The Following User Says Thank You to Q-M242-is-Papuan-related For This Useful Post:

     Mansamusa (09-19-2021)

  17. #10
    Registered Users
    Posts
    72
    Sex
    Y-DNA (P)
    J2a - L70
    mtDNA (M)
    N1a1a1a2

    What happens when you use Mota? I.e (Chimp, Mota, Eurasian, Natufian)

Page 1 of 23 12311 ... LastLast

Similar Threads

  1. What is Basal Eurasian?
    By Tsakhur in forum Autosomal (auDNA)
    Replies: 204
    Last Post: 07-19-2021, 12:30 AM
  2. Replies: 3
    Last Post: 06-15-2020, 02:32 PM
  3. Is haplogroup M1 Basal Eurasian?
    By NetNomad in forum M
    Replies: 25
    Last Post: 10-12-2018, 06:27 PM
  4. Is there a need for Basal Eurasian now?
    By ren in forum Ancient (aDNA)
    Replies: 0
    Last Post: 10-14-2017, 02:58 AM
  5. Basal Eurasian and ASI Split
    By Dr_McNinja in forum Ancient (aDNA)
    Replies: 158
    Last Post: 11-06-2015, 07:18 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •