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Thread: Ancient DNA from North Africa (this time with formal stats)

  1. #321
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    Quote Originally Posted by mephisto View Post
    I merged myself a small dataset which I ran through admixture a few days ago. I will make better ones, but I think the charts are (to a specific degree) interesting for now. I used very few SNPs, this was just a small experiment to see how Taforalt samples are handled.
    To the samples (in the next graphs I will name them by their population, it is somehow unhandy):
    TAF[...], are the new Taforalt samples.
    WC1, is an early Neolithic Iranian (7500-7000 BC)
    I0124, is a Samaran HG (5650-5555 BC, Mesolithic)
    I1069, is a Natufian (12000-9700 BC)
    I1690, is a Natufian
    I1685, is a Natufian
    MA1 (Mal'ta-Buret' culture, 22 000 BC, Siberia)
    Loschbour, is a WHG
    I0861, is a Natufian
    Villabruna, is a WHG
    AfontovaGora3, 15 000-14 500 BC Siberia
    I1293, is from Mesolithic Iran (9100-8600 BC)
    I1072, is a Natufian
    Bichon, is a WHG
    KK1, CHG
    SATP, CHG
    Attachment 22390
    Attachment 22391
    I will make better admixture graphs, also with modern samples. The light purple ancestral population is also interesting.

    You need to run about 1000 samples through admixture in order to not get some funky looking stuff like that. More than three clusters are probably going to be needed too.

  2. #322
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    Tonight I received a new SNP set for Africans. I can test this out here in the next few days. We will see if pre-Basal Eurasian works.

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  4. #323
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    Quote Originally Posted by Chad Rohlfsen View Post
    Tonight I received a new SNP set for Africans. I can test this out here in the next few days. We will see if pre-Basal Eurasian works.
    Including which populations? How many Individuals & how many variants?

  5. #324
    Quote Originally Posted by Chad Rohlfsen View Post
    Tonight I received a new SNP set for Africans. I can test this out here in the next few days. We will see if pre-Basal Eurasian works.
    Any updates on this or can I assume basal para-Eurasian did not work?

  6. #325
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    Resurrecting this thread from the dead for a minute, but I was reading the Supplement for this paper the other day and stumbled on this paragraph on page 11:

    Finally, we tried to detect additional signatures of admixture between the Eurasian and sub424
    Saharan African gene pools, using f3 statistics with Taforalt as the target and a linkage
    425 disequilibrium (LD) decay-based method implemented in the ALDER v1.3 program (78). We
    426 could not find any Eurasian and sub-Saharan African population pairs with negative f3(Taforalt;
    427 Eurasian, sub-Saharan African), suggesting a strong post-admixture genetic drift in our Taforalt
    428 individuals (Z > 44.320 SE)
    . Neither could we detect a decay of admixture LD in our Taforalt
    429 individuals, suggesting that the admixture may not be a recent event
    (Fig. S17)
    These samples are about 15,000 years old, and the Iberomaurusian first appears around 25,000 years ago, following the Middle Stone Age Aterian culture which lasted until around 30,000 ybp. So there's a couple thousand year gap between the Aterian and the Iberomaurusian, but as some people here have speculated admixture with Aterians could account for some of this cryptic SSA affiliation that these guys have.

    For those more familiar with ALDER, is it sensitive enough to detect admixture in a given population going back 10,000-15,000 years, which in this instance would be when you would expect the ancestors of these folk to have moved into the Maghreb and absorbed some remnant MSA populations, some point between 25,000-30,000 years ago?

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  8. #326
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    This paper by Fregel "Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe" :

    https://anthrogenica.com/showthread....l=1#post413906

    was previously posted as a preprint in 2017 (so before the Iberomaurusians genomes were released in March 2018) and is now published in Pnas.

    We can notice Fregel et al. changed the 2017 abstract a little bit from "We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, indicating long-term genetic continuity in the region" to "We show that Early Neolithic Moroccans (-5000 BCE) are similar to Later Stone age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region." as they could now compared the Early Neolithic Moroccans with Iberomaurusians.

    EDIT:
    From the paper :

    "The recent publication of Iberomaurusian samples from the Taforalt site in Morocco has allowed us to directly compare IAM to Later Stone Age samples from the Maghreb"

    "FST and outgroup-f3 distances indicate a high similarity between IAM and Taforalt. As observed for IAM, most Taforalt sample ancestry derives from Epipaleolithic populations from the Levant. However, van de Loosdrecht et al. (17) also reported that one third of Taforalt ancestry was of sub-Saharan African origin. To confirm whether IAM individuals show a sub-Saharan African component, we calculated f4(chimpanzee, African population; Natufian, IAM) in such a way that a positive result for f4 would indicate that IAM is composed both of Levantine and African ancestries. Consistent with the results observed for Taforalt, f4 values are significantly positive for West African populations, with the highest value observed for Gambian and Mandenka (Fig. 3 and SI Appendix, Supplementary Note 10). Together, these results indicate the presence of the same ancestral components in ~15,000-yold and ~7,000-y-old populations from Morocco, strongly suggesting a temporal continuity between Later Stone Age and Early Neolithic populations in the Maghreb. However, it is important to take into account that the number of ancient genomes available for comparison is still low and future sampling can provide further refinement in the evolutionary history of North Africa"
    Last edited by rz1706; 06-12-2018 at 09:02 PM.
    Geno 2.0: Mediterranean 48%, North Euro 25%, SWAsian 16%, SSA 9%
    Basal K7: Basal 43.7%, Villabruna 42.7%, ANE 7.7%, SSA 4.7%, EastEurasian 1%
    Global 25 Ancient: Later Stone Age Northwest Africa (Iberomaurusian) 10%, Neolithic Levant 15%, Bronze Age Western Europe 70%, SSA 5%

    Il est très rare que l'ethnie à laquelle appartient l'auteur racialiste ne se trouve pas au sommet de sa hiérarchie., T.Todorov

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  10. #327
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    Quote Originally Posted by rz1706 View Post
    This paper by Fregel "Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe" :

    https://anthrogenica.com/showthread....l=1#post413906

    was previously posted as a preprint in 2017 (so before the Iberomaurusians genomes were released in March 2018) and is now published in Pnas.
    The updated, published Fregel paper has improved significantly since they were able to make use of the Taforalt samples. They are also finally actually testing for SSA-related admixture in the IAM samples, which was somehow missed in the preprint.

    Interestingly, PCA revealed that IAM individuals are similar to North African Later Stone Age samples from the Taforalt site in Morocco, dated ∼15,000 y ago (Fig. 2 and SI Appendix, Supplementary Note 6). When projected, IAM samples are halfway between Taforalt and modern North Africans, in the Levantine corner of the PCA space (Fig. 2). Southern Iberian Neolithic individuals from TOR cluster with Sardinians and with other Anatolian and European Neolithic samples. Moreover, KEB samples are placed halfway between the IAM and Anatolian/European farmer clusters, in close proximity to Levant aDNA samples and also to Guanche samples (16) (from the indigenous population of the Canary Islands known to have a Berber origin; ref. 23).
    Recent aDNA analysis of Moroccan Later Stone Age samples from the Taforalt site indicates that at least one-third of Taforalt ancestry derives from sub-Saharan African populations. When Taforalt and sub-Saharan African samples are included in the unsupervised clustering analysis (SI Appendix, Supplementary Note 7), we observe that IAM and Taforalt cluster together at K = 7, as observed for the MEGA-HGDP ADMIXTURE analysis. However, as reported by van de Loosdrecht et al. (17) for Taforalt, we can detect both West African (maximized in Gambians and Yoruba) and East African (maximized in Hazda) components in IAM at lower K values. In contrast, TOR does not show any sub-Saharan African ancestry and KEB is again in an intermediate position, with lower sub-Saharan African ancestry than IAM.

    To compare our samples directly to the genomes of ancient and modern populations, we calculated pair-wise fixation index (FST) distances, which, unlike PCA and global ancestry analyses, are insensitive to the inclusion of large numbers of individuals from modern populations. FST values (noted in parentheses) indicate that the IAM samples are as differentiated from all other populations as Yoruba are from non-Africans (SI Appendix, Supplementary Note 9), with the exceptions of Taforalt (0.049) and, to a lesser extent, KEB (0.090; similar to the distance between Yoruba and Mbuti), the Guanches (0.125; similar to the distance between Somali and Mbuti), and modern North African populations (0.115 to 0.138). The same pattern is observed for Taforalt samples, which shows its lower FST distance with IAM, followed again by KEB (0.129), the Guanches (0.150), and modern North Africans (0.130 to 0.149). Given the relatively low heterozygosity and high identity-by-descent proportions observed in IAM (SI Appendix, Supplementary Note 8), this differentiation could be driven by isolation and genetic drift. IAM is divergent from the other populations, with the exception of populations that either could have shared genetic drift with them or received genetic influx from them. This raises the possibility that Taforalt/IAM people were isolated in North Africa since Paleolithic times, when a back migration from Eurasia brought mtDNA haplogroups M1 and U6 to the Maghreb (19). Although IAM is clearly more similar to KEB than most populations, the converse is not true. KEB has lower FST distances with ancient Anatolian (0.032), Armenian (0.025 to 0.053), European (0.036 to 0.041, excluding European hunter-gatherers), Levantine (0.020 to 0.079), and Iranian (0.081 to 0.081) populations, as compared with IAM. In the modern DNA reference panel, KEB is similar to North African, European, and Middle Eastern populations. Among the ancient populations, TOR is more similar to Middle Neolithic/Chalcolithic Europeans (0.029 to 0.031), and, among modern populations, TOR is more similar to those from Spain, North Italy, and Sardinia.
    To further investigate the genetic affinities of IAM, KEB, and TOR samples, we conducted outgroup f3-statistic analysis (24). When using an outgroup population that has not experienced any postdivergence gene flow with either one of the compared populations, the f3-statistic calculated in the form f3(PopA, PopB; outgroup) allows us to determine the amount of shared drift between two populations, PopA and PopB. We selected the Ju\ʼhoan population as the outgroup, and compared our three ancient populations (IAM, KEB, and TOR) against all of the ancient populations in the Human Origins panel, as well as the Taforalt and Guanche samples. The highest f3 values for IAM are observed for Taforalt (0.3060) and KEB (0.2296). Consistent with previous results, when Taforalt, KEB, and Guanches (f3 = 0.2196) are excluded, IAM shares more drift with ancient Levantine populations, such as Epipaleolithic communities (Natufians; f3 = 0.2296) and Pre-Pottery Neolithic individuals (f3 = 0.2167) (Fig. 3 and SI Appendix, Supplementary Note 10), than with any other ancient population. This confirms previous results for Taforalt (17) indicating a Levantine intrusion in North Africa in Paleolithic times.

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  12. #328
    Quote Originally Posted by Lank View Post
    The updated, published Fregel paper has improved significantly since they were able to make use of the Taforalt samples. They are also finally actually testing for SSA-related admixture in the IAM samples, which was somehow missed in the preprint.
    I may be wrong but there are a lot of unsound theories and weird results in this paper. Taforalt and IAM are 100% North African while Ancient Levantine populations appear to be a mix of IBM and Anatolia N(Figure 7.2 to Figure 7.4) yet the author insist heavily that they are of "Levantine" origin, Iberomaurusians(Taforalt and IAM) show the highest FST distance(higher than CHG, EHG, Iran_N) with Natufian and SSA populations(Figure 9.1) yet they are 30% SSA and are somehow of "Paleolithic Levantine origin" according to the author.
    Last edited by Shamayim; 06-13-2018 at 03:14 PM.

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  14. #329
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    Quote Originally Posted by Shamayim View Post
    I may be wrong but there are a lot of unsound theories and weird results in this paper. Taforalt and IAM are 100% North African while Ancient Levantine populations appear to be a mix of IBM and Anatolia N(Figure 7.2 to Figure 7.4) yet the author insist heavily that they are of "Levantine" origin, Iberomaurusians(Taforalt and IAM) show the highest FST distance(higher than CHG, EHG, Iran_N) with Natufian and SSA populations(Figure 9.1) yet they are 30% SSA and are somehow of "Paleolithic Levantine origin" according to the author.
    I think it's best to avoid looking too much into the ADMIXTURE or Fst results. The f3 stats (Fig. 3A) show that out of the Eurasian aDNA samples, Natufians share the most drift with the IAM samples. This is perfectly sensible as they are the Mesolithic sample closest to Africa, share Y-DNA E-M35 with the IAM/Taforalt samples, and the Taforalt paper already demonstrated that the Eurasian component in Taforalt is "Natufian-related". But the Iberomaurusian predates the Natufian by thousands of years, so the Eurasian component rather seems derived from earlier Paleolithic West Asians.

    There is a lot of speculation that Natufians probably have North African admixture (which seems likely IMO), but this doesn't mean there weren't earlier migrations going the other way, into North Africa from the Levant.

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  16. #330
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    Here is fig. 2 from the Fregel paper with better spacing for readability:



    PCA from the supp. material:


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