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Thread: Torsten Günther at al 2018 - Population genomics of Mesolithic Scandinavia

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    Torsten Günther at al 2018 - Population genomics of Mesolithic Scandinavia

    Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation(PLOS Biology)

    https://journals.plos.org/plosbiolog...l.pbio.2003703
    Abstract
    Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500–6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east–west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

    Main discussion topic:
    https://anthrogenica.com/showthread....ic+Scandinavia

    This topic is dedicated to Steigen individ:
    https://anthrogenica.com/showthread....er-on-GEDmatch

    ID Age (cal BP) Sex mt Y(orignal) Contamination (based on X) Contamination (based on autosomes) Y(detailed)
    Hum1 9452-9275 XX U5a1 NA 0,00%
    HUM2 9452-9275 XY U5a1d I2-M438 0,63% 0,73% pre I2-S6635
    Steigen 5950-5764 XY U5a1d I2-M423 0,4% 0,0% I2-M423*
    SF9 9300-8988 XX U4a2 NA 0,0%
    SF11 9023-8760 XY U5a1 NA NA 10,16% pre-I1?
    SF12 9033-8757 XX U4a1 NA 0,93%
    SBj 8963-8579 XY U4a1 I2-L68 1,4% 0,06% I2-L68

    Brief results: 2 out of 4 Ychromosomes likely belong to ancient long dead branches.
    I have checked the *.bam files myself and used 2019 version of ISOGG tree (several months old though).

    Most samples have high coverage, so I will not post here (even under spoiler) all the list of upstream positives and downstream negatives as it will make a too long post.

    HUM2
    Out of S6635 synonimes he is positive to 25 and negative to 2. It could happen, that those 2 negatives are just problems with the data, but I desided here to state that he is pre-S6635, as if those two negatives where both correct.
    What is more important that these two negative SNPs, is that he is negative for both known downstream SNP branches: I-PF3885 and I-Y5334.

    He lived 9452-9275 ybp, while his terminal Ychr branch has TMRCA 10100 ybp.
    Closest surviving branch is at least 600 years from him, but it is likely a bit more as he is likely pre-S6635, but not full S6635.
     

    S6635 synonimes
    Positive:
    PF6915
    PF3881
    PF3892
    PF3904
    PF3914
    PF3924
    PF3930
    PF3933
    S6635
    S6648
    S6661
    S6685
    S6701
    S6705
    S6711
    S10911
    S15422
    S17911.2
    S23479
    S23817
    FGC18596
    FGC18630
    PF3926
    PF3928
    S6724

    Negative:
    S6716 (4 reads)
    FGC18615 (6 reads, five of them at the begining/end of a read)

    I-PF3885 synonimes:
    All negatives:
    BY431
    A10439
    PF3885
    PF3905
    PF3913
    PF3916
    PF3920
    PF3921
    S18870
    S23632
    Z45426
    Z45427
    Z45429
    PF6909
    Z45428
    S10292
    S12457
    S18874

    I-Y5334 synonimes:
    All negatives:
    FGC18124
    FGC18541
    FGC18587
    FGC18594


    Steigen

    If we use y-full tree we will see that he is positive to all the M423 synonimes, but negative to both Y3104 and Y24694 branches.
    Y24694 branch is not in ISOGG 2019 jet, so I had to manually copy SNP's from y-full to make this check. He is ancestral to all 10 Y24694 SNP's where he has calls.

    So, this hunter-gather is I2a1a2* (ISOGG 2019). He lived 6,000–5,800 cal BP, while his terminal Ychr branch has TMRCA 13900 ybp.
    This means his Y-chromosome branch is about 8000 years away from the closest surviving branch.

     

    M423 synonimes (y-full)
    Positive:
    M423
    AM01256
    AM01270
    AM01282
    AM01284
    AM01290
    AM01291
    FGC7074
    FGC7084
    S11650
    Y3114
    Z2601
    Z2575
    AM01259
    AM01264
    AM01268
    AM01271
    AM01272
    AM01286
    AM01296

    Y3104 synonimes:
    Negative:
    AM01253
    AM01258
    AM01266
    AM01289
    AM01292
    FGC7066
    FGC7067
    FGC8114
    S7721
    S12378
    AM01273
    AM01283
    AM01299
    Z2587

    Y24694 synonimes:
    All negatives:
    Y130032
    Y128076
    Y128343
    Y129078
    Y128442
    Y151128
    Y136309
    Y128271
    Y32698
    Y80035


    SF11
    This sample seems to be a good candidate for an ancestor of modern Scandinavian I1.
    But it has high percent of estimated contamination, so it could happen he is positive to so many I1 SNPs because of contaminated modern DNA.

    Hope, we will have more pre-I1 samples from any part of Europe. In this case we will be able to compare positive and negative SNPs from different pre-I1 samples.

    Positive:
    CTS1748
    CTS6221
    CTS6629
    FGC2433
    YSC0000301
    Z2726
    Z2731
    CTS5887
    FGC7747

    Negative:
    CTS3268
    CTS6547
    CTS9258
    FGC2425
    L121
    L509

    SBj
    He is positive to I2a happlogroup (ISOGG 2019) - those SNPs are still listed as synonimes just to root I2 on y-full.
    He is also negative to important known downstream branches: P37, M436 and L596 (no calls for L460).

    L460 has TMRCA at 20800 ypb, and this hunter-gather lived 8963-8579 ybp. So, his Ychr branch is at least 11 837 years away from the closest known survived branch - but likely even more, as he could be negative for L460 SNPs.
    Given a few negatives I could even suggest this could be some pre-I2, but he is positive to all SNPs marked as I2a, so I will think this 3 cases are just some errors.

     

    I2/I2a synonimes:
    Positives:
    CTS4568
    CTS6096
    CTS10247
    L68
    PF3644
    PF3664.1
    PF3669
    PF3812
    CTS11806
    PF3810
    PF3850
    CTS1799
    CTS2257
    CTS3529
    CTS4047

    Undesided:
    CTS6479(1 read for ancestral, 1 for derived)

    Negatives:
    CTS7965(8 reads)
    PF3648(2 reads)
    PF3650(1 read for derived, 5 reads for ancestral)

    P37 synonimes:
    Negative:
    CTS6825 (24 reads)

    Positive:
    CTS1279 (1 read, this is a C->T mutation, so we should not wory he could be pre P-37)

    M436 synonimes:
    All negative:
    CTS4314
    CTS5017
    CTS8302
    CTS11311
    FGC3524
    FGC3526
    FGC3530
    FGC3537
    FGC3538
    P217
    P218
    PF6895

    L596 synonimes:
    All negative
    L597
    FGC18092
    FGC18599
    M3935
    PF3906
    PF3911
    PF3931
    FGC18542
    PF3907
    Last edited by artemv; 09-30-2019 at 04:55 PM.

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    Regarding SF11, I wouldn't say there's enough strong evidence to say this is a good candidate for an ancestor of modern Scandinavian I1. I think it's more likely that SF11 is representative of an extinct lineage that didn't result in the modern I1, but they would share a common ancestor, although the available data really isn't conclusive enough so could be either. I'd add that SF11 has several derived SNPs that are associated with other haplogroups and not found in modern I1 individuals, but as you say some of these might be due to contamination and some might be due to DNA damage such as deamination. All of the derived calls are one-read SNPs so could be false positives.

    I'm using the YFull tree as reference for the 312 SNPs that they define haplogroup I1 - I had a few differences in the I1 SNP calls for SF11 - most were the same but I also had a derived read for Z2683 (1T) and ancestral reads for Y1831/FGC2468 (1T), CTS9845 (1A), FGC7871/Y1906 (1G), Z2690 (1G). There's definitely some sections of the genome where the BAM file shows a lot of derived reads close together close to some of these SNPs, so I'm overall less confident about some of these calls.

    We might have a better idea of correllating the ancestral and derived versus the sample age if there were more reads for the I1 SNPs in SF11's BAM file, which would help lock down if SF11 was a transition between I and I1 or a brother lineage that didn't make it, but unfortunately SF11 is no call for more than 290 of the I1 SNPs (>93%), so it's difficult to say with any certainty.

    Of the other pre-I1 samples that I'm aware of that have a mixture of derived and ancestral I1 SNPs, there are two in a couple of the recent ancient Iberian papers:

    BAL051 from "Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula" Villalba-Mouco et al., 2019, Current Biology 29, 1–9; Derived SNPs: Z2699 2C, Z2751 2A, Z2869 1G, Z2885 1T, Z2887 1T, CTS7751 1T, Z2812 1T, Z2860 1A, L124 1C, CTS4532 1A, Z2724 2G, FGC2441 2G, CTS10140 1A. Ancestral SNPs:Z2886 1T, Z2679 1T, Z2727 1C, Z2850 1A, Y1962 4T, P40 1C, Z2747 1A, FGC2422 1C, CTS3506/Z2765 1A, FGC33327 1T, CTS11534 1A, Y1863 1T, L848 2C, FGC2433 1G, Y1950 1C, FGC2427 1C, Y1932 1A, Z2870 1T, S22865 1G, Z2806/CTS6765 1T.

    Car1 from "The genomic history of the Iberian Peninsula over the past 8000 years" Olade et al 2019, Science 363, 1230–1234; Derived I1 SNPs: Z2699 1C, Z2880 3A, Z2729 1T, Z2779 1C, CTS10338 1C, Z2885 1T, V5190/Z2742 1A, CTS11036/Z2863 1T, Z2730 1G, Z2720 1T, Z2887 1T, Z2847 1T, CTS1739 1G, Y1950 CGGA, Z2852 1T, CTS6022 1A, CTS4532 1A, Z2859 2A, Z2695 1T; Ancestral I1 SNPs: L840 1C, FGC7747 1T, Z2718 2C, Z2679 2T, Z2727 3C, CTS6140 1T, Y1872 1G, Z2747 1A, CTS11042 2T, Z2826 1T, Z2858 1G, V5203 2G, CTS11534 1A, Y1863 3T, CTS8394 1G, Z2825 1G, L848 1C, CTS9486 1G, Z2705 1C, Z2790 1G, Y1860 1A, Y1871 1C, FGC2427 1C, L764 1C, L1439 2C 1G (ambiguous, but likely ancestral), Z2870 1T, CTS9487 1G, Z2775 1G, CTS9368 2T, Y1876 1T,Z6116 1A, Z2832 2G, CTS7386 1T, CTS8708 1T, FGC2462 1C - also one SNP that has a mutation at the described position for FGC2445, but to a different nucleotide (1A rather than T).

    There are a few more that are not enough information to tell. Three samples (RISE175, RISE179, RISE210) from the Allentoft 2015 paper have some derived I1 SNPs, but are low coverage and >97% of the I1 SNPs are not read, so could have some that are ancestral, or could be all derived - there's no way to tell. BAB5 from Szécsényi-Nagy 2014
    only had a single SNP (M253) relevant to I1 tested, but predates the TMRCA of modern I1, so was probably a mix of derived and ancestral I1 SNPs. But there's no way to tell with the information we have.

    Also, check out my Ancient I1 samples map - I include SNP calls from all the ancient I1 samples that I'm aware of. The confirmed pre-I1 (mixture of derived and ancestral I1 SNPs) are on the map in black with skull and crossbones while the uncertain ones are brown with a "?" - link to the map in my signature.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by deadly77 View Post
    Regarding SF11, I wouldn't say there's enough strong evidence to say this is a good candidate for an ancestor of modern Scandinavian I1. I think it's more likely that SF11 is representative of an extinct lineage that didn't result in the modern I1, but they would share a common ancestor, although the available data really isn't conclusive enough so could be either. I'd add that SF11 has several derived SNPs that are associated with other haplogroups and not found in modern I1 individuals, but as you say some of these might be due to contamination and some might be due to DNA damage such as deamination.
    Of course we cannot know for sure about each individ if it is exactly on the branch going to modern happlogroups or somewhere near. But given its time and location we can suppose that the example is on or somewhere near the branch leading to modern I1.
    I usually check files for a high number of SNPs, I've cheked SF11 for all the SNPs in trunk tree, I1 and I2 tree, and results always contain some noise, approximately one of 30-40 SNPs is usually false.
    For example, nucleotids, located very close to known or unkonwn "del" or "insert" mutations have a chance to have a wrong position number.

    Quote Originally Posted by deadly77 View Post
    All of the derived calls are one-read SNPs so could be false positives.
    This is the data we have for this sample - we usually have only 1 read for each position, rarely 2 reads. Very few cases for more than 2 reads for SF11.
    As I've said, I've checked SF11 for all the I1/I2 SNPs in ISOGG2019 tree.
    And the results do not look like they are heavily contaminated. For example there are 195 calls for downstream I1 SNPs and all 100% of them are ancestral.
    For I2 SNPs I have the following stats: total 314 calls, out of them 6 derived, 4 "new"(means replaced by a different nucleotide).

    Quote Originally Posted by deadly77 View Post
    I'm using the YFull tree as reference for the 312 SNPs that they define haplogroup I1 - I had a few differences in the I1 SNP calls for SF11 - most were the same but I also had a derived read for Z2683 (1T) and ancestral reads for Y1831/FGC2468 (1T), CTS9845 (1A), FGC7871/Y1906 (1G), Z2690 (1G). There's definitely some sections of the genome where the BAM file shows a lot of derived reads close together close to some of these SNPs, so I'm overall less confident about some of these calls.
    All these SNPs are not in a current ISOGG SNP list.
    By the way, how did you download the SNP list from Y-full? I saw there only definition of SNPs, that start with Y.

    Quote Originally Posted by deadly77 View Post
    We might have a better idea of correllating the ancestral and derived versus the sample age if there were more reads for the I1 SNPs in SF11's BAM file, which would help lock down if SF11 was a transition between I and I1 or a brother lineage that didn't make it, but unfortunately SF11 is no call for more than 290 of the I1 SNPs (>93%), so it's difficult to say with any certainty.
    I meant that we should check which I1 SNPs appeared "earlier" and which appeared "later", and if we get contradicting results this means we got errors due to damaged aDNA, contamination, e.t.c.
    Quote Originally Posted by deadly77 View Post
    Of the other pre-I1 samples that I'm aware of that have a mixture of derived and ancestral I1 SNPs, there are two in a couple of the recent ancient Iberian papers:

    BAL051 from "Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula" Villalba-Mouco et al., 2019, Current Biology 29, 1–9; Derived SNPs: Z2699 2C, Z2751 2A, Z2869 1G, Z2885 1T, Z2887 1T, CTS7751 1T, Z2812 1T, Z2860 1A, L124 1C, CTS4532 1A, Z2724 2G, FGC2441 2G, CTS10140 1A. Ancestral SNPs:Z2886 1T, Z2679 1T, Z2727 1C, Z2850 1A, Y1962 4T, P40 1C, Z2747 1A, FGC2422 1C, CTS3506/Z2765 1A, FGC33327 1T, CTS11534 1A, Y1863 1T, L848 2C, FGC2433 1G, Y1950 1C, FGC2427 1C, Y1932 1A, Z2870 1T, S22865 1G, Z2806/CTS6765 1T.

    Car1 from "The genomic history of the Iberian Peninsula over the past 8000 years" Olade et al 2019, Science 363, 1230–1234; Derived I1 SNPs: Z2699 1C, Z2880 3A, Z2729 1T, Z2779 1C, CTS10338 1C, Z2885 1T, V5190/Z2742 1A, CTS11036/Z2863 1T, Z2730 1G, Z2720 1T, Z2887 1T, Z2847 1T, CTS1739 1G, Y1950 CGGA, Z2852 1T, CTS6022 1A, CTS4532 1A, Z2859 2A, Z2695 1T; Ancestral I1 SNPs: L840 1C, FGC7747 1T, Z2718 2C, Z2679 2T, Z2727 3C, CTS6140 1T, Y1872 1G, Z2747 1A, CTS11042 2T, Z2826 1T, Z2858 1G, V5203 2G, CTS11534 1A, Y1863 3T, CTS8394 1G, Z2825 1G, L848 1C, CTS9486 1G, Z2705 1C, Z2790 1G, Y1860 1A, Y1871 1C, FGC2427 1C, L764 1C, L1439 2C 1G (ambiguous, but likely ancestral), Z2870 1T, CTS9487 1G, Z2775 1G, CTS9368 2T, Y1876 1T,Z6116 1A, Z2832 2G, CTS7386 1T, CTS8708 1T, FGC2462 1C - also one SNP that has a mutation at the described position for FGC2445, but to a different nucleotide (1A rather than T).
    I've checked beforehad the BAL051 results, unfortunately no SNPs that show up in both samples (SF11 and BAL051).
    But at least we have FGC7747, that is derived in SF11 and ancestral in Car1.

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    Quote Originally Posted by artemv View Post
    I've checked beforehad the BAL051 results, unfortunately no SNPs that show up in both samples (SF11 and BAL051).
    But at least we have FGC7747, that is derived in SF11 and ancestral in Car1.
    Both SF11 and BAL051 have a read for FGC2433 - SF11 has derived (1A), BAL051 has ancestral (1G). Although this doesn't contradict earlier/later since BAL051 is older than SF11.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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