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Thread: The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe - Olalde

  1. #11
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    Quote Originally Posted by rafc View Post
    The first tab also gives the haplogroups, if you scroll left, the other tabs provide detailed calls.
    You just saved my sanity.

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  3. #12
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    Quote Originally Posted by Jean M View Post
    The list of samples, just giving location, is in Supplementary table 1. Supplementary table 2 gives the mtDNA haplogroup of the samples, and supplementary table 3 the Y-DNA haplogroups. In both of the latter tables, the samples are numbered. To find out which samples are which, you then have to find the number in Supplementary Information. What fun! Heaven knows how long it will take me to get all this data into my online tables.
    You can combine the three tables using an Index Match function so at least you only have to compare a table and the Supplementary Information.

    =IFERROR(INDEX(column to return a value from, (MATCH (lookup value, column to lookup against, 0))),"")
    For example, to copy over Derived SNPs in Table 3 to the matching ID in Table 1 make a new column header in Table 1 named Derived SNPs in Column X then past this into cell X2

    =IFERROR(INDEX(SupplementaryTable3!E:E,(MATCH(A:A, SupplementaryTable3!A:A,0))),"")
    then to fill the column with the same double click on the bottom right of cell X2

    then in order to have just the values in each cell - highlight the column, copy, right-click, past values

    You will now see the corresponding Derived SNPs for each sample in column X.

    You can do that for each column of data you want copied over into a single table

    so if you want copy over SNPs against rCRS then use the following in the 2nd cell of another column -

    =IFERROR(INDEX(SupplementaryTable2!F:F,(MATCH(A:A, SupplementaryTable2!A:A,0))),"")
    Last edited by ArmandoR1b; 05-10-2017 at 07:04 PM.

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  5. #13
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    Quote Originally Posted by Mikewww View Post
    This Beaker paper is using the ISOGG haplogroup labels. I found their citation in the paper. Here is the ISOGG tree for haplogroup R with all of the SNPs.
    https://isogg.org/tree/ISOGG_HapgrpR.html
    According to page 11 they are using version 11.110 (21 April 2016) so it will be similar to the 2016 tree available at https://isogg.org/tree/2016/ISOGG_HapgrpR16.html

    Y-chromosome analysis
    374 We determined Y-chromosome haplogroups for both new and published samples
    375 (Supplementary Information, section 3). We made use of the sequences mapping to 1240k Y376
    chromosome targets, restricting to sequences with mapping quality ≥30 and bases with quality
    377 ≥30. We called haplogroups by determining the most derived mutation for each sample, using
    378 the nomenclature of the International Society of Genetic Genealogy (http://www.isogg.org)
    379 version 11.110 (21 April 2016). Haplogroups and their supporting derived mutations can be
    380 viewed in Supplementary Table 3.
    381

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  7. #14
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    Quote Originally Posted by Bas View Post
    delete-data cannot be seen
    What are these?

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  9. #15
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    It seems there is a DF21 man, whose remains were found in Scotland.

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  11. #16
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    Quote Originally Posted by r_r_abril View Post
    It seems there is a DF21 man, whose remains were found in Scotland.
    That was the Raithlin sample which they incorporated into their data.

    As near as I can collect from their tables this is the list of L21 samples. The "Major SNP" column is my own add for readability and I listed their terminal SNP and where applicable in parentheses the equivalent SNP that we normally use within L21 to refer to that line.

    For clarity I should note because of equivalents that does NOT mean the SNP in parentheses is always positive in those samples, it just refers to the sample's branch. If the SNP in parentheses occurred after their lifetime it would naturally be negative in that person.

    ID Major SNP Date (95% CI) Location Country
    I2453 CTS8221 (DF13) 2289–2041 calBCE (3760±35 BP, Poz-83404) West Deeping Great Britain
    I2452 CTS8221 (DF13) 2277–1920 calBCE [2277–2030 calBCE (3735±35 BP, Poz-83405); 2195–1920 calBCE (3700±30 BP, Beta-444979)] Dairy Farm, Willington Great Britain
    I2445 CTS8221 (DF13) 2137–1930 calBCE (3650±35 BP, Poz-83407) Yarnton Great Britain
    I2447 CTS8221 (DF13) 2400–2040 BCE Yarnton Great Britain
    I2565 L21 2470–2140 calBCE (3829±38 BP, OxA-13562) Amesbury Down, Wiltshire Great Britain
    I3256 CTS8221 (DF13) 2204–2029 calBCE (3722±31 BP, SUERC-49483) Trumpington Meadows Great Britain
    I2457 L21 2480–2031 calBCE [2480–2280 calBCE (3890±30 BP, SUERC-36210), 2200-2031 calBCE (3717±28 BP, SUERC-69975)] Amesbury Down, Wiltshire Great Britain
    I3082 L21 1500–1390 calBCE (NZA-34643) Canada Farm, Sixpenny Handley, Dorset Great Britain
    I2568 CTS8221 (DF13) 2287–2039 calBCE (3755±35 BP, SUERC-4078) Scotland, Dryburn Bridge Great Britain
    I2653 S868 (L1066) 1500–1300 BCE Scotland, Longniddry, Evergreen Great Britain
    rath1.SG DF21 2026-1885 calBCE (3591±29 BP, UBA-8707) Rathlin Island, County Antrim Ireland
    rath2.SG CTS8221 (DF13) 2024-1741 calBCE (3539±54 BP, UBA-8705) Rathlin Island, County Antrim Ireland
    rath3.SG L21 1736-1534 calBCE (3354±28 BP, UBA-8706) Rathlin Island, County Antrim Ireland

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  13. #17
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    Equally important in terms of placing L21, here are the other P312 lines with the same translation (i.e. Major SNP column is my add):

    ID Major SNP Date (95% CI) Location Country
    I1390 P312 2566–2299 calBCE [2566–2524 calBCE (3910±35 BP, Poz-41227); 2489–2299 calBCE (3875±35 BP, Poz-41226)] Sierentz, Les Villas d'Aurele, Haut-Rhin France
    I1389 P312 2468–2278 calBCE [2481–2289 calBCE (3935±35 BP, Poz-41229); 2468–2278 calBCE (3925±30 BP, Poz-41228)] Sierentz, Les Villas d'Aurele, Haut-Rhin France
    I1382 P312 2435–2136 calBCE (3805±35 BP, GrA-4468) Mondelange, PAC de la Sente, Moselle France
    I3875 L2 2459–2242 BCE Villard France
    I2478 P312 2200–1930 calBCE (3671±40 BP, LTL-5035A) via Guidorossi, Parma Italy
    I4068 P312 2300–1900 BCE [from other dates of the same site] De Tuithoorn, Oostwoud, Noord-Holland The Netherlands
    I4069 P312 2188–1887 calBCE (3640±50 BP, GrA-6477) De Tuithoorn, Oostwoud, Noord-Holland The Netherlands
    I4073 P312 2196–1903 calBCE (3660±50 BP, GrA-15598) De Tuithoorn, Oostwoud, Noord-Holland The Netherlands
    I4074 P312 2278–1914 calBCE (3690±60 BP, GrA-15597) De Tuithoorn, Oostwoud, Noord-Holland The Netherlands
    I2365 L2 2465-2205 calBCE [2465-2205 calBCE (3858±32 BP, DeA-6762); 2465-2213 calBCE (3858±32 BP, DeA-7220)] Budapest-Békásmegyer Hungary
    I3599 P312 2300–2150 BCE Alburg-Lerchenhaid, Spedition Häring, Stkr. Straubing, Bavaria Germany
    I3589 L2 2300–2150 BCE Alburg-Lerchenhaid, Spedition Häring, Stkr. Straubing, Bavaria Germany
    I3597 L2 2300–2150 BCE Alburg-Lerchenhaid, Spedition Häring, Stkr. Straubing, Bavaria Germany
    E09569 L2 2397–2149 calBCE (3819±24 BP, MAMS-18949) Unterer Talweg 85 (Augsburg) Germany
    I4144 P312 2572–2512 calBCE (3955±35 BP, Poz-84553) Osterhofen-Altenmarkt Germany
    I0806 P312 2431–2150 calBCE (3824±25 BP, MAMS-22820) Quedlinburg Germany
    I1775 P312 1693–1600 calBCE (3344±27 BP, OxA-14308) Great Orme Mines, Llandudno, North Wales Great Britain
    I2566 P312 2210–2030 calBCE (3734±25 BP, NZA-32490) Amesbury Down, Wiltshire Great Britain
    I2602 P312 1900–1690 calBCE (3490±30 BP, SUERC-40290) Thanet, Kent Great Britain
    I2421 P312 1931–1756 calBCE (3524±28 BP, OxA-26256) Hasting Hill, Sunderland, Tyne and Wear Great Britain
    I2569 P312 2140–1916 calBCE (3650±40 BP, SUERC-5318) Scotland, Eweford Cottages Great Britain
    I2567 P312 2275–1884 calBCE [2131–1884 calBCE (3615±40 BP, SUERC-4072); 2275-2024 calBCE (3725±35 BP, SUERC-4083)] Scotland, Dryburn Bridge Great Britain
    Last edited by Dave-V; 05-10-2017 at 10:57 PM.

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  15. #18
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    Quote Originally Posted by Romilius View Post
    What are these?
    It was a desperate attempt to take screenshots from the excel file, of all the Y Haps with locations and dates, and paste them in a paint image, but in the end it just ended up being really blurry. Never mind

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  17. #19
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    Skimming through so far, these parts I found quite interesting:

    ''Among the different continental Beaker Complex groups analysed in our dataset, individuals from Oostwoud (Province of Noord-Holland, The Netherlands) are the most closely related to the great majority of the Beaker Complex individuals from southern Britain (n=14). They had almost identical Steppe ancestry proportions (Fig. 2a), the highest shared genetic drift(Extended Data Fig. 4b) and were symmetrically related to other ancient populations using f4- statistics (Extended Data Fig. 4a), showing that they are consistent with being derived from the same ancestral population without additional mixture into either group''

    (On British BA population turnover) ''In either case, our results imply a minimum of 93±2% local population turnover by the Middle Bronze Age''

    ''Derived alleles at rs12913832 (SLC45A2) and rs16891982 (HERC2/OCA2), which contribute to reduced skin and eye pigmentation in Europeans,dramatically increased in frequency during the Beaker and Bronze Age periods. Thus, the arrival of migrants associated with the Beaker Complex significantly altered the pigmentation phenotypes of British populations. However, the lactase persistence allele at SNP rs4988235 remained at very low frequencies in our dataset both in Britain and continental Europe, showing that the major increase in its frequency in Britain, as in mainland Europe,occurred in the last 3,500 years''

    ''We find that the great majority of Beaker Complex individuals outside of Iberia derive a large portion of their ancestry from Steppe populations whereas in Iberia, such ancestry is absent in all sampled individuals, with the exception of two (I0461 and I0462) from the Arroyal I site in northern Spain''

    ''A new finding that emerges from our analysis is that Neolithic individuals from southern France and Britain also show a greater affinity to Iberian Early Neolithic farmers than to central European Early Neolithic farmers (Fig. 2b), similar to previous results obtained in a Neolithic farmer genome from Ireland''

    And also U152-L2 in BB Hungary, which could mean something for Italic or Italo-Celtic

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  19. #20
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    Quote Originally Posted by Dave-V View Post
    Equally important in terms of placing L21, here are the other P312 lines with the same translation (i.e. Major SNP column is my add):

    [TABLE="width: 1094"]
    [TR]
    [TD]ID[/TD]
    [TD]Major SNP[/TD]
    [TD]Date (95% CI)[/TD]
    [TD]Location[/TD]
    [TD]Country[/TD]
    [/TR]
    [TR]
    [TD]I0806[/TD]
    [TD]P312[/TD]
    [TD]2431–2150 calBCE (3824±25 BP, MAMS-22820)[/TD]
    [TD]Quedlinburg[/TD]
    [TD]Germany[/TD]
    [/TR]
    I0806 (not one of the new samples from this paper) has previously been identified as DF27, by Rich Rocca. We expect that to be the case with a number of additional P312 samples from this paper, once the raw data are available for more tightly targeted subclade analysis.

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