Results 1 to 10 of 10

Thread: Francalacci 2015 - What went wrong?

  1. #1
    Legacy Account
    Posts
    7,362
    Sex
    Location
    United Kingdom
    Nationality
    British
    mtDNA (M)
    H

    United Kingdom

    Francalacci 2015 - What went wrong?

    Francalacci 2013* was a study of Y-Chromosome Phylogeny, based on modern samples from Sardinia. No ancient DNA was included, but it was a good example of what can be done with modern DNA alone, by detecting the deep phylogeny. It estimated times of arrival in Sardinia of various haplogroups, by noting the number of Sardinian-specific mutations. As they said "The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7700 years ago."

    So they appeared aware that Sardinia was settled in the Neolithic by makers of Cardial Ware pottery.

    They made sensible deductions:

    Haplogroup I ... is of special interest because it is mostly represented by the I2a1a clade, identified by the M26 marker, which is at high frequencies in Sardinia but is rare or absent elsewhere. .... To estimate points of divergence between Sardinian and continental clades, we sequenced two samples from the Basque Country and northern Italy, belonging to haplogroup I .... The Basque individual separates from the basal position of the I2a1a branch that encompasses 11 Sardinian individuals. The northern Italian sample, instead, most likely reflecting the last step of I2a1 lineages before their arrival in Sardinia, is at the basal point of most of the remaining I2a1a samples. Considering two other basal lineages encompassing only Sardinian samples, we can infer that when the I2a1a sub-haplogroup entered Sardinia, it had already differentiated into four founder lineages that then accumulated private Sardinian variability.

    Two other founder clades show similar divergence after entry into the island: one belonging to haplogroup R1b1c (xV35) (whose differentiation is identified contrasting the Sardinian data with the ISOGG and 1000 Genome data) ...
    Now we have the paper revised**, one can scarcely say updated, since it represents a falling back to the bad old days.

    I2a1a-M26... In agreement with previous observations, this ... subhaplogroup is by far the most common in Sardinia. Still, the distribution of I2a1a-M26 in Europe, and in particular the rare but constant presence in the Iberian Peninsula, with significant occurrence in Basques, suggests marking refuges during the last glaciation.
    We have this howler:

    The R1a1a-M417 subclade ... has its maximum occurrence in Eastern Europe, with frequencies over 50% among Slavic people. Its subclade R1a1a1b1a1 (formerly R1a1a7)-M458, present in our sample in 6 of 15 individuals ..., has been linked to the spread of Bronze Age horsemen, associated with the Andronovo culture from the Central Asian steppe
    for which piece of ignorance they cite Keyser 2009, who did not test for M458 (now recognised as a Slavic marker). We now have Sintashta samples which are R1a-Z93, as expected.

    Is anyone thinking of submitting a correction?


    *Paolo Francalacci et al., Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny, Science, vol. 341 (2013), pp. 565-569.
    **Paolo Francalacci et al., Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample, BMC Research Notes 2015, 8:174.
    Last edited by Jean M; 06-28-2015 at 04:47 PM. Reason: Typo.

  2. The Following 7 Users Say Thank You to Jean M For This Useful Post:

     ADW_1981 (06-28-2015),  Agamemnon (06-28-2015),  GailT (06-28-2015),  Krefter (06-28-2015),  Michał (06-28-2015),  N21163 (06-28-2015),  Tomenable (03-01-2016)

  3. #2
    Registered Users
    Posts
    1,950
    Sex
    Omitted

    I thought we were at the point where with any study on modern phylogeny, the setup was this...
    1) Abstract/Introduction
    2) Materials/Methods
    3) Data/Supplementary info
    4) Conclusion(Comedy)

    You've never heard of wrapping up a speech with a joke?

  4. #3
    Gold Class Member
    Posts
    2,718
    Sex

    Although YFull's haplotree contains very few of the Sardinian samples, the subtree for I-Z105 suggests that the Sardinian variety of I-M26 diverged from non-Sardinian roughly 4800 years ago.

    The geographical origin of R-M458 is not fully settled, although the two singleton cases surrounding it (R-PF6155* and R-M458*) are both Polish. Its immediately downstream clade, R-Y2604 (TMRCA 4500 ybp), quickly divided into two tribes:
    - CTS11962 barely survived for 1000 years, then divided into tribes YP515 and L1029 (3500 years ago), each of which barely survived for another 1000 years before expanding about 2500 ybp
    - L260 barely survived for 2000 years before starting to expand about 2500 ybp
    Last edited by lgmayka; 06-28-2015 at 03:04 PM.

  5. The Following 5 Users Say Thank You to lgmayka For This Useful Post:

     Agamemnon (06-28-2015),  Jean M (06-28-2015),  Krefter (06-28-2015),  Michał (06-28-2015),  vettor (06-28-2015)

  6. #4
    Registered Users
    Posts
    5,789
    Sex
    Location
    Australia
    Ethnicity
    Italian Alpine
    Nationality
    Australian and Italian
    Y-DNA (P)
    T1a2b- SK1480
    mtDNA (M)
    H95a
    Y-DNA (M)
    R1b-S8172
    mtDNA (P)
    T2b17

    Australia Italy Veneto Friuli Italy Trentino Alto Adige Italy Ladinia Austria Tirol
    Quote Originally Posted by Jean M View Post
    Francalacci 2013* was a study of Y-Chromosome Phylogeny, based on modern samples from Sardinia. No ancient DNA was included, but it was a good example of what can be done with modern DNA alone, by detecting the deep phylogeny. It estimated times of arrival in Sardinia of various haplogroups, by noting the number of Sardinian-specific mutations. As they said "The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7700 years ago."

    So they appeared aware that Sardinia was settled in the Neolithic by makers of Cardial Ware pottery.

    They made sensible deductions:



    Now we have the paper revised**, one can scarcely say updated, since it represents a falling back to the bad old days.



    We have this howler:



    for which piece of ignorance they cite Keyser 2009, who did not test for M458 (now recognised as a Slavic marker). We now have Sintashta samples which are R1a-Z93, as expected.

    Is anyone thinking of submitting a correction?


    *Paolo Francalacci et al., Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny, Science, vol. 341 (2013), pp. 565-569.
    **Paolo Francalacci et al., Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample, BMC Research Notes 2015, 8:174.
    As with ALL papers from the past, present and in the future...........all will have some errors...........some errors, does not make a bad paper. There are always many results still valued in some of these past "erred" papers.


    Lets not go down the Goiello path of.......... "rip the paper into a million pieces" syndrome ..............we are better than this.
    Last edited by vettor; 06-28-2015 at 06:35 PM.


    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-Y33791 ydna
    Great grandmother paternal side = T1a1e mtdna

  7. The Following 2 Users Say Thank You to vettor For This Useful Post:

     Gravetto-Danubian (03-01-2016),  Krefter (06-28-2015)

  8. #5
    Registered Users
    Posts
    5,453
    Sex
    Location
    Poland
    Ethnicity
    Polish
    Y-DNA (P)
    R1b-Z2552
    mtDNA (M)
    W6a

    Poland European Union Poland Pomerania
    Sardinia was part of the Vandal-Alan North African realm in years 456 to 534 AD.

    Francalacci et al. 2013, tested 1204 Sardinian males for Y-DNA, among them these 21:

    - 6 samples of R1a-M458
    - 5 samples of R1a-Z280
    - 4 samples of R1a-Z93
    - 2 samples of I2a-M423
    - 2 samples of I1-M253
    - 2 samples of R1b-U106

    As for other types of R1b-M269 (apart from 2 samples of U106):

    - 10 samples of R1b-M269*
    - 9 samples of R1b-L23*
    - 3 samples of R1b-L151*
    - 25 samples of R1b-P312*
    - 4 samples of R1b-DF27
    - 2 samples of R1b-L21
    - 2 samples of R1b-L513
    - 128 samples of R1b-U152

    In total 183 samples, including 128 of U152.

    Other haplogroups in that sample of 1204 Sardinians:

    I2a1a - 465
    G2a - 131
    E1b1b1 - 126
    J2 - 98
    J1c - 63
    R1b1c - 29
    T - 28
    I2c - 11
    I2a2a - 10
    R2a1 - 10
    L - 8
    A1b1b2b - 7
    F3 - 7
    E1a1 - 6
    Q1a3c - 1

    In total exactly 1000. Plus 183 + 21 = 1204.
    Last edited by Tomenable; 03-01-2016 at 12:14 AM.

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

     kingjohn (01-10-2017)

  10. #6
    Junior Member
    Posts
    2
    Sex
    Location
    US
    Ethnicity
    French
    Nationality
    US
    Y-DNA (P)
    I2a1a1 I-M26
    mtDNA (M)
    H5

    France Spain United States of America
    Quote Originally Posted by lgmayka View Post
    Although YFull's haplotree contains very few of the Sardinian samples, the subtree for I-Z105 suggests that the Sardinian variety of I-M26 diverged from non-Sardinian roughly 4800 years ago.
    Below I-Z105
    I-Z99 CTS10530 * Z126 * CTS787+25 SNPs formed 5400 ybp, TMRCA 3500 ybp
    has also been found in Sardinia (PF4183).
    The divergence would therefore be much more recent than Francalacci anticipated.
    I tested positive for I-Z106 under I-Z99. My paternal lineage up to the 1600 is from the south west of France in the vallÚe dĺOssau of the PyrÚneans mountains in SÚvignacq-Meyracq in BÚarn next to the Basque country.
    Based on FTDNA results, Z106 has been found also in several Basque people from Viscaya, and one from Pilsdon, Dorset in South West England.
    More questions than answers so far.

  11. #7
    Banned
    Posts
    380
    Sex
    Location
    Caen
    Ethnicity
    81% FRA+13% ITA+6% SPA
    Nationality
    French
    Y-DNA (P)
    R1b U152 Z56 BY3538
    mtDNA (M)
    J2a1a1, H13a1a1

    France New Caledonia Italy Spain Luxembourg Switzerland
    I have one question, How many Y snps were analyzed by Francalacci in his paper ? (Big Y analysed 8 millions snps if i'm not mistaken) Because I'm supposed to share 5 private SNPs with this guy ERS257070ITA [IT-CA] on YFULL.


    My other question but related to Yfull this time, is I appear on the Z56 tree but as Z56* with my Y-cousin ERS257070ITA [IT-CA], aren't we supposed to form a new clade ? (well my results aren't completed, maybe that's why)
    Last edited by Il PapÓ; 01-10-2017 at 07:43 PM.

  12. #8
    Gold Class Member
    Posts
    2,718
    Sex

    Quote Originally Posted by Il PapÓ View Post
    well my results aren't completed, maybe that's why
    Yes. After your results are substantially complete and you pay YFull's fee, the next version of the tree will show your new subclade.

  13. #9
    Registered Users
    Posts
    5,789
    Sex
    Location
    Australia
    Ethnicity
    Italian Alpine
    Nationality
    Australian and Italian
    Y-DNA (P)
    T1a2b- SK1480
    mtDNA (M)
    H95a
    Y-DNA (M)
    R1b-S8172
    mtDNA (P)
    T2b17

    Australia Italy Veneto Friuli Italy Trentino Alto Adige Italy Ladinia Austria Tirol
    Quote Originally Posted by Il PapÓ View Post
    I have one question, How many Y snps were analyzed by Francalacci in his paper ? (Big Y analysed 8 millions snps if i'm not mistaken) Because I'm supposed to share 5 private SNPs with this guy ERS257070ITA [IT-CA] on YFULL.


    My other question but related to Yfull this time, is I appear on the Z56 tree but as Z56* with my Y-cousin ERS257070ITA [IT-CA], aren't supposed to form a new clade ? (well my results aren't completed, maybe that's why)
    All yFull noted "paper" samples starting with either ERS or HG , will only form a new clade if a person's Ftdna sample matches is found..........

    I do not see an issue here


    My Path = ( K-M9+, TL-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-Y33791 ydna
    Great grandmother paternal side = T1a1e mtdna

  14. #10
    Banned
    Posts
    380
    Sex
    Location
    Caen
    Ethnicity
    81% FRA+13% ITA+6% SPA
    Nationality
    French
    Y-DNA (P)
    R1b U152 Z56 BY3538
    mtDNA (M)
    J2a1a1, H13a1a1

    France New Caledonia Italy Spain Luxembourg Switzerland
    Quote Originally Posted by vettor View Post
    All yFull noted "paper" samples starting with either ERS or HG , will only form a new clade if a person's Ftdna sample matches is found..........

    I do not see an issue here
    There's no issue, I just wanted to be sure, why all the ................. ? and what about Yelite sample, they can't match ERS or HG sample ?


    Also I'm still curious to know how many snps Francalacci tested ? Couldn't find any answer.
    Last edited by Il PapÓ; 01-10-2017 at 08:17 PM.

Similar Threads

  1. Am I doing something wrong?
    By punk_knitter in forum Forum Support
    Replies: 8
    Last Post: 07-12-2017, 03:25 AM
  2. Replies: 0
    Last Post: 05-15-2015, 08:41 AM
  3. Karmin 2015 got M458 wrong
    By lgmayka in forum R1a-Z283
    Replies: 0
    Last Post: 03-17-2015, 03:51 AM
  4. U152 in Sardinia - Francalacci et al. 2013
    By R.Rocca in forum R1b-U152
    Replies: 39
    Last Post: 11-23-2013, 07:25 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
  •