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Thread: Basal Haplogroup R classification for 24,000-year-old individual (MA-1), from Malíta

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    Basal Haplogroup R classification for 24,000-year-old individual (MA-1), from Malíta

    Here are the details behind the grouping of basal Y-haplogroup R for the Ma'lta sample:

    Y chromosome haplogroup of MA-1

    Due to low depth-of-coverage of the MA-1 individual (1.5X on 5.8 million bases),
    genotyping at each site on the Y chromosome was performed by selecting the allele
    with the highest frequency of bases with a base quality of 13 or higher. Additionally,
    a multi-fasta file was generated from the variable positions on the Y chromosomes
    available from 24 Complete Genomics public genomes. SNPs were filtered for
    quality (using VQHIGH as the threshold, as defined by Complete Genomics), with
    tri-allelic positions excluded and only those Y chromosome regions determined as
    being phylogenetically informative being used2. This yielded a final dataset of 22492
    positions. MA-1 Y chromosome data was then included, and MEGA phylogenetic
    software was used to construct a Neighbor Joining (NJ) tree with default parameters
    (Figure SI 5a). MA-1 is placed as a basal lineage to hg R. Phylogenetically
    informative positions and their state in MA-1 were then determined to confirm the
    placement of MA-1 on the tree. In the course of this analysis, the original dataset was
    severely pruned. Non-informative positions, including those with more than four Ns
    in the public dataset, were excluded (633 positions). Moreover, the following
    positions were also excluded which were 1) in reference state in all individuals
    including MA-1 (7172 positions); 2) N in MA-1 and either N or reference state
    among the rest of the individuals (9682 positions); 3) ‘N-ref’ – those with only N or
    reference state among all individuals (586 positions) and ‘N-alt’ - positions with
    alternative alleles, but difficult to classify (11 positions); 4) reference specific (79
    positions); and, 5) recurrent (28 positions). This resulted in 4301 positions being
    retained that were classified according to their hg affiliations. Among those
    phylogenetically informative positions, 1889 non-N positions were retrieved from
    MA-1. When counting from the split of hg DE on the unrooted phylogenetic tree,
    MA-1 is determined to be carrying the derived allele in 183 sites and the ancestral
    allele in 1706 sites. The position of MA-1 on the phylogenetic tree is established by
    the state of the 313 basal mutations separating hgs DE and R, where MA-1 has 143
    informative positions. Of these, 138 are in the derived and 5 in the ancestral state,
    placing MA-1 as a lineage basal to hg R. With only a few exceptions characterized
    below, all other informative positions in MA-1 are in the ancestral state, further
    supporting the phylogenetic positioning of MA-1 on the tree.
    Among the derived markers in the final dataset only a few (11) mutations were
    detected that are likely to be false positives based on the phylogenetic analysis, where
    it is assumed that recurrent mutation is less likely than a sequencing error. One
    position among the 35 private to MA-1 is characteristic of a distant hg – namely
    C3c14. Based on current data, 10 additional phylogenetically non-concordant
    positions in MA-1 were found – 1 position for hgs E, G, Q, R1b, R1 each, 2 defining
    positions for hg I and 3 private mutations for R1b individuals (shown in red on Figure
    SI 5a). Additionally, among the mutations originally excluded (the reference-private
    mutations), two positions were found where MA-1 is in derived state.


    Figure SI 5a An unrooted Neighbor Joining tree of 24 Y chromosomes from the
    publicly available Complete Genomics dataset1 and MA-1. The tree is based on
    22492 Y chromosome SNPs and constructed with MEGA using default parameters.
    MA-1 is ancestral to haplogroup R, based on 5 sites that are in ancestral state
    compared to all other individuals belonging to this haplogroup. The phylogenetic
    analysis of sites underlying the tree resulted in a pruned dataset of 4301 informative
    positions. The derived (d) or ancestral (a) states of called (non-N) sites in the MA-1 Y
    chromosome are noted on the edges of the tree. The overall number of informative
    sites at those edges is shown in parentheses. For example, “(232) MA-1: 109a, 1d,
    122N ” on the hg Q edge means that out of the 232 positions in derived state at this
    edge, 109 were ancestral, one derived and 122 N in MA-1.
    Last edited by R.Rocca; 11-20-2013 at 07:43 PM.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    Where is the data from?

    [Added] It's OK. I see you announced the paper on another thread. http://www.nature.com/nature/journal...ture12736.html
    Last edited by Jean M; 11-20-2013 at 06:57 PM.

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    Quote Originally Posted by Richard A. Rocca View Post
    Here are the details behind the grouping of basal Y-haplogroup R for the Ma'lta sample:
    MA-1 is placed as a basal lineage to hg R2,4. Phylogenetically
    informative positions and their state in MA-1 were then determined to confirm the
    placement of MA-1 on the tree.
    Based on current data, 10 additional phylogenetically non-concordant
    positions in MA-1 were found – 1 position for hgs E, G, Q, R1b, R1 each, 2 defining
    positions for hg I and 3 private mutations for R1b individuals (shown in red on Figure
    SI 5a).
    Please explain! Is it R2 or R1b?

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    Quote Originally Posted by Joe B View Post
    Please explain! Is it R2 or R1b?
    If I understand correctly it looks like a basal branch of R1b1 or R1b, and if I am looking at the tree correctly. Hopefully others can chime in with additional input or correct me why this is not so.

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    Quote Originally Posted by Joe B View Post
    Please explain! Is it R2 or R1b?
    Sorry, when I copy and pasted the test, the references to other sudies went from super-script to normal. It is now fixed...it is basal R, not R2.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    Quote Originally Posted by Richard A. Rocca View Post
    Sorry, when I copy and pasted the test, the references to other sudies went from super-script to normal. It is now fixed...it is basal R, not R2.
    Looks R(xR2) right? Pre-R1?

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    Basal R = R*.

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    Quote Originally Posted by parasar View Post
    Looks R(xR2) right? Pre-R1?
    Correct. It looks like the sample has some false positives in some positions, but there are more than enough positives (derived) to make him R+ and enough negatives (ancestral) to make him R1- and R2-.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    http://www.nature.com/nature/journal...re12736-s1.pdf

    10 additional phylogenetically non-concordant positions in MA-1 were found – 1 position for hgs E, G, Q, R1b, R1 each, 2 defining
    positions for hg I and 3 private mutations for R1b individuals
    Do we know why R1 is phylogenetically non-concordant?
    Last edited by parasar; 11-20-2013 at 07:35 PM.

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    Quote Originally Posted by parasar View Post
    http://www.nature.com/nature/journal...re12736-s1.pdf

    Do we know why R1 is phylogenetically non-concordant?
    If I am reading the image legend correctly, it looks like it is non-concordant because, while a single R1b SNP was derived, all other R1 defining mutations with reads between it and basal R were ancestral.
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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