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.
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Originally Posted by Richard A. Rocca
