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Archiver > GENEALOGY-DNA > 2013-08 > 1376418748


From: Vince Tilroe <>
Subject: Re: [DNA] New results for TMRCA of Y-Haplogroups - based ofComplete Genomics data
Date: Tue, 13 Aug 2013 12:32:28 -0600
References: <CAOMvN50n8ym+z4uh_=7F3J0wXDQZO0znSuFZ2=17OMa98aWRng@mail.gmail.com><5209AE58.4010100@earthlink.net>
In-Reply-To: <5209AE58.4010100@earthlink.net>


In most cases, the phylogenetic root is implied by the inclusion of an
out-group. Unfortunately we have not found a viable out-group with
sufficient sequence data beyond A00 as yet, and even A00 itself is
insufficiently tested. However, from what we have, A00 as such has played
the role of the out-group, and has consequently but tentatively positioned
the Y-root ancestral to haplogroups A00 and A0.

We now have sequenced data at 50x coverage from a few members of
haplogroups G and R, as well as the NCBI reference sequence that is a
composite of both haplogroups G and R. The coverage spans slightly over 25
million bases of the Y-chromosome, but of those, several million bases were
filtered out during variant calling due to heterozygousity resulting from
inter-chromosomal and intra-chromosomal similarities.

My own sequence has provided a preliminary SNP candidate list of at least
45 SNPs positioned below R-U106 (after filtering), including L199.1. If
U106 is approximately 4500 years old, that implies one Y-SNP occurrence per
100 years. This rate is in roughly the same ball-park as a previous
preliminary estimate I and a co-author had made (but left unpublished)
during research of the Rocca et al (2012) R1b1a2 paper from the 1000
Genomes Project data, which studied dozens of genomes sequenced at 2x to 4x
coverage, belonging to haplogroup R-L11.

Getting comparable chrY sequence data from multiple members of haplogroups
A1, A0 and A00 will greatly assist in providing supporting evidence for or
against an implied homo sapiens Y-root ancestral to these haplogroups. As
Anatole says, we need data, not speculation.

Vince Tilroe

On 12 August 2013 21:56, Susan Hedeen <>wrote:

> There is a fundamental difference between a true phylogenetic tree based
> on actual data and a list labeled as the 2013 phylogenetic tree as in
> the ISOGG link below, as well as a diagram in representation as the wiki
> example.
>
> These representations may contain actual information; the information
> may and likely will change as more is determined. In regard to the
> actual by data interpretive phylo trees which I have looked at in the
> publications, I see no root...and I believe those trees are not rooted
> trees. Perhaps the difficulty in argument here has everything to do
> with how the concept of phylogenetic tree is defined by interpretation.
> To the best of my knowledge the root has not yet been determined; there
> are theories based on a multitude of investigations of certain data; but
> as far as I know, a root has not been specified beyond theory. Susan
> Hedeen
>


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