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  #1  
Old 6th March 2017, 06:51 AM
Slithy Tove Slithy Tove is offline
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Phylotree question

Hi all,

Phylotree has, on occasion, a branch with a mutation listed but no subclade reference for the node.

See the attachment for an example.

In this case is phylo saying that T152C! is a back mutation present in subclades U5a1a1a, U5a1a1b, and U5a1a1h but not in U5a1a1c?

Or is it something different?

regards
Gavan
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Old 6th March 2017, 02:41 PM
GST GST is offline
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Quote:
Originally Posted by Slithy Tove View Post
In this case is phylo saying that T152C! is a back mutation present in subclades U5a1a1a, U5a1a1b, and U5a1a1h but not in U5a1a1c?
Yes, you interpreted this correctly. However, I don't think it is useful to include highly volatile markers like 152, 195, 16362, etc as unnamed branch point in the phylotree. There will be some people in U5a1a1a with C152T!! and some people in U5a1a1c with T152C! These markers might (or might not) have some value when you are looking at your closest matches, but they don't add much informational value to the phylotree. FTDNA includes these branch names in subclade assignments, and I think mostly just confuses people.

Gail
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Old 8th March 2017, 04:23 AM
Slithy Tove Slithy Tove is offline
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Quote:
Originally Posted by GST View Post
highly volatile markers ... don't add much informational value to the phylotree.
Gail
Thanks, Gail.

Is this why Phylotree says "309.1C(C), 315.1C, AC indels at 515-522, A16182c, A16183c, 16193.1C(C) and C16519T/T16519C were not considered for phylogenetic reconstruction"?

Gavan
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Old 10th March 2017, 11:22 AM
GST GST is offline
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Quote:
Originally Posted by Slithy Tove View Post
Thanks, Gail.

Is this why Phylotree says "309.1C(C), 315.1C, AC indels at 515-522, A16182c, A16183c, 16193.1C(C) and C16519T/T16519C were not considered for phylogenetic reconstruction"

Yes - in general, these are the most volatile of the hyper variable region (HVR) markers. But other markers can also be very volatile, for example, in some haplogroups 16093 seems to be much less stable than 16519. When you see large variability in an HVR marker, I would discount the value of that marker. Some HVR markers can be much more "hyper" than others.
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