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Ebizur
03-15-2015, 06:31 AM
According to Figure S21 of Monika Karmin et al. (2015), "A recent bottleneck of Y chromosome diversity coincides with a global change in culture," Japanese C1a1-M8 and European & Nepalese C1a2-V20 together comprise one branch (C1a-CTS11043) of what they have called C1'8-CTS824. The other primary branch of this haplogroup, C8-CTS5573, has been found in a Japanese individual sampled in Tokyo (JPT).

This should tend to support a hypothesis that a common ancestor of European & Nepalese C1a2-V20 has lived in Palaeolithic East Asia.

palamede
03-15-2015, 12:21 PM
According to Figure S21 of Monika Karmin et al. (2015), "A recent bottleneck of Y chromosome diversity coincides with a global change in culture," Japanese C1a1-M8 and European & Nepalese C1a2-V20 together comprise one branch (C1a-CTS11043) of what they have called C1'8-CTS824. The other primary branch of this haplogroup, C8-CTS5573, has been found in a Japanese individual sampled in Tokyo (JPT).

This should tend to support a hypothesis that a common ancestor of European & Nepalese C1a2-V20 has lived in Palaeolithic East Asia.
Why C8 and C1'8 ? I know C1 and C2 in the last ISOGG version only.

http://isogg.org/tree/ISOGG_HapgrpC.html
https://sites.google.com/site/compositeytree/c

Otherwise there were C1,C2, C3,C4, C5 and C6 in an old ISOGG version. and C1'8 would be a group within C.

lgmayka
03-15-2015, 02:15 PM
The caption of Figure S21 makes clear that the entire branch labeled C1'8 (CTS824) is based on poor sequencing and sheer speculation. Do you see the other branch labeled C2'7 (K30)? YF02502, YF02660, and YF02678, who all belong to C-V20, are all derived at K30 and ancestral at CTS824.

Actual high-quality sequencing is much more reliable than low-quality sequencing and speculation.

Ebizur
03-15-2015, 04:52 PM
The caption of Figure S21 makes clear that the entire branch labeled C1'8 (CTS824) is based on poor sequencing and sheer speculation. Do you see the other branch labeled C2'7 (K30)? YF02502, YF02660, and YF02678, who all belong to C-V20, are all derived at K30 and ancestral at CTS824.

Actual high-quality sequencing is much more reliable than low-quality sequencing and speculation.

"Figure S21. Refined topology of the Y chromosome haplogroup C1'7. Grey dashed lines denote known branches with no sequence data and branches based on low coverage sequencing."

So, judging from other data available to you, you think that all their "refined topology" (at least where it appears with grey dashed lines) is unreliable, right? That is good to know, but I wonder why the authors would have constructed such a complex, "refined" phylogenetic tree without valid evidence to support it.

Ebizur
03-15-2015, 09:57 PM
lgmayka, what is your opinion regarding their C5'9-K281 and C5'7-B66 branches? These have been drawn with solid black lines, so I presume that they have based this topology on data derived from high-quality sequencing.

Their C9-B68 and C7-B65 should account for at least some part of the C-M130(xM8, M38, M217) Y-DNA that has been found in Maritime Southeast Asia (especially central Indonesia). I find it interesting that the phylogeny suggests an origin in Maritime Southeast Asia with a subsequent spread of one branch (C5-M356) to South Asia and beyond.

lgmayka
03-15-2015, 11:57 PM
So, judging from other data available to you, you think that all their "refined topology" (at least where it appears with grey dashed lines) is unreliable, right? That is good to know, but I wonder why the authors would have constructed such a complex, "refined" phylogenetic tree without valid evidence to support it.
I was only referring to the dashed lines. The authors themselves caution us that the dashed lines are provisional at best and speculative at worst.

We have now arrived at the point in yDNA that we reached in mtDNA a few years ago: Citizen scientists are accumulating high-quality data faster than all the academics put together. We already take it for granted that most of the complete mtDNA sequences in the world originated from FTDNA; we must now recognize that FTDNA and FullGenomes have amassed more high-quality nearly-full-Y sequences than all other sources combined. YFull's sequence numbers show it has about 1600 user-submitted sequences, and we can be sure that there are hundreds if not thousands more that have not been submitted to YFull.

lgmayka
03-16-2015, 12:28 AM
lgmayka, what is your opinion regarding their C5'9-K281 and C5'7-B66 branches? These have been drawn with solid black lines, so I presume that they have based this topology on data derived from high-quality sequencing.

Their C9-B68 and C7-B65 should account for at least some part of the C-M130(xM8, M38, M217) Y-DNA that has been found in Maritime Southeast Asia (especially central Indonesia). I find it interesting that the phylogeny suggests an origin in Maritime Southeast Asia with a subsequent spread of one branch (C5-M356) to South Asia and beyond.
K281 is on the SNP list for YFull's C1b (http://yfull.com/tree/C1b/). But YFull has no user-submitted sequences in that clade, only South Asian samples from the 1000 Genomes project.

I share your interpretation of that part of the tree. But of course, haplogroup C itself splits into C-M217 and C-K29. C-M217 is mostly Central Asian (by the UNESCO definition) (http://en.wikipedia.org/wiki/Central_Asia#/media/File:Central_Asia_borders4.png).

It is intriguing that C-V20 was found in a Nepalese sample. More data will eventually give us answers.