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Analysis of Huang et al.
Topic Started: Jun 21 2007, 11:18:37 PM (306 Views)
custodian
Unregistered

From your own findings which I saved,

Huang's results:
hts 1, 13: M9, M89, M117, M122, M134, M175, M214, 021354, 25 men.
hts 3, 9: M9, M89, M122, M134, M175, M214, 021354, 21 men.
hts 4, 6: M9, M89, M122, M175, M214, LY1, 21 men.
hts 17, 21: M9, M89, M122, M175, M214, 021354, 5 men.
hts 18, 33: M7, M9, M89, M122, M175, M214, 021354, 4 men.
hts 24, 29: M7, M9, M89, M122, M175, M214, LY1, 021354, 2 men.
hts 34, 35: M9, M89, M122, M175, M214, LY1, 021354, 2 men.


Note:
-While Huang et al. shows M134 as derived from Line1, they have not been found together in other studies. In Hammer et al. 2006, for example, M134 and Line1 are separate branches under O3/M122.

-The conclusions lead to more questions then answers:
1. In either of the scenarios, 2 things have to occur (in red). And it's not likely for any one of them. If Line1 was found in other non-O3a lineages, then Scenario 1 would earn some credit, but since these weird repeats seem to only occur in O3a, something is amess.

2. Why would Line1 keep recurring and deleting in the O3 lineage and not anywhere elese?

Santos [/I]. tested Line1 in 633 y-chromosomes from all around the world and was found in 15 Asians. For this reason it might have been considered a reliable marker by some researchers (e.g. Hammer and Karafet). But as Santos et al. explained, there are two methods of detection: one being apparently more reliable than the other. That could be one potential error source for researchers.

And why did it mutate back since a mutation of the same allele in exactly the same haplogroup is statistically less likely than the mutation of this allele in countless other haplogroups?

2. If given that Line is mentioned as an unreliable marker, than Scenario 1 is most likely.

3. 002611 is mentioned as a reliable point mutation (comapred to Line1) in Nonaka, and it's safe to assume that M7 and 021345 are too.

-----------------------------------------------------------------------------------------------

update:
Quote:
 
- Line1+, 002611- (men in five populations, Nonaka et al.)
- Line1+, 002611+ (men in seven populations, Nonaka et al.)
- Line1-, 002611+ (men in seven populations, Nonaka et al.)

Adding 002611+ into the mix, assuming it is a reliable point mutation as Nonaka claims, it would fall under Line1 as an immediate branch exclusive of the other branches in the below scenarios.

black man
May 3 2007, 09:07 PM
Huang's "O3" samples:

see also http://z6.invisionfree.com/orient/index.php?showtopic=1268

hts 1, 13: M9, M89, M117, M122, M134, M175, M214, 021354, 25 men.
hts 3, 9: M9, M89, M122, M134, M175, M214, 021354, 21 men.
hts 4, 6: M9, M89, M122, M175, M214, LY1, 21 men.
hts 7, 8: M9, M89, M122, M175, M214, 14 men.
hts 17, 21: M9, M89, M122, M175, M214, 021354, 5 men.
hts 18, 33: M7, M9, M89, M122, M175, M214, 021354, 4 men.

Given that 021345 occurs with and without M134, it would seem that it is upstream from M134.

>021354
>>M134
>>>M134, M117


Given that Line1 occurs without 021345 and vice versa, it seems that they are parallel branches.

>Line1
>021345


Given that 021345 occurs with or without M7, it seems that 0212345 is upstream from M7. Given that M134 does not occur with M7 and vive versa, it seem they are parallel branches below 021345.

>021345
>>M7
>>M134
>>>M134, M117


The consolidated tree up to this point would be

>Line1

>021345
>>M7
>>M134
>>>M134, M117


-----------------------------------------------------------------------------------------------


So far, no problem, but then we run into trouble:
Quote:
 
hts 24, 29: M7, M9, M89, M122, M175, M214, LY1, 021354, 2 men.
hts 25, 32: M9, M89, M121, M122, M175, M214, 2 men.
hts 34, 35: M9, M89, M122, M175, M214, LY1, 021354, 2 men.


Given that Line1 suddenly appears with 021345 and 021345+M7, we have to assume A), B ), or C).


-----------------------------------------------------------------------------------------------


A) Line1 occurs as an insertion and then 021345 is derived from it, but than Line1 becomes a deletion, in which case you'd get 021345 without Line1 and the appearance of it as a parallel branch to the Line1 branch. In this case, Line1 could've occurred as a deletion twice, once with 021345 and once with 021345 + M7, or Line1 could be occur as a deletion once, in which case M7 is recurrent also.

Scenario 1a:
>Line1
>>021345
>>>021345 + Line del
>>>M7
>>>>M7 + Line1 del
>>M134
>>>M134, M117


Scenario 1b:
>Line1
>>021345
>>>021345 + Line del
>>>>021345 + Line1 del + M7

>>>M7
>>M134
>>>M134, M117[/b


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B ) Or Line1 recurred twice, once with 021345 and once with 021345 + M7:

>021345
>>021345 + Line1
>>M7
>>>M7 + Line1


The consolidated tree would be,

Scenario 2:
>Line1

>021345
>>021345 + Line1
>>M7
>>>M7 + Line1
>>M134
>>>M134, M117


Or Line1 could have recurred only once in this case, and then M7 is also a recurrence.

Scenario 3:
>Line1

>021345
>>M7
>>M134
>>>M134, M117
>>021345 + Line1
>>>021345 + Line1 + M7



-----------------------------------------------------------------------------------------------


C) 021345 and M7 are recurrent mutations. If 021345 is the recurrent mutation, then M7 is also recurrent and a derivative of 021345 + Line1.

Scenario 4:
>Line1
>>021345
>>>021345 + M7


>021345
>>M7
>>M134
>>>M134, M117


-----------------------------------------------------------------------------------------------

Alternative phylogenies with "conventionalized" names:

Scenario 1a:
>O3a3 - Line1
>>O3a3a - 021345
>>>O3a3a1 - 021345 + Line del
>>>O3a3b - M7
>>>>O3a3b1 - M7 + Line1 del
>>O3a3c - M134 (O3a5 in ISOGG tree, formerly O3d)
>>>O3a3c1 - M134, M117 (O3a5a in ISOGG tree, formerly O3d1)

Scenario 1b:
>O3a3 - Line1
>>O3a3a - 021345
>>>O3a3a1 - 021345 + Line del
>>>>O3a3a1a - 021345 + Line1 del + M7

>>>O3a3a1b - M7
>>O3a3b - M134 (O3a5 in ISOGG tree, formerly O3d)
>>>O3a3b1 - M134, M117 (O3a5a in ISOGG tree, formerly O3d1)

Scenario 2:
>Line1

>021345
>>021345 + Line1
>>M7
>>>M7 + Line1
>>M134 (O3a5 in ISOGG tree, formerly O3d)
>>>M134, M117


Scenario 3:
>Line1

>021345
>>M7
>>M134 (O3a5 in ISOGG tree, formerly O3d)
>>>M134, M117
>>021345 + Line1
>>>021345 + Line1 + M7


Scenario 4:
>Line1
>>021345
>>>021345 + M7


>021345
>>M7
>>M134 (O3a5 in ISOGG tree, formerly O3d)
>>>M134, M117


-----------------------------------------------------------------------------------------------

I dunno how much you can trust Huang. Here's 2 mistakes I found in examining Haplogroup 1:

1. In table 2, M9 (G to C) is a mistake as it is written C/G, unless they put the mutation in front, but that would contradict with their M7 info, in which they put the mutation in the back.
2. M119 is defined by A to C mutation; nowhere is T involved, but a T shows up in Table 3 for M119.

-----------------------------------------------------------------------------------------------
Haplogroup 1: K-M9 positive,

M7(C to G) negative http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=3898
M9 (C to G) positive
M88 (A to G) negative
M89 (T to C) negative
M95 (C to T) negative
M111 (TT to del TT) negative
M117 (ATCT to del ATCT) positive
M119 (A to C) ---> T in Huang's Table 3; mistake
M121
M122
M134
M175
M214
Line1 (- to +) negative
MSY2
RPS4Y
SRY
IMS-JST 164520
IMS-JST 021354
IMS-JST 003305

-----------------------------------------------------------------------------------------------

Case# 24: Line1 positive, IMS-JST 021354 positive
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black man
The Right Hand
[ *  *  * ]
custodian
Jun 21 2007, 11:18:37 PM
021345
Occurs by far more than once in your post. That's why I mention it. It's 021354 or, since Hammer et al. published their results, P201.

In "An updated tree of Y chromosome Haplogroup O and revised phylogenetic position of mutations P164 and PK4" Yan Shi, Li Hui et al. introduced some new upstream markers.

Looks like that, now (according to the tree of Yan Shi et al. and some data not from Yan Shi et al.):
- L127, KL1, KL2*: wide distribution at least among Han
---- M121: found in relatively many (though at a low frequency) in Taiwan Han by Lin Yi-Wen et al. (2007)
---- M164: absent from Wuhan Han (Huang et al. 2006); in Yan's study there is also nobody with the M164+ mutation; I don't know (or forgot) whether Ivan Shim already resolved the relation to 002611 via private testing; could be an "inland" marker because Lin et al. didn't find it in their Taiwanese large-scale study ==> UPDATE: Mirabal et al. (2011) reported having found it in a Samoan from Tutila. If I'm not mistaken, not even Cai Xiaoyun et al. reported having found it in their (more than 700?!) AA and HM samples from Laos.
---- 002611: a very common mutation in China according to Yan Shi et al. and in Japan according to Nonaka et al.: includes both LY1+ and LY1- individuals
- P201 (021354)*: low percentage in comparison to the M134+ sub-branch in China (Yan Shi 2011) but relatively high percentage in Japan (Nonaka 2007)
---- M159: M159: includes LY1+ individuals only
---- M7: includes both LY1+ and LY1- individuals
---- P164*: "southern Chinese" sample size of Yan Shi et al. too small for an inter-regional comparison
---------- M134...
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