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Y-Chromosome and mtDNA phylogeny
Topic Started: Jun 17 2006, 07:16:05 PM (1,991 Views)
Ibra
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Y-Chromosome: http://www.isogg.org/tree/index.html

mtDNA: http://www.phylotree.org/
Edited by Ibra, May 15 2009, 05:00:54 AM.
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Maju
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Great reference. We just need something half as good for MtDNA.

As a comment, I'm more and more fascinated by the apparent key role played by India/South Asia in the differentiation and early distribution of most lineages of Eurasia (F derivates). In a sense, we are all "Indians" (except A, B and DE lineages).
Chaos never died,
the Empire was never founded.
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Ibra
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Hi Mayu, the Y-chromosome tree seems to be constantly refined and in addition the changes are kept on record. mtDNA needs something like this, but so far it’s unavailable. As it turns out predefined mutations represented by variable names are mere twigs on much larger haplogroups. For example:

M9<E *Edit*: May or may not be true.
M8<C,Z
N1<I
N9<Y
N2<W
R0<H, V, PreHV etc
JT<J, T
U<U8<K

The human mtDNA in Eurasia is probably simpler than once thought. Here is East Eurasian mtDNA so far. European and Middle Eastern mtDNA will probably simplify as well.

http://rapidshare.de/files/21325488/Updati...logeny.pdf.html
Credit to Ren for this
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Maju
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Hey, cool! Tanks to both.

Guess that, as research efforts go ahead the correct mapping of all (or near all) human MtDNA across the planet will become more and more clear.

I was already pretty much aware of JT, K being a U subgorup and HV. That makes the European female lineages' map pretty much more simple: 3 main groups (all part of R), plus a copuple of minor NxR groups (I and X).
Chaos never died,
the Empire was never founded.
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Ibra
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Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock

New age estimates of mtDNA haplogroups adjusted for the effects of purifying selection. img file via Dienekes blog.

http://2.bp.blogspot.com/_Ish7688voT0/Sig86h9ZS6I/AAAAAAAABkI/GZ35t27okZo/s1600-h/mtdna_chronology.jpg

Attached is a calculator made by the author that adjusts for the effects of selection. Simply insert the rho value and optional standard error.
Attached to this post:
Attachments: mtDNA_Calculator.xls (33.5 KB)
Edited by Ibra, Jun 5 2009, 10:14:25 PM.
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manju
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So N is older than M? Again this study also says M in East Asia is older than India. I think that will weaken Coastal Migration Theory.
Edited by manju, Jun 6 2009, 03:23:53 AM.
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ren
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N is definitely older than M. It was established in SW Asia and produced R possibly before M came into existence. The profusion of M lineages is probably due to the opportunity to expand once it got to South Asia.

I don't know if I can believe M is older in East Asia than in South Asia. But it's posible that M did go through Central Asia. I was against the idea before because we don't find M in Europe, as woudl be expected if M expanded in Central Asia, but it seems that NOP also didn't expand directly into Europe but was via SW Asia. The Siberian (too cold) and Khazakh steppe passage (no caves) seems to be too cold and insurmountable for early Moderns.

So, now a Central Asian path into East Asia for some M, N and R is at least possible.
Edited by ren, Jun 9 2009, 02:58:00 AM.
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Ibra
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Quote:
 
Again this study also says M in East Asia is older than India.

There is an explanation for the lower age estimates. According to (Kong et al. 2006),

“The ages of macrohaplogroup M in India, Southeast Asia, East Asia, and Oceania are displayed in table 1. With the exception of M in India, the estimated ages are not significantly different and match the postulated age (60 x 103 to 70 x 103 years) of the three Eurasian founder types (Kong et al. 2003 ; Macaulay et al. 2005 ). The abnormal younger age ( 44 x 103 years) of the Indian M lineages may be attributed to the unequal age contributions from different M haplogroups to the total M age estimate. The frequency composition of the particular M haplogroups in a population sample from India then matters a lot because the ages contributed by the different branches range from 21 x 103 years (M30a) to 93 x 103 years (M6b). Our sample drawn for complete sequencing does not reflect the natural frequencies and therefore could bias the age estimation.”



“To investigate this, we simulated a natural frequency distribution by assigning the mtDNAs sampled from the Chenchu and Koya populations (Kivisild et al. 2003 ) to their respective haplogroups by (near) matching control-region motifs (Yao et al. 2002 ). Fewer than 5% of the mtDNAs were virtually unassignable, so that the remaining 142 mtDNAs could be used to evaluate the natural frequency of each M branch in Indian population (table 2). Based on this frequency information, the M age was recalculated by using the complete sequence data. The resulting age, 54.1 x 103 years, is indeed considerably larger than the value obtained for an unweighted estimation and falls into the range of the age estimates from the other geographical regions (see table 1).”

By the same reasoning the age of Indian M haplogroup according to (Soares et al. 2009) should translate to 57 kyr, which is roughly the same age of M haplogroups observed in East Eurasia.
Edited by Ibra, Jun 6 2009, 06:16:24 AM.
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manju
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Is M1 phylogenetically closer to East Eurasia than South Asia? Sorry if I misinterpreted the graph.
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Ibra
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manju
Jun 6 2009, 09:12:19 AM
Is M1 phylogenetically closer to East Eurasia than South Asia? Sorry if I misinterpreted the graph.
M1 is an out group in that there is not other M haplogroups in West Eurasia. Rather that establish a West Eurasian M node they arbitrary group it with the East Eurasian M haplogroups (perhaps).
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ren
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M1 is unrelated to other M clades, so it might be that M started in SW Asia and due to chance drift did not explode int oa major lineage, or that a back migration from South or Central Asia brought it there early in M's diversification.

Anyway, it clearly should be considered a West Eurasian lineage, just like R and N clades in East Eurasia, South Asia, and Oceania are East Eurasian, South Asian, etc.
Edited by ren, Jun 7 2009, 02:51:06 AM.
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Ibra
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Pre-U2 trickled passed the desert barriers across Iran and into in South Asia by 30kyr. Could the rare exception of an M population moving in opposite direction around the same time be the reason why we only have M1 in West Eurasia?
Edited by Ibra, Jun 7 2009, 07:23:56 AM.
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ren
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It seems to be not a basal U lineage but part of U2'3'4'7'8'9.

I thought U4 was mostly found among Uralic people, and argued as a autochthonous product of the Urals, but yet it seems to be found in Anatolia in significant numbers as well. U2 seems to have unique branch in SW Asia and Europe (U2d, e): http://s6.zetaboards.com/man/topic/528974

How reliable is the dating of U2?



From "Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages"
Quote:
 
The dominant subcluster in India is
U2. Although rare in Europe, the South-Asian form differs
from the western-Eurasian one: western-Eurasian U2
includes a further characteristic transversion at nucleotide
position (np) 16,129 [12], which is absent in Indian U2
varieties (Figure 2). We calculated the coalescence age
essentially as described in [15,17] and estimate the split
between the Indian and western-Eurasian U2 lineages as
53,000 ± 4,000 years before present (BP).


From "Mitochondrial Haplogroup U2d Phylogeny and Distribution"
Quote:
 
The sequencing of the entire mitochondrial DNA belonging to haplogroup U2d reveals that this clade is defined by four coding-region mutations at positions 1700, 4025, 11893, and 14926. Phylogenetic analysis suggests that western Eurasian haplogroup U2d appears to be a sister clade with the Indo-Pakistani haplogroup U2c. Results of a phylogeographic analysis of published population data on the distribution of haplogroup U2d indicate that the presence of such mtDNA lineages in Europe may be mostly a consequence of medieval migrations of nomadic tribes from the Caucasus and eastern Europe to central Europe.


U2
-U2a (SouthAsian)

_U2b (South Asian)

_U2c'd'e
__c (South Asian)
__d (West Asian, European)
__e (European, West Asian)

That would be U2e, which seems to form a branch with U2c and d as the third leg of U2:

the other two being U2a and b.
Edited by ren, Jun 8 2009, 02:30:31 AM.
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Ibra
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Quote:
 
I thought U4 was mostly found among Uralic people, and argued as a autochthonous product of the Urals, but yet it seems to be found in Anatolia in significant numbers as well. U2 seems to have unique branch in SW Asia and Europe (U2d, e):


Interestingly U4 and U9 are jointed together as well.

Ren
 
How reliable is the dating of U2?


Thanks for the breakdown of U2 clades, Ren. The age of U2 seems to be consistent with the rest of the literature although the variance is slightly smaller since it was corrected for selection; this would slightly reduce the age of U2. The age of U2a and U2b are around the 40- 35kyr as are the Majority of Indian M haplogroups so it possible that populations expanded in the Upper Paleolithic after improved conditions perhaps. It’s intriguing if the populations that carried U2 to India also had a unique y-chromosome signature or the part of West Eurasia that U2 originated in. Anyone have any ideas?
Edited by Ibra, Jun 8 2009, 08:59:29 PM.
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manju
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Is this paper related to the new paper?
Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates

http://mbe.oxfordjournals.org/cgi/content/full/26/1/217
Edited by manju, Jun 10 2009, 09:54:21 AM.
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Ibra
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The newest paper offers a solution to the question posed by the first. Variance doesn’t grow exactly linearly with time because of selection. The new paper corrects for that problem.
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