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GailT
10-19-2012, 03:37 PM
A new open access paper was just published with analysis of mtDNA from the 1000 Genomes Project (link) (http://www.nature.com/srep/2012/121018/srep00745/full/srep00745.html).

I've compared the U5 results with other FMS results, and the 1000 Genome seems to have good quality - I've only found a few sequence where they appeared to have missed expected mutations (although there might also be some private mutations that they missed), and there are some close matches to previously unique FMS results.

Also covered in Science Daily (link) (http://www.sciencedaily.com/releases/2012/10/121018130834.htm).

Rathna
10-19-2012, 07:47 PM
Many thaks, Gail, for having posted this link. I'll study it soon.

Rathna
10-20-2012, 12:49 PM
Europeans. The Neolithic transition in Europe has been debated for
decades5,19,20. Agriculture in Europe was not developed independently,
but was brought from farmer influx in Middle East. In the
Eastern Europe, agriculture appeared in Greece about 9 kya15, which
could be considered as the first farming in Europe. It is still
controversial whether the farmers replaced the majority of the
original Palaeolithic European residents or they only had limited
contribution to the gene pool of modern Europeans when bringing
agriculture to the land of Europe. According to previous mtDNA
evidence which are mainly based on the analysis of hypervariable
regions, the farmer influx only account for a very little proportion,
about 20%5. The 1000 Genome Project provides 413 Europeans (103
CEU, 97 FIN, 94 GBR, 14 IBS and 105 TSI) in this study. As shown
in Table S2, most of the European samples belonged to the
Macrohaplogroup N, with 2 exceptions found in TSI (1 L1 and 1
D4). HV accounted for about a half of the gene pool, and frequencies
of lineage U and JT were the next highest.
According to the median-joining network analysis, 15 star lineages
were observed in Figure 4. Most of them (HV, H, H1, H3, J1c, T1, T2,
U5a1, U5a, K1, V, W, U2’3’4’7’8’9) coalesced before 10 kya although
2 lineages (J1c3 and T2b) might expand in 10 kya. Except HV and
U2’3’4’7’8’9, other lineages expanded about after LGM. A very distinct
and major expansion in Figure 4 is the H lineage, and subsequent
expansions of haplogroups H1 and H3 were also important
in Europe. About 44.5% of European samples in current analysis
belonged to the H expansion, which happened right after LGM
according to our calculation (Table S3).
To further verify that the lineage expansions indeed occurred in
Europe, we extended the analysis to the populations in Middle East.
In the network of Middle East which were mainly based on the data
from Schönberg et al.21 and whole mtDNA sequence data on Pakistan
and Israel individuals from CEPH-HGDP (HX Zheng, unpublished
data), we found 13 expansions (HV, H, I, L2a1, M4’67, M, N, R, T2b,
T2, U2’3’4’7’8’9, U7 and X2) in Middle East, five of which were
identical to European expansion lineages (HV, H, T2b, T2,
U2’3’4’7’8’9). HV and U2’3’4’7’8’9 were too old for the discussion
in this context.
In the following, we focused on the analysis of the relatively
younger lineages, including Haplogroup H. The H lineage in the
Middle East was estimated ,15 kya, which was younger than
European H (,18 kya). Although haplogroup H was thought to
have a Middle East origin, previous work also supported that it
expanded in Europe22. In Europe, H expanded 18–16 kya, which is
definitely in Palaeolithic Time. In addition, high frequency of H was
observed in many European populations, almost about 40% or
more23–26. Thus, the expansion of H lineage contributed greatly to
current European gene pool. Another young lineage, T2b, was
,12210 kya in Middle East, which is older than T2b in Europe
(1029 kya), and T2b was previously suggested a Middle Eastern
origin26. Although T1 and T2 were previously thought to associate
with agriculture development11, we did not find any expansion in T1
lineage while T2 lineage coalesced at 19 kya, which is much earlier
than farming time, which was also concordant to a recent study
considering T might in fact reflect dispersal from Near Eastern refugia
in Post-LGM period27. Furthermore, H1, H3, and V were considered
to expand northwards from the Southwestern European
refuge right after LGM in former analysis22,28. Compared to the estimations
of European lineages, our estimation might be lower in some
lineages but still before the agriculture occurred in Europe16,29. Other
expansions K1, W and J1c, were also ambiguous for their origins26.
However, their ages (.14 kya) indicated that these lineages had little
chances for playing a role in agriculture transmission.
To conclude, H, H1, H3, J1c, K1, U5a, U5a1, V and W represent
pre-Neolithic expansions, of which V, H1, H3, U5a and U5a1 were
definitely autochthonous in Europe, indicating that main lineages in
Europe began to expand before the agriculture while none of the
lineages were found to expand in Europe after Neolithic Time.
From the European BSP plots (Figure 2), 3 populations (CEU, FIN
and TSI) were found that they began distinct growth ,14212 kya,
which were concordant to previous analysis in Middle East21. As
expected, from the BSP plot including all European samples in
Macrohaplogroup N (Figure 5B), we found that the expansion began
,13 kya and showed a continuous trend to nowadays, which is very
similar to the result of BSP analysis of East Asian14. The population
expansion began , 13 kya might correlate to lineages H1, H3, J1c,
J1c3, K1, T1, U5a1, V and W (Hong-Xiang Zheng et al., MtDNA analysis
of global populations support that major population expansions began before
Neolithic Time).

GailT
10-20-2012, 07:34 PM
I have several criticisms of this report, and I think it is typical of the poor scholarship and uneven peer review that we frequently see in papers on mtDNA. So I don't have any confidence in the conclusions they reach.

The samples are not random (as the authors claim). In fact, the samples are selected from narrowly defined regions and many large regions are not evaluated at all. It would make sense to include results from other studies to represent data from other regions.

The approach used to define star patterns is not described but is obviously flawed. For example, H1 and U5a are both treated as star patterns, even though H1 has nearly 100 unique daughters while U5a has only two. There is something very obviously different in the patterns of these two groups that is entirely ignored.

The report presents results from a model with no context, no scholarship, no reference or discussion of ancient DNA, and no critical evaluation of the model to assess if the results are meaningful.

GTC
10-21-2012, 01:58 AM
As soon as I noticed some grammatical errors I began to lose interest in the paper. Properly reviewed papers don't contain those.

Rathna
10-21-2012, 05:21 AM
As soon as I noticed some grammatical errors I began to lose interest in the paper. Properly reviewed papers don't contain those.

The scholars are Chinese. It is possible that they have done some mistakes for an English ear, but this shouldn’t be the yardstick to judge their work.
They have put at our disposal 910 FGSs, amongst them 105 Tuscans, and, if you do exam them, I assure you that they are very interesting. One, NA 20505, is a K1a1b1e, about which I have written a lot, about its origin in Italy and its expansion to the Isles (with the mutation 477C).
The work hasn’t been published in the Western reviews, funded by the same people who want that the same things are written. For this it is more reliable than all these ones.

GailT
10-21-2012, 05:45 PM
The paper is published in Nature's "Reports" which is designed for expedited peer review and rapid publication - and I give the authors great credit for making the 1000 genomes data accessible to a wider audience, and that alone might justify publication regardless of the depth of the analysis. Some other peer reviewed publications on mtDNA suffer from the same superficial analysis of the data and facile conclusions, so it might be unfair to single out these authors for criticism when publications from western researchers often have the same flaws.