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Clinton P
10-22-2014, 07:30 PM
"DNA analysis of a 45,000-year-old human has helped scientists pinpoint when our ancestors interbred with Neanderthals."

Click here (http://www.bbc.co.uk/news/science-environment-29649499) to read more about this story.

Clinton P

Jean M
10-22-2014, 07:43 PM
Dienekes covers this paper: http://dienekes.blogspot.co.uk/2014/10/high-coverage-genome-from-45000-year.html
High coverage genome from 45,000-year old Siberian (Ust'-Ishim)


This is the oldest full genome of a modern human published to date and it also comes from a time (45 thousand years ago) that coincides with the Upper Paleolithic revolution in Eurasia...

The Y chromosome sequence of the Ust’-Ishim individual is similarly inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT)) that occurs across Eurasia today (Supplementary Information section 9).

The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’), which occurs today across Eurasia (Supplementary Information section 8).

Details of the paper have been posted here on the new DNA papers thread.

palamede
10-22-2014, 10:37 PM
For Mt dna , Ust'Ishim man was R+3107d as compared to rCRS sequence : 73G, 263G, 750G, 1438G, 2706G, 3107d, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G...
but what is the meaning of d in 3107d (3107 doesn't appear in the mt phylogeny from rCRS, therefore possible unique mt mutation in R )

For Y dna, he was K(xLT)-M526 plus 6 additional mutations unknown in the subgroups of K-M526.

It was thought the couple (Y:K-M526, Mt:R) migrated to South-East Asia (where NO diverged from K), then Indonesia

ISOGG
• K2 M526/PF5979 -This was previously classified as K(xLT)
• • K2* -
• • NO or K2a M214/Page39 etc.
• • • N or K2a1 M231/Page91
• • • O or K2a2 M175 etc.
• • K2b M1221/P331/PF5911
• • • K2b* -
• • • K2b1 P397, P399
• • • • K2b1* -
• • • • K2b1a CTS5650/F3744/P405
• • • • • K2b1a* -
• • • • • K2b1a1 P60, P304, P308
• • • • • K2b1a2 P79/P299, P307
• • • • • K2b1a3 P315
• • • • • • K2b1a3* -
• • • • • • K2b1a3a P401
• • • • • S or K2b1a4 M230, etc.
• • • • K2b1b P336
• • • • K2b1c P378
• • • • M or K2b1d P256, etc.
• • • P or K2b2 P295/PF5866/S8, etc.
• • • K2c P261, P263
• • • K2d P402, P403
• • • K2e M147

Below K2-M526, The groups are NO and K2b in ISOGG, but between K2-M526 (1 mutation) and NO (48 mutations) , YFULL introduces K-M2335 with 7 mutations (CTS11667 * S22380/M2335/F549 * M2346/F650 * Z4829 * M2308/Z4842... 2 SNPs) with one test HG03742 ITU (Indian/Telugu).

K-Ust'Ichim would be an independant sub-group which went northwards into West Siberian and if the 6 mutations are confirmed not to be in the present sub-branches, either the sub-branch exists and hasn't fount yet or has disappeared. Maybe, the same reasoning with mt hg R+3107d should give the same conclusion.

Personnaly, I am very surprised
1) The Y-hg K and the mt-hg R dates from about a little more than 45,000 years ago only.

2) They are found in a so northern latitude, I waited for Y-hg P or R or Q or NO or C and mt-hg U, Ux, HV, H, Rx or other descendants of M, N or R.
U (derived from R) is frequently given more than 50,000 years.

3) The expansion area of Y-K and mt-R is generally considered as being into the South-East Asia and Indonesia . This supposes a lost branch went to South Siberia in the same time. It was contemporary of the first Upper Paleolithic in Siberia but was unsuccessful and disappeared while the less culturally advanced Indonesian P arrived later to Siberia and from Siberia, P knew a very big success towards Europe, South Asia (hg R) and America (hg Q).

Gisele H
10-23-2014, 12:28 AM
"For Mt dna , Ust'Ishim man was R+3107d as compared to rCRS sequence : 73G, 263G, 750G, 1438G, 2706G, 3107d, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G... but what is the meaning of d in 3107d (3107 doesn't appear in the mt phylogeny from rCRS, therefore possible unique mt mutation in R "

None of the differences from the CRS listed above signify haplogroup R. In fact, nearly all human sequences have the same differences including those belonging to the M and L clusters. See Ingman's listing of polymorphic sites here:

http://www.mtdb.igp.uu.se/

The 3107 difference emerged during a reference sequence amendment and is not meaningful. The only informative mtDNA mutation provided in the article is 16150T.

parasar
10-23-2014, 01:05 AM
...
Personnaly, I am very surprised
1) The Y-hg K and the mt-hg R dates from about a little more than 45,000 years ago only.

...

That is about the same age I had obtained calibrating Karafet and Anzick-1.
http://www.anthrogenica.com/showthread.php?1507-Some-provisional-calculations-for-haplogroup-R1a-based-on-the-first-FGC-result/page11


four hg Q samples for whom the false negative rate is minimized due to haploid coverage of at least 5× (HGDP00877, HGDP00856, HG01124, and Anzick-1) ... We infer an average of approximately 36.7 (48.7 – 12) transversions to have accumulated in the past 12.6 ky and therefore estimate the divergence time of Q-M3 and Q-L54*(xM3) to be approximately 16.8 ky (12.6 ky × 48.7 / 36.7) ... Poisson process model for mutations on the tree and used the constrOptim() function in R to compute a maximum likelihood TMRCA estimate of 16.9 ky. We then repeated this for 100,000 bootstrap simulations to yield a 95% confidence interval of 13.0–19.7 ky.

Using their averaging and maximum likelihood calculation, we have 16.9 - 12.6 (age of Anzick-1) = 4.3 ky as the spacing of Anzick-1 from Q-M3, Q-L54 divergence, which going backwards on the same scale gives us about 32.7 ky for R, Q divergence.

I think this lower age is quite possibly the age of P-M45. I would definitely put a much higher age for P-P295 at about 46000 years ...
Going by Karafet et al that the K-M9 is about 17 ky distant from R,Q divergence we get 33 (calibration with Anzick-1) + 17 = 50 ky as the approximate age for K-M9.



So as Ust-Ishim is 45000years old and is 6 mutations down from K-M526, a 50000ybp age for K-M9 is reasonable.

parasar
10-23-2014, 03:46 AM
"For Mt dna , Ust'Ishim man was R+3107d as compared to rCRS sequence : 73G, 263G, 750G, 1438G, 2706G, 3107d, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G... but what is the meaning of d in 3107d (3107 doesn't appear in the mt phylogeny from rCRS, therefore possible unique mt mutation in R "

None of the differences from the CRS listed above signify haplogroup R. In fact, nearly all human sequences have the same differences including those belonging to the M and L clusters. See Ingman's listing of polymorphic sites here:

http://www.mtdb.igp.uu.se/

The 3107 difference emerged during a reference sequence amendment and is not meaningful. The only informative mtDNA mutation provided in the article is 16150T.

So which is the indicator mutation for Ust-Ishim's mtDNA R determination?

Gisele H
10-23-2014, 04:39 AM
So which is the indicator mutation for Ust-Ishim's mtDNA R determination?

16223C and 12705C, when found on an 'N' background (8701A 9540T 10873T 10398A), are indicative of R. We have not been told the status of any of these, though.

alan
10-23-2014, 08:15 AM
Archaeologically and chronologically speaking this seems to be a person from the first wave of humans into southern Siberia c. 45000 years ago. I dont know the details of the material culture of this find, if any, but the date and location places it in what is known as the Initial Upper Palaeolithic of southern Siberia - the first modern humans to take the northern route eastwards. Archaeologists believe the technology associated with this culture suggests a route from SW Asia to Iran to Uzbekistan to south Siberia. So, the y-DNA seems to fit such a model. I believe P emerged shortly after this in the same area and culture.

In general I believe the SE Asian idea that emerged this year is a red herring caused by later movements south from Siberia during times of climate decline which at times made previously settled areas of south Siberia impossible to live in. From memory there was a bad climatic period at some point in the 30 thousands BC and another, the LGM, had driven people out of much of southern Siberia by c. 22000BC . It seems far more likely to me that people went south from Siberia in this period than some sort of very hard to believe movement of P from SE Asia into Siberia. I would always also be wary of using islands to deduce much.

alan
10-23-2014, 08:29 AM
Interestingly there is a very broad similarity in the technology of these groups who went into north central Asia and Siberia c. 45000 years ago and those like the ill fated Bohunician of Europe around the same time - both also having there best ultimate origins in the Levant but taking different routes I think the Levantine group they appear to have derived from was the Emiran culture a transitional technology between the Levallois-Mousterian and Upper Paleolithic in the Palestinian region

alan
10-23-2014, 08:56 AM
Of course lets also not forget the range of Neanderthals with whom this guy's ancestors mixed maybe 5-15000 years earlier. There are not too many places where humans and Neanderthals lived together c. 50-60000BC. This is a map of the Neanderthal range

http://www.nature.com/nature/journal/v449/n7164/images/nature06193-f1.2.jpg

Again this points to a movement from SW Asia into northern Eurasia

Jean M
10-23-2014, 09:20 AM
Razib Khan comments on this paper. http://www.unz.com/gnxp/basal-eurasians-and-pre-out-of-africa-population-structure/

The text and the supplements both mention that this individual lacks the “Basal Eurasian” component which seems ubiquitous in modern West Eurasians, and was likely brought by Middle Eastern farmers.

Muircheartaigh
10-23-2014, 10:42 AM
Qiaomei Fu et al.
We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.


Does the paper report the procedure in arriving at these mutation rates. The Y chromosome rate of 0.7 x 10-9 to 0.9 x 10-9 per site per year seems to agree with the rate derived from Q-M3 age calculations.

parasar
10-23-2014, 12:35 PM
Of course lets also not forget the range of Neanderthals with whom this guy's ancestors mixed maybe 5-15000 years earlier. There are not too many places where humans and Neanderthals lived together c. 50-60000BC. This is a map of the Neanderthal range

http://www.nature.com/nature/journal/v449/n7164/images/nature06193-f1.2.jpg

Again this points to a movement from SW Asia into northern Eurasia

I would agree that the point where this Neandertal contact occurred is key to determining where his ancestors came from, but SW Asia is unlikely as West Eurasians show some of lowest Neandertal admixture among Eurasians.
Their basal portion has even lower. So I think the admixture point is somewhere between the Altai and Vietnam.
http://m.pnas.org/content/109/51/E3523/F1.large.jpg

GailT
10-23-2014, 01:26 PM
For Mt dna , Ust'Ishim man was R+3107d as compared to rCRS sequence : 73G, 263G, 750G, 1438G, 2706G, 3107d, 4769G, 7028T, 8860G, 11719A, 14766T, 15326G.


None of the differences from the CRS listed above signify haplogroup R. In fact, nearly all human sequences have the same differences including those belonging to the M and L clusters. The 3107 difference emerged during a reference sequence amendment and is not meaningful. The only informative mtDNA mutation provided in the article is 16150T.

The results above were reported relative to the rCRS reference, H2a2a1, so you need to start there and work up the tree, which takes you to mtDNA haplogroup R. None of the defining mutations for R are listed because they are all shared with H2a2a1. Nearly all human sequences in M and L share these mutations (when reported relative to the rCRS) because these are the reverse of the mutations in the line from R to H2a2a1

GailT
10-23-2014, 01:39 PM
I would agree that the point where this Neandertal contact occurred is key to determining where his ancestors came from, but SW Asia is unlikely as West Eurasians show some of lowest Neandertal admixture among Eurasians.
Their basal portion has even lower. So I think the admixture point is somewhere between the Altai and Vietnam.

It was proposed in another recent paper that present day West Eurasians include a large contribution from the ancestors of Middle East farmers (the Basal Eurasian component?), who descend at least in part from a population who diverged about 60,000 years ago and remained isolated from the main OoA migration. If Neandetal admixture occured after that divergence, it's possible that the ancestors of Middle Eastern farmers also had little or no Neandertal admixture. I don't think we know where the ancestors of Middle Eastern farmers lived or how they remained separate from other Eurasian populations for so long. And I think the key to determining the location of admixture is the accuracy of the date of admixture. Anatolia might be a possibility, it would include the main OoA expansion, but perhaps not include ancestors of Middle East farmers who, perhaps, were isolated in the Arabian Peninsula.

Ebizur
10-23-2014, 02:48 PM
So as Ust-Ishim is 45000years old and is 6 mutations down from K-M526, a 50000ybp age for K-M9 is reasonable.I note that Ust-Ishim's estimated age and Y-DNA haplogroup assignment are in contradiction with the coalescence estimates of several recent studies, such as Yan et al. (2014), "Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers." The authors of that study have estimated the TMRCA of K2a and K2b to be approximately 33,000 years (95% confidence interval "ignoring uncertainty in mutation rate" 30,900 years to 35,200 years) and the TMRCA of G and IJK to be approximately 35,800 years (95% CI 33,300 years to 38,300 years). K-M526 must be younger than the MRCA of G and IJK, so the age of the Ust-Ishim specimen sets a lower bound on the TMRCA of {G+IJK}. Disregarding the uncertainty inherent in the estimation of the age of the Ust-Ishim specimen, this means that the TMRCA estimates of Yan et al. (2014) should be multiplied by a factor of at least 1.257 (and probably closer to 1.425) in order to be consistent with this new piece of ancient DNA evidence. Using 1.425 as a scale factor would result in each of their "Neolithic Super-Grandfathers" originating in the early Neolithic of East Asia (e.g. Nanzhuangtou, Pengtoushan, or Peiligang culture) rather than in a mid-Neolithic culture (e.g. Yangshao, Hongshan, Dawenkou) as their published estimates have suggested.

parasar
10-23-2014, 03:02 PM
I note that Ust-Ishim's estimated age and Y-DNA haplogroup assignment are in contradiction with the coalescence estimates of several recent studies, such as Yan et al. (2014), "Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers." The authors of that study have estimated the TMRCA of K2a and K2b to be approximately 33,000 years (95% confidence interval "ignoring uncertainty in mutation rate" 30,900 years to 35,200 years) and the TMRCA of G and IJK to be approximately 35,800 years (95% CI 33,300 years to 38,300 years). K-M526 must be younger than the MRCA of G and IJK, so the age of the Ust-Ishim specimen sets a lower bound on the TMRCA of {G+IJK}. Disregarding the uncertainty inherent in the estimation of the age of the Ust-Ishim specimen, this means that the TMRCA estimates of Yan et al. (2014) should be multiplied by a factor of at least 1.257 (and probably closer to 1.425) in order to be consistent with this new piece of ancient DNA evidence. Using 1.425 as a scale factor would result in each of their "Neolithic Super-Grandfathers" originating in the early Neolithic of East Asia (e.g. Nanzhuangtou, Pengtoushan, or Peiligang culture) rather than in a mid-Neolithic culture (e.g. Yangshao, Hongshan, Dawenkou) as their published estimates have suggested.

I agree. That is close to what I had pointed out based on Anzick-1.
http://www.anthrogenica.com/showthread.php?1507-Some-provisional-calculations-for-haplogroup-R1a-based-on-the-first-FGC-result&p=48531&viewfull=1#post48531

So a correction factor of 1.51 should be applied to Yan et. al.'s ages. This correction would actually bring their three Chinese neolithic Super-grandfathers more in line with the beginning of Chinese agriculture

Gisele H
10-23-2014, 03:26 PM
The results above were reported relative to the rCRS reference, H2a2a1, so you need to start there and work up the tree, which takes you to mtDNA haplogroup R.

That classification method only works when there are few ambiguous nucleotide sites. I am assuming there are many in a 45,000 yo sequence and so would feel more confident about the classification if we were given key mutations relative to a basal sequence.

I would not expect basal R sequences in Siberia either. SE Asia, instead.

parasar
10-23-2014, 03:36 PM
It was proposed in another recent paper that present day West Eurasians include a large contribution from the ancestors of Middle East farmers (the Basal Eurasian component?), who descend at least in part from a population who diverged about 60,000 years ago and remained isolated from the main OoA migration. If Neandetal admixture occured after that divergence, it's possible that the ancestors of Middle Eastern farmers also had little or no Neandertal admixture. I don't think we know where the ancestors of Middle Eastern farmers lived or how they remained separate from other Eurasian populations for so long. And I think the key to determining the location of admixture is the accuracy of the date of admixture. Anatolia might be a possibility, it would include the main OoA expansion, but perhaps not include ancestors of Middle East farmers who, perhaps, were isolated in the Arabian Peninsula.

Yes I have considered that possibility that two populations were in Western Eurasia - one admixed with Neanderthals and the other did not.
The one that did moved east. The one that did not stayed put.

But at present I am persuaded by the string lengths and proportions that the admixture occurred further east.
http://2.bp.blogspot.com/-iPjWPx5aHF0/UulquRDwSEI/AAAAAAAAJew/XCKk9JDFwsQ/s1600/neandertal.png

But it is also possible Meyer et.al. is correct that potentially there were at least two events or that 24% of European is late African. See also Wall et.al.
http://www.anthrogenica.com/showthread.php?2573-New-DNA-Papers-General-Discussion-Thread&p=52721&viewfull=1#post52721

alan
10-23-2014, 04:33 PM
I would agree that the point where this Neandertal contact occurred is key to determining where his ancestors came from, but SW Asia is unlikely as West Eurasians show some of lowest Neandertal admixture among Eurasians.
Their basal portion has even lower. So I think the admixture point is somewhere between the Altai and Vietnam.
http://m.pnas.org/content/109/51/E3523/F1.large.jpg

Well the route normally suggested for the first settlement of Siberia does involve Iran and the Stan countries and I suppose one couldnt rule out the Caucasus route either. So, although Europe and Siberia probably both derive much of their upper palaeolithic population from an ultimate Eurasian starting point of the Levant, they then diverged nearly 50000 years ago taking routes than may never have crossed again for 40000 years. The routes may have shared nothing in common once they left the Levant.

The relationship with Neanderthals that the European branch of modern humans heading west and the north Eurasian branch heading east may have been very different - a lot would depend on timing and other factors. We would need a good map showing where and when of Neanderthal settlements c. 50-38000BC and compare them to the routes and chronology of the early humans to truly understand how Neanderthal admixture could come to vary among groups who both originated in an area with Neaderthals and also passed through other areas with Neaderthals.

To give a short answer though, or rather a speculation, there is one very important difference between the groups who left the Levant heading towards Europe and the groups who heading towards Siberia via Iran etc. This difference is that the very early initial upper palaeolithic groups of c. 45000BC who headed into Europe (Bohunician etc) floundered and were replaced by later waves while this is not true for those who headed into Siberia.

The Siberian wave seems to have been the one and only major wave of hunter into northern Asia until post-LGM. Therefore in a sense they were a closer representative of Levantines of 45000BC than Europeans.

European hunters may derive more from later Levantine waves such as the Aurignacian and Gravettian after 40000BC

yxc
10-23-2014, 07:01 PM
...that present day West Eurasians include a large contribution from the ancestors of Middle East farmers (the Basal Eurasian component?), who descend at least in part from a population who diverged about 60,000 years ago and remained isolated from the main OoA migration. If Neandetal admixture occured after that divergence, it's possible that the ancestors of Middle Eastern farmers also had little or no Neandertal admixture. I don't think we know where the ancestors of Middle Eastern farmers lived or how they remained separate from other Eurasian populations for so long. And I think the key to determining the location of admixture is the accuracy of the date of admixture. Anatolia might be a possibility, it would include the main OoA expansion, but perhaps not include ancestors of Middle East farmers who, perhaps, were isolated in the Arabian Peninsula.
if they had no Neandertal admixture then they were like the uncontacted Andamanese and Jarawa. are latter the sames as the Onge or what. On the scene in the Arabian Peninsula.
I always propageted that DE and D with M mtdna had inhabited the temperate latitudes that possibly were all forested in between Africa and at least Burma.
it's N , R mtdna and its descendents like U and B who were isolated for a while with the mammoths in the northern zones.

parasar
10-27-2014, 03:03 PM
I think Genetiker is correct on this one:

I’ll check the Ust’-Ishim data later, but I can already confidently predict that he didn’t have the Mongoloid EDAR mutation. It was estimated here that the mutation arose around 30,000 years ago, which was 15,000 years after Ust’-Ishim. Also, Ust’-Ishim was located near South Asians in the principal component analyses. He was Veddoid. Veddoids were the race from which both Caucasoids and Mongoloids evolved.

Ust’-Ishim probably would have looked like the Veddas in this video, with brown skin, straight (but not stiff) black hair, and an absence of Caucasoid, Mongoloid, and Negroid physical features.

https://genetiker.wordpress.com/2014/10/24/analyses-of-an-iron-age-hungarian-genome/#comments



Meanwhile, Vedda people had the lowest frequency of haplogroup M (17.33%). It is quite astonishing to see such a lower frequency of M haplogroup in the Vedda population when compared with southern Indian tribal groups (70–80%) as well as southern Indian caste populations (65%).30 This is probably due to the effect of genetic drift in the smaller population of Vedda. This is supported by other observation of reduced intrapopulation diversity among the subgroups of Vedda people.

On the other hand, Vedda people and Low-country Sinhalese showed relatively high frequencies of haplogroup R (45.33 and 25%, respectively) which was contributed mainly by sub-haplogroup R30b (38.67 and 20%). The haplogroup was less frequent in Up-country Sinhalese, Sri Lankan Tamils and Indian Tamils. Haplogroup U was mostly found in Vedda (29.33%) and Up-country Sinhalese (23.33%), with highest contribution from sub-haplogroups U1a’c (12 and 5%, respectively) and U7a (13.33 and 11.67%, respectively).

The haplogroup frequency of Vedda people from each site is shown in Supplementary Table S7. Low frequency of M haplogroup and high frequencies of R and U haplogroups were found to be the unique characteristics of Vedda. However, the frequencies of these haplogroups varied among Vedda from different sites. Two Vedda groups (VA-Dam and VA-Hen) posses the frequency of M haplogroup close to that of Up-country Sinhalese, Low-country Sinhalese and Sri Lankan Tamils, indicating the genetic admixture between these two Vedda groups and the other three populations. The Vedda subgroups shared haplogroup R30b/R8a1a3 at relatively high frequencies, the characteristic not found among subgroups of other ethnic populations on the island, suggested a common shared origin of the Vedda population. Median Joining network of HVS-1 and part of HVS-2 sequence of haplogroups R (62 individuals, 21 haplotypes) and U (52 individuals, 25 haplotypes) from five Sri Lankan populations were constructed (Supplementary Figure S3). In general, the network was in agreement with the mtDNA haplogroup analysis. Although posses less frequency of both haplogroups, the haplotypes, belonging to these haplogroups, of the other four Sri Lankan populations were more diverse than Vedda haplotypes, which were also highly derived within the tree. The Median Joining network incorporating data of HVS-1 and part of HVS-2 sequences of haplogroups R and U24, 25 from Indian populations was also performed (Supplementary Figure S4). The Median Joining network map does not reveal a basal status of the Vedda's sequences for the genetic differentiation of haplogroups R and U. It is more likely that these two haplogroups, found to be particularly prevalent in the Vedda, were derived from ancestors on the Indian subcontinent.

http://www.nature.com/jhg/journal/v59/n1/full/jhg2013112a.html

On a separate note, Princess Diana's mtDNA line was discerned to be M30b

Because mtDNA is passed down the female line, Prince William carries Eliza Kewark’s mtDNA and
so do all other matrilineal or motherline descendants of Eliza. Through genealogy we traced two
such living direct descendants and by reading the sequence of their mtDNA, we showed not only
that they matched, but also that it belongs to a haplogroup called R30b, thus determining Eliza
Kewark’s haplogroup. Comparison to databases totalling over 65,000 individuals from around the
world show that only 14 examples have been reported, 13 of whom were Indian and one Nepalese.
Moreover the other related branches of R30a and R30* are also entirely South Asian.

http://www.britainsdna.com/files/press-release/Indian%20Ancestry%20of%20William.pdf

parasar
10-29-2014, 03:37 PM
The results above were reported relative to the rCRS reference, H2a2a1, so you need to start there and work up the tree, which takes you to mtDNA haplogroup R. None of the defining mutations for R are listed because they are all shared with H2a2a1. Nearly all human sequences in M and L share these mutations (when reported relative to the rCRS) because these are the reverse of the mutations in the line from R to H2a2a1

GailT,

How many mutations, if any, down-stream of R are you reading on Ust-Ishim?

Thanks.

lgmayka
10-30-2014, 09:54 AM
G. Magoon just announced this on a mailing list:
---
I've just been taking a look at the chrY data for the ancient genome described here: http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html (data just became available today). The authors of the paper classify him as K(xLT), but that is based on an older tree. I've been looking at the results in the context of our tree and a preliminary look suggests that this will split the SNPs we have as defining "Hg-X" into two levels. In particular, his results suggest he is:
CTS11667+
Z4842/M2308+
Z12216-
Z4845/M2313-
Z12176-
Z4952/M2339-
F650/M2346-
---

On YFull's haplotree, then, this man from 45,000 years ago has some but not all of the SNPs associated with K-M2335 (http://yfull.com/tree/K-M2335/), which is essentially pre-NO.

Shaikorth
10-30-2014, 10:14 AM
G. Magoon just announced this on a mailing list:
---
I've just been taking a look at the chrY data for the ancient genome described here: http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html (data just became available today). The authors of the paper classify him as K(xLT), but that is based on an older tree. I've been looking at the results in the context of our tree and a preliminary look suggests that this will split the SNPs we have as defining "Hg-X" into two levels. In particular, his results suggest he is:
CTS11667+
Z4842/M2308+
Z12216-
Z4845/M2313-
Z12176-
Z4952/M2339-
F650/M2346-
---

On YFull's haplotree, then, this man from 45,000 years ago has some but not all of the SNPs associated with K-M2335 (http://yfull.com/tree/K-M2335/), which is essentially pre-NO.

Well that is interesting. Good thing enthusiasts are willing to go through this stuff. If Ust-Ishim's Y-DNA is closer to NO than to MSP then someone should find a precursor to the latter in ancient Siberia some day. Or perhaps there'll be a variant of the Karafet hypothesis with NO taking the northern route from Persia to South Siberia and pre-MSP going to SE-Asia through India. :pop2:

parasar
10-30-2014, 01:59 PM
So per Magoon, Ust-Ishim is:

CTS11667+
Z4842/M2308+

Z12216-
Z4845/M2313-
Z12176-
Z4952/M2339-
F650/M2346-

HG03742, Indian Telugu is:

CTS11667+ (23208284 G>A)
Z4842, M2308+ (7690182 A>T)

Z12216+ (3909630 T>C)
Z4858, M2313+ (8674808 C>T)
Z12176+ (9978055 C>A)
Z4952, M2339+ (21797754 T>C )
F650, M2346+ (23617006 G>A)

M214-
P188-
P192-
P193-
P194-
P195-

So essentially we can think of the defining NO branch markers as CTS11667+ and Z4842/M2308+.

While Karafet did not investigate the NO side, in SE Asia/Oceania M214 was found everywhere but in Australia, and it would be interesting to see how many, if any, of the unresolved M526* found in Sumatra and Sulawesi are positive for these SNPs.

Table 1. Frequencies (%) of K-M526-derived Y-chromosome haplogroups in 7462 worldwide samples
Unresolved K-M526* 5/38 Sumatrans 1/177 Sulawesi
http://www.nature.com/ejhg/journal/vaop/ncurrent/fig_tab/ejhg2014106t1.html#figure-title

Maju's depiction based on table above:
http://1.bp.blogspot.com/-xIyCVSPSm3I/U5LqVD5nawI/AAAAAAAACsM/TEjs1OTRu7k/s1600/Karafet-Y-DNA-K-tree-annotated.png

parasar
10-30-2014, 05:17 PM
Well that is interesting. Good thing enthusiasts are willing to go through this stuff. If Ust-Ishim's Y-DNA is closer to NO than to MSP then someone should find a precursor to the latter in ancient Siberia some day. Or perhaps there'll be a variant of the Karafet hypothesis with NO taking the northern route from Persia to South Siberia and pre-MSP going to SE-Asia through India. :pop2:

We have to consider these Siberian finds with caution and not ascribe to them a precursor status. Lack of DNA preservation in more tropical locales should not detract from the proposition that these people showing up in northern regions in the Upper Paleolithic came in from tropical regions. Their morphology show tropical adaptations indicating long periods of stay in tropical climates. In the pre-LGM timeframe, IMO, they are more likely dead-end lines.

http://www.kunstkamera.ru/en/temporary_exhibitions/virtual/gerasimov/09
"Certain cranial features, including very narrow braincase, low and narrow face, marked prognathism (anterior protrusion of the midface), and very wide nose, are typical of tropical populations. The trait combination links the cranium with those of Papuans and Melanesians ... Bodily proportions of Early Upper Paleolithic people reveal southern characteristics as well. This also concerns the arm proportions of the Markina Gora individual, whose forearm was relatively long compared to the shoulder."

http://www.academia.edu/6822954/Siberian_Migration_Theory_of_Human_Species

Homo sapiens are examined prior to the Last Glacial Maximum (24,000–22,000 years ago) they are virtually all of the morphology of a tropical group; long and slender limbs, only after the Last Glacial Maximum did Homo sapiens gain the shorter stouter morphology of what is seen in some modern populations (Hoffecker, 2004:95)

alan
10-30-2014, 05:39 PM
G. Magoon just announced this on a mailing list:
---
I've just been taking a look at the chrY data for the ancient genome described here: http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html (data just became available today). The authors of the paper classify him as K(xLT), but that is based on an older tree. I've been looking at the results in the context of our tree and a preliminary look suggests that this will split the SNPs we have as defining "Hg-X" into two levels. In particular, his results suggest he is:
CTS11667+
Z4842/M2308+
Z12216-
Z4845/M2313-
Z12176-
Z4952/M2339-
F650/M2346-
---

On YFull's haplotree, then, this man from 45,000 years ago has some but not all of the SNPs associated with K-M2335 (http://yfull.com/tree/K-M2335/), which is essentially pre-NO.

That wouldnt entirely surprise me either. I just have a suspicion that they also arrived by the Siberia route. Maybe all of MNOP. I think when we get back to 45000 we must remember that some epic climatic downturns took place since then that would have made Siberia a hard spot to hold on in and surely many went south in the downturns in the 30000s and the LGM from 25000 especially. Its well known from archaeological dating that there was a big retraction from 25000BC years ago and Mal'ta is the latest dated site at that latitude until the end of the LGM. Some clearly made a shorter retreat to Altai but others may have headed further south.

alan
10-30-2014, 05:44 PM
A date around 30000 ya for EDAR is interesting in that about 27000 years ago the LGM turned places like central and eastern Siberia, Mongolia and northern China into very brutally cold places to live. Mal'at didnt have it but he was the very last dated guy from his middle upper palaeolithic culture - no other sites of this culture have been found after 27000ya.

vettor
10-30-2014, 06:08 PM
That wouldnt entirely surprise me either. I just have a suspicion that they also arrived by the Siberia route. Maybe all of MNOP. I think when we get back to 45000 we must remember that some epic climatic downturns took place since then that would have made Siberia a hard spot to hold on in and surely many went south in the downturns in the 30000s and the LGM from 25000 especially. Its well known from archaeological dating that there was a big retraction from 25000BC years ago and Mal'ta is the latest dated site at that latitude until the end of the LGM. Some clearly made a shorter retreat to Altai but others may have headed further south.

It still makes IJ and K1 group older and westward of this man ...............you need to fit these groups in the logic of age before origin of Uta makes sense

Megalophias
10-30-2014, 09:02 PM
Awesome! I hope we see another survey of K soon using all these new SNPs. And while they're at it, have a good look at P*-M45.

Of course, since we already had pre-NO in India, this actually makes one *less* branch west of SE Asia. Easy come, easy go I guess.


I just have a suspicion that they also arrived by the Siberia route. Maybe all of MNOP. I think when we get back to 45000 we must remember that some epic climatic downturns took place since then that would have made Siberia a hard spot to hold on in and surely many went south in the downturns in the 30000s and the LGM from 25000 especially. Its well known from archaeological dating that there was a big retraction from 25000BC years ago and Mal'ta is the latest dated site at that latitude until the end of the LGM. Some clearly made a shorter retreat to Altai but others may have headed further south.

And... then they migrated en masse down through already populated South Asia, retaining high Y-hg diversity without bestowing it where they passed through, reached Southeast Asia, switched to Southeast Asian lithic technology, conquered all of Southeast Asia while being archaeologically indistinguishable from everyone else there, and lived happily ever after? I think I'm missing something here. :)

vettor
10-31-2014, 05:00 AM
On YFull's haplotree, then, this man from 45,000 years ago has some but not all of the SNPs associated with K-M2335 (http://yfull.com/tree/K-M2335/), which is essentially pre-NO.

Is this pre-NO the new X ( ydna) created in June 2014 as per the tree?

parasar
10-31-2014, 12:22 PM
Is this pre-NO the new X ( ydna) created in June 2014 as per the tree?

Not exactly but close. The Indian Telugu referred to in post 26 is at the X node.

parasar
10-31-2014, 12:29 PM
Apparently modern human fossils were also described from Tam Pa Ling Cave in Laos, with an age estimate of more than 46,000 years8. A direct U/Th date of 61 ka was obtained on the human remains, but the indirect 14C and OSL dates of between 45 and 50 ka on the deposits are considerably younger. The dates have been questioned9, but the Tam Pa Ling specimen seems to be one of the earliest modern humans in mainland Asia ... The Ust’-Ishim fossil is the oldest directly 14C-dated modern human in Northern Eurasia



http://i.imgur.com/gYn3HWy.jpg?1

http://3.bp.blogspot.com/-VaHQZo9wITM/VEf9tMQhktI/AAAAAAAAJ00/aRlFR-Z6Nts/s1600/nature13810-f3.jpg

If Ust-Isim was a recent OoA (~15000years from 60000ybp), why is he so much closer to the Ongee compared to Africans?

parasar
10-31-2014, 12:35 PM
Awesome! I hope we see another survey of K soon using all these new SNPs. And while they're at it, have a good look at P*-M45.

Of course, since we already had pre-NO in India, this actually makes one *less* branch west of SE Asia. Easy come, easy go I guess.



And... then they migrated en masse down through already populated South Asia, retaining high Y-hg diversity without bestowing it where they passed through, reached Southeast Asia, switched to Southeast Asian lithic technology, conquered all of Southeast Asia while being archaeologically indistinguishable from everyone else there, and lived happily ever after? I think I'm missing something here. :)

SE Asian islands were a destination and in those pre Internet days global transmission of top hot spots was telepathic!

Silesian
10-31-2014, 02:19 PM
It still makes IJ and K1 group older and westward of this man ...............you need to fit these groups in the logic of age before origin of Uta makes sense

If Ust-Ishim's genes had longer segments[showing his ancestors had possible contact 50K-60K] of Neanderthal genes in the same region as hair and skin it would have helped adapt to colder climate.

http://blogs.discovermagazine.com/d-brief/2014/01/29/neanderthal-genes-helped-modern-humans-adapt-to-cold/#.VFOUoBZz_p4

Regions like Tuscany have also have Neaderthal.

https://www.youtube.com/watch?v=6Dgm8zeGqb4

Ebizur
10-31-2014, 04:15 PM
So, when the Ust-Ishim specimen's autosomes are analyzed as if he were a present-day human, the largest portion is attributed to a "Central and South Asian" (Kalash-centered) component, followed by an "Oceanian" (Papuan-centered) component, which is again very closely followed by a "Southeast and East Asian" (Southern Chinese-centered) component.

What is that dark blue segment in Ust-Ishim's bar? Is it supposed to be the Pima-centered component or the Yoruba-centered component? I think the color looks slightly more similar to that of the Yoruba-centered component on my computer screen, but I'm not sure.

ArmandoR1b
10-31-2014, 04:47 PM
What is that dark blue segment in Ust-Ishim's bar? Is it supposed to be the Pima-centered component or the Yoruba-centered component? I think the color looks slightly more similar to that of the Yoruba-centered component on my computer screen, but I'm not sure.

It looks more Yoruba-centered and darker than the Pima-centered component.

parasar
10-31-2014, 05:32 PM
So, when the Ust-Ishim specimen's autosomes are analyzed as if he were a present-day human, the largest portion is attributed to a "Central and South Asian" (Kalash-centered) component, followed by an "Oceanian" (Papuan-centered) component, which is again very closely followed by a "Southeast and East Asian" (Southern Chinese-centered) component.

What is that dark blue segment in Ust-Ishim's bar? Is it supposed to be the Pima-centered component or the Yoruba-centered component? I think the color looks slightly more similar to that of the Yoruba-centered component on my computer screen, but I'm not sure.

I believe it is PIMA. The dark tan near the bottom looks to be San.
You may have to compare at 100% here: pg 58 http://www.nature.com/nature/journal/v514/n7523/extref/nature13810-s1.pdf
The Yoruba is a shade lighter blue to my eyes!

Megalophias
10-31-2014, 05:54 PM
If Ust-Isim was a recent OoA (~15000years from 60000ybp), why is he so much closer to the Ongee compared to Africans?
He probably wasn't that recent. CDEF broke from B about 100 kya (using the mutation rate in the new paper) and remained isolated for nearly 50 ky, before E, C, and F all spread around 55 kya. (Although neither Fu et al nor the recent Scozzari et al paper included D, much less DE*, so D might have already been out there.) I *think* the autosomal data agrees with an early split from Africans, or at least Dienekes says it does, using the slow mutation rate as measured in this new paper. So he had been out of Africa already for a very long time (or at least very isolated if somewhere in Africa).

The mitochondrial clock still ticks like something from a Dali painting, so who knows there. There may or may not have been matrilineal genetic exchange with Africa.


I believe it is PIMA. The dark tan near the bottom looks to be San.
You may have to compare at 100% here: pg 58 http://www.nature.com/nature/journal/v514/n7523/extref/nature13810-s1.pdf
The Yoruba is a shade lighter blue to my eyes!
The dark blue component is actually Yoruba. I had to paste the image to GIMP and check the colour values to be sure.

ArmandoR1b
10-31-2014, 06:09 PM
I believe it is PIMA. The dark tan near the bottom looks to be San.
You may have to compare at 100% here: pg 58 http://www.nature.com/nature/journal/v514/n7523/extref/nature13810-s1.pdf
The Yoruba is a shade lighter blue to my eyes!

I zoomed in on the image in two different instances. Yoruba shows be lighter than Pima once I did that but the blue in Ust-Ishim still looks closer to Yoruba than to Pima.

http://i.imgur.com/hHHbZUZl.png

Shaikorth
10-31-2014, 06:17 PM
It's definitely Yoruban shade of blue. The Native American component in Ust-Ishim is almost nonexistent.

parasar
11-03-2014, 06:07 PM
I think Genetiker is correct on this one:
...

update:
https://genetiker.wordpress.com/2014/11/01/analyses-of-the-ust-ishim-genome/

... South Asian or Indian components were the largest components for Ust’-Ishim for all of the calculators that had such components. The second-largest components tended to be Mongoloid Southeast Asian or East Asian components, which is consistent with Ust’-Ishim belonging to a Y haplogroup that was ancestral to the main Mongoloid Y haplogroup ... Ust’-Ishim didn’t have the Mongoloid EDAR mutation. The only derived alleles that Ust’-Ishim had were those in the genes ASIP and KITLG which gave Veddoids brown rather than black skin ...

parasar
11-16-2014, 10:48 PM
When you say P you have to define which P you mean? Because P-P295 is very different in age from P-P27.
For example the Aeta folk have P-P295* (exclusive of P-P27).
Aeta: 12.0% M214 60.0%P378 28.0%P295* http://www.nature.com/ejhg/journal/vaop/ncurrent/fig_tab/ejhg2014106t1.html
It is the age of P295 that is in the ballpark of the age Ust-Ishim around 50000-45000ybp. P27 is much younger.

Therefore to me this Aeta closeness to Ust-Ishim is significant. Obviously the direction of movement is not known. You think that the movement was from Siberia or West Asia which would involve the Siberians bringing their tools and genes to SE Asia.
I think on the other hand, due to the minimal if any basal European in Ust-Ishim, that the movement cannot be from West Asia (or even South Asia, unless South Asian populations at that time lacked basal European*) which had basal European per K14, but was from the Laos-Vietnam region.

*The reason I have been calling it basal European or the "so called basal Eurasian" is because the ancient DNA is from Europe, and it is the Ust-Ishim type that I think of as the real basal Eurasian.

Ust-Ishim
Harappaworld
Using 1 population approximation:
1 great-andamanese @ 25.363333
2 onge @ 29.846519

MDLP k23b
1 Ayta_AE @ 24.783888
2 Nepalese @ 27.270012

"Extended Ust-Ishim map (added South and South-East Asia) http://s020.radikal.ru/i700/1411/99/39e84d81c245.png

Epicenter is somewhere in Burma. Interestingly, Papuans and Melanesians are close."
http://eurogenes.blogspot.com/2014/11/treemix-graphs-with-kostenki14-and-ust.html
http://s020.radikal.ru/i700/1411/99/39e84d81c245.png

parasar
11-16-2014, 10:53 PM
When you say P you have to define which P you mean? Because P-P295 is very different in age from P-P27.
For example the Aeta folk have P-P295* (exclusive of P-P27).
Aeta: 12.0% M214 60.0%P378 28.0%P295* http://www.nature.com/ejhg/journal/vaop/ncurrent/fig_tab/ejhg2014106t1.html
It is the age of P295 that is in the ballpark of the age Ust-Ishim around 50000-45000ybp. P27 is much younger.

Therefore to me this Aeta closeness to Ust-Ishim is significant. Obviously the direction of movement is not known. You think that the movement was from Siberia or West Asia which would involve the Siberians bringing their tools and genes to SE Asia.
I think on the other hand, due to the minimal if any basal European in Ust-Ishim, that the movement cannot be from West Asia (or even South Asia, unless South Asian populations at that time lacked basal European*) which had basal European per K14, but was from the Laos-Vietnam region.

*The reason I have been calling it basal European or the "so called basal Eurasian" is because the ancient DNA is from Europe, and it is the Ust-Ishim type that I think of as the real basal Eurasian.

Ust-Ishim
Harappaworld
Using 1 population approximation:
1 great-andamanese @ 25.363333
2 onge @ 29.846519

MDLP k23b
1 Ayta_AE @ 24.783888
2 Nepalese @ 27.270012

"Extended Ust-Ishim map (added South and South-East Asia) http://s020.radikal.ru/i700/1411/99/39e84d81c245.png

Epicenter is somewhere in Burma. Interestingly, Papuans and Melanesians are close."
http://eurogenes.blogspot.com/2014/11/treemix-graphs-with-kostenki14-and-ust.html
http://s020.radikal.ru/i700/1411/99/39e84d81c245.png

For comparison K14:
http://s013.radikal.ru/i325/1411/80/9c75759aae62.png

And, basal European rich Stuttgart:
http://s52.radikal.ru/i135/1411/ac/cd8bfb0a4137.png

parasar
11-16-2014, 11:54 PM
TreeMix graphs posted by Davidski at Eurogenes blog:
https://drive.google.com/file/d/0B9o3EYTdM8lQYUFpRV9EQlNRNU0/view?pli=1
https://lh5.googleusercontent.com/-XsLe4LFeqdo/VGkcJipwVOI/AAAAAAAAB6Q/klTkw2yPIW4/w350-h228-no/TreeMix5b_14-11-2014_small.png
https://drive.google.com/file/d/0B9o3EYTdM8lQLWg1MkJpTVRHQVE/view?pli=1

https://lh4.googleusercontent.com/-qxmjlRxMswM/VGkcI9tiHII/AAAAAAAAB6Y/zMtifLAMjko/w350-h228-no/TreeMix4_13-11-2014_small.png

https://drive.google.com/file/d/0B9o3EYTdM8lQZ19xWHA4OGtvd1U/view?pli=1
https://lh5.googleusercontent.com/-xIPnovO_7i8/VGkcJNzk_ZI/AAAAAAAAB6I/ChG7iJQ06js/w350-h228-no/TreeMix5_13-11-2014_small.png

Jean M
11-23-2014, 10:21 PM
There is a reconstruction here: http://www.t4mag.com/news/3219/genome-man-lived-45-000-years-ago-sequenced-scientists/

3059

parasar
11-24-2014, 12:36 AM
There is a reconstruction here: http://www.t4mag.com/news/3219/genome-man-lived-45-000-years-ago-sequenced-scientists/

3059
Cool!
Technically a visualization as only his femur was found.

Another visualization:
http://static1.businessinsider.com/image/544821f15afbd33b178b4567-480/a-femur-found-by-chance-on-the-banks-of-a-west-siberian-river-in-2008-is-that-of-a-man-who-died-around-45000-years-ago-scientists-said-shedding-light-on-modern-humans-colonisation-of-the-planet.jpg
A femur found by chance on the banks of a west Siberian river in 2008 is that of a man who died around 45,000 years ago, scientists said, shedding light on modern humans' colonisation of the planet
http://www.businessinsider.com/afp-oldest-dna-ever-found-sheds-light-on-humans-global-trek-2014-10#ixzz3JwRjuMQw

Megalophias
11-24-2014, 07:52 AM
What are these pictures based on? I know older modern humans were more robust, but he makes Neanderthals look pretty.

R.Rocca
11-24-2014, 12:47 PM
Cool!
Technically a visualization as only his femur was found.



Another words, they took creative liberties :D

parasar
11-25-2014, 04:28 AM
The results above were reported relative to the rCRS reference, H2a2a1, so you need to start there and work up the tree, which takes you to mtDNA haplogroup R. None of the defining mutations for R are listed because they are all shared with H2a2a1. Nearly all human sequences in M and L share these mutations (when reported relative to the rCRS) because these are the reverse of the mutations in the line from R to H2a2a1


To date everyone who has tested the FMS is in one of the 9 named U haplogroups. There are a few interesting HVR test results in the U* project that might possibly be a new U branch, but I expect if they test the full sequence they might turn out to be in one of the named groups.

Ust-Ishim is R plus an extra mutation at 16150, The path from R to H2a2a1 is copied below. The results are reported relative to the rCRS, so R is the opposite of this list. 3107d is a dummy to account for an error in the original CRS and should be ignored.

R0 73A
H2a2a1 263A
H2a2 750A
H2 1438A
H 2706A
H2a 4769A
H 7028C
H2a2a 8860A
R0 11719G
HV 14766C
H2a2a 15326A

So if he is just one mutation downstream of R, do you suppose some of the calculated ages are overestimates?
For example:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182158/

Since there is thus no evidence that the offshoots R5, R6, R7, R8, R30, and R31 arose west of the Indian subcontinent, one can approximately calculate the time of the arrival of the predicted founder R haplotype in India by stipulating that all of the variation seen in this part of the phylogeny arose in situ. Then, we estimate the age of the root type of R on the basis of these lineages, in the same way as Kong et al. (2003), by assuming the rate of one substitution (other than a deletion or insertion) in the coding region per 5,140 years (Mishmar et al. 2003). This yields an age (mean ± SD) of 64,200±6,300 years, so the actual entry of the R root has a point estimate of ∼65 kya. The only other branch of macrohaplogroup N that could have arisen in India that early is haplogroup N5, but more data on the diversity and geographic distribution of this haplogroup are needed.

Haplogroup U2 as a subhaplogroup of haplogroup U is definitely younger than this early diversification of R in India. Taking the mtDNA lineages from the autochthonous subhaplogroups U2a, U2b, and U2c, we estimate a potential founder age of 49,900±7,900 years for this part of the phylogeny. The age calculated here, however, depends on the relative frequency of U2a versus U2b, since the latter contributes to higher ages in view of the large number of coding-region mutations in the U2b stem of the phylogeny. Control-region estimates for the Indian U2 lineages are slightly higher (∼50–55 kya [Kivisild et al. 1999a]). On the other hand, unless further screening of the Near Eastern mtDNA pool would exhibit early offshoots of U2a, U2b, or U2c, an entry of U2 in India more recent than 40 kya is not plausible.

Il Papŕ
11-25-2014, 05:05 AM
Cool!
Technically a visualization as only his femur was found.

Another visualization:
http://static1.businessinsider.com/image/544821f15afbd33b178b4567-480/a-femur-found-by-chance-on-the-banks-of-a-west-siberian-river-in-2008-is-that-of-a-man-who-died-around-45000-years-ago-scientists-said-shedding-light-on-modern-humans-colonisation-of-the-planet.jpg
A femur found by chance on the banks of a west Siberian river in 2008 is that of a man who died around 45,000 years ago, scientists said, shedding light on modern humans' colonisation of the planet
http://www.businessinsider.com/afp-oldest-dna-ever-found-sheds-light-on-humans-global-trek-2014-10#ixzz3JwRjuMQw
This picture is actually a representation of neanderthall .

parasar
11-25-2014, 05:17 AM
This picture is actually a representation of neanderthall .

Another:
http://www.neanderthal.de/en/press-pictures/pictures/neanderthals/index.html
http://www.neanderthal.de/en/press-pictures/pictures/neanderthals/index.html?tx_reddownloads%5Bfile%5D=991&cHash=917cab9482d2c51b6f975d9d36e2864b

GailT
11-25-2014, 05:42 AM
So if he is just one mutation downstream of R, do you suppose some of the calculated ages are overestimates?


Behar's age estimate for R is 56,000 years, so the question is whether it is plausible that a 45,000 sample could be R with only 1 extra mutation, and yes, it is possible. There are cases of modern samples who have had no mutations in their line in 15,000 years, although this is extremely rare. The 64,200 year age estimate seems less likely given only one extra mutation.

This also illustrates the challenge of using ancient samples to date the mtDNA phylotree. The variation in the mutation rate is so large that a single sample is not conclusive. At most you can say that R is older than 45,000 years, but you can't set a reliable upper limit.

Another possibility might be that this sample had extra mutations that they failed to detect.

parasar
11-25-2014, 06:04 AM
Behar's age estimate for R is 56,000 years, so the question is whether it is plausible that a 45,000 sample could be R with only 1 extra mutation, and yes, it is possible. There are cases of modern samples who have had no mutations in their line in 15,000 years, although this is extremely rare. The 64,200 year age estimate seems less likely given only one extra mutation.

This also illustrates the challenge of using ancient samples to date the mtDNA phylotree. The variation in the mutation rate is so large that a single sample is not conclusive. At most you can say that R is older than 45,000 years, but you can't set a reliable upper limit.

Another possibility might be that this sample had extra mutations that they failed to detect.

I was think about the detection issue too, but the coverage is supposed to be very high ["4,439-fold of the mtDNA"].

parasar
07-15-2015, 12:17 AM
Ust-Ishim:
CTS11667+
Z4842/M2308+
Z12216-
Z4845/M2313-
Z12176-
Z4952/M2339-
F650/M2346-


HG03742, Indian Telugu:
CTS11667+ (23208284 G>A)
Z4842, M2308+ (7690182 A>T)
Z12216+ (3909630 T>C)
Z4858, M2313+ (8674808 C>T)
Z12176+ (9978055 C>A)
Z4952, M2339+ (21797754 T>C )
F650, M2346+ (23617006 G>A)
M214-
P188-
P192-
P193-
P194-
P195-


Oase1:
Z4842+
F650-

So Z4842/M2308+ can be thought of as the defining mutation for this branch.

malleus
07-15-2015, 11:06 AM
Behar's age estimate for R is 56,000 years, so the question is whether it is plausible that a 45,000 sample could be R with only 1 extra mutation, and yes, it is possible.

I heard that Ust Ishim's maternal line is now assigned to B, an early form of B.