Login

tipirneni · 03-08-2024, 02:36 PM

Massilani et al. generated genome-wide data from a 34,000-year-old female individual from the Salkhit Valley in eastern Mongolia and conducted a detailed modeling of her ancestry with regard to other Pleistocene human genomes. They found evidence for Denisovan ancestry in ancient human genomes from at least 6000 years before the Salkhit individual lived and determined that the Denisovan contribution differed from that of another ancient Asian individual, as well as from the ancient Denisovan contribution to extant Australasians. Following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.
[Image: 370_579_f1.jpeg]

This individual was more closely related to present-day East Asians than to ancient Europeans but, surprisingly, shared more alleles with a ~35,000-year-old individual from Belgium (Goyet Q116-1) than with other ancient Europeans (7). In Siberia, which neighbors East Asia to the north, four modern human individuals older than 20,000 years BP have been studied: a ~45,000-year-old individual from Ust’-Ishim in West Siberia who did not contribute ancestry to present-day populations (8); a ~24,000-year-old individual from Mal’ta 1 in South Central Siberia who was more related to Western Europeans than to East Asians and was part of a population that contributed approximatively one-third of the ancestry of present-day Native Americans (9); and two ~31,000-year-old individuals from the Yana Rhinoceros Horn Site in northeastern Siberia who show affinities to early modern humans in both West and East Eurasia (10).
[Image: 370_579_f1.jpeg]

The Salkhit individual and her relationship to ancient and present-day humans.
(A) The Salkhit skull cap. [Image © Institute of Archaeology, Mongolian Academy of Sciences (Mongolia)] (B) Heat map illustrating the genetic similarity between the Salkhit individual and modern humans from Eurasia older than 20,000 years (20 ka) (diamonds) as well as present-day human populations (circles) determined by f3 statistic of the form f3(Salkhit, X; Mbuti). The warmer the color, the higher the genetic similarity between the Salkhit individual and a population or individual. (C) Relative amounts of allele sharing between the Salkhit and Tianyuan genomes and ancient and present-day humans determined by D statistics of the form D(Salkhit, Tianyuan, X, Mbuti). The D statistic is positive when the individual/population shares more alleles with the Salkhit individual than with the Tianyuan individual. The colors of the diamonds indicate whether the Z-score is significant (red), weakly significant (pink), or not significant (white).

[Image: 370_579_f2.jpeg]

Our models suggest that the Tianyuan individual and the ~37,000-year-old Kostenki14 individual from Russia are unadmixed representatives of early East and West Eurasian populations, respectively. The Salkhit individual, who lived in Mongolia about 6000 years after the Tianyuan individual, carries ~75% of its ancestry from a Tianyuan-related East Eurasian population and the remaining ~25% from a population related to the Siberian Yana individuals, who lived some 3000 years later than the Salkhit individual.

We estimate the proportion of Neanderthal ancestry in the Salkhit genome to be ~1.7% (table S17 and fig. S15), similar to other early Eurasians. As is the case for other Eurasian individuals, the Neanderthal ancestry in the Salkhit individual is equally related to the two Neanderthals from Vindija Cave in Croatia and Chagyrskaya Cave in Siberia who are ~50,000 and 80,000 years old, respectively, and less related to the ~120,000-year-old Siberian “Altaï” Neanderthal from Denisova Cave

Using data from ~1.7 million SNPs where Neanderthal and/or Denisovan genomes differ from present-day African genomes, we detected 18 segments of Denisovan ancestry longer than 0.2 cM in the Salkhit genome (Fig. 3, table S18, and figs. S17 and S28) and 20 such segments in the Tianyuan genome (table S18 and figs. S19 and S28). We detected about one-third as many segments of Denisovan DNA in the genomes of the ancient Siberians Yana 1, Yana 2, and Mal’ta 1 (table S18, figs. S19 to S21, and fig. S28), consistent with the proportion of their East Asian ancestry. In contrast, no Denisovan ancestry was detected in the genome of the ~45,000-year-old Siberian individual from Ust’Ishim in West Siberia, nor in any European individual older than 20,000 years (table S18, figs. S22 to S25, and fig. S28). Thus, the Salkhit and Tianyuan genomes provide direct evidence that ancestors of modern humans who lived in East Asia 40,000 years ago had met and mixed with Denisovans.

[Image: 370_579_f4.jpeg]

Fig. 4 Overlap of Denisovan segments in the Salkhit genome and present-day non-African populations.
(A) Correlation coefficient of the overlap between the Denisovan segments larger than 0.2 cM in the Salkhit genome and Denisovan segments larger than 0.05 cM in 45 present-day Eurasian populations (see fig. S28 for the same with 111 present-day populations). Numbers above the bars give the number of overlapping segments and the number of segments in the present-day population. The range of correlation coefficients generated by 500 bootstraps is indicated. (B) Geographic locations of present-day populations for which Denisovan ancestry segments overlap significantly with the Salkhit individual (orange circles). Sizes of circles are proportional to the correlation coefficients.

the 34,000-year-old Salkhit individual carried more West Eurasian ancestry than the 40,000-year-old Tianyuan individual, indicating that after the major West/East Eurasia split, gene flow from West Eurasia to East Asia occurred earlier than 34,000 years ago, probably mediated by populations related to the Siberian Yana individuals. We also show that these early East Asians carried segments of Denisovan DNA that come from admixture events that also contributed Denisovan DNA to populations across mainland Asia today, but not to Papuans and Aboriginal Australians.

from Denisovan ancestry and population history of early East Asians | Science

tipirneni · 03-08-2024, 02:40 PM

I share more than 625 SNPs with this 44kya Salkhit sample

[Image: salkhit-denisov.png]

rp48 · 03-10-2024, 06:29 PM

(03-08-2024, 02:36 PM)tipirneni Wrote: Massilani et al. generated genome-wide data from a 34,000-year-old female individual from the Salkhit Valley in eastern Mongolia and conducted a detailed modeling of her ancestry with regard to other Pleistocene human genomes. They found evidence for Denisovan ancestry in ancient human genomes from at least 6000 years before the Salkhit individual lived and determined that the Denisovan contribution differed from that of another ancient Asian individual, as well as from the ancient Denisovan contribution to extant Australasians. Following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

This individual was more closely related to present-day East Asians than to ancient Europeans but, surprisingly, shared more alleles with a ~35,000-year-old individual from Belgium (Goyet Q116-1) than with other ancient Europeans (7). In Siberia, which neighbors East Asia to the north, four modern human individuals older than 20,000 years BP have been studied: a ~45,000-year-old individual from Ust’-Ishim in West Siberia who did not contribute ancestry to present-day populations (8); a ~24,000-year-old individual from Mal’ta 1 in South Central Siberia who was more related to Western Europeans than to East Asians and was part of a population that contributed approximatively one-third of the ancestry of present-day Native Americans (9); and two ~31,000-year-old individuals from the Yana Rhinoceros Horn Site in northeastern Siberia who show affinities to early modern humans in both West and East Eurasia (10).

The Salkhit individual and her relationship to ancient and present-day humans.
(A) The Salkhit skull cap. [Image © Institute of Archaeology, Mongolian Academy of Sciences (Mongolia)] (B) Heat map illustrating the genetic similarity between the Salkhit individual and modern humans from Eurasia older than 20,000 years (20 ka) (diamonds) as well as present-day human populations (circles) determined by f3 statistic of the form f3(Salkhit, X; Mbuti). The warmer the color, the higher the genetic similarity between the Salkhit individual and a population or individual. (C) Relative amounts of allele sharing between the Salkhit and Tianyuan genomes and ancient and present-day humans determined by D statistics of the form D(Salkhit, Tianyuan, X, Mbuti). The D statistic is positive when the individual/population shares more alleles with the Salkhit individual than with the Tianyuan individual. The colors of the diamonds indicate whether the Z-score is significant (red), weakly significant (pink), or not significant (white).

Our models suggest that the Tianyuan individual and the ~37,000-year-old Kostenki14 individual from Russia are unadmixed representatives of early East and West Eurasian populations, respectively. The Salkhit individual, who lived in Mongolia about 6000 years after the Tianyuan individual, carries ~75% of its ancestry from a Tianyuan-related East Eurasian population and the remaining ~25% from a population related to the Siberian Yana individuals, who lived some 3000 years later than the Salkhit individual.

We estimate the proportion of Neanderthal ancestry in the Salkhit genome to be ~1.7% (table S17 and fig. S15), similar to other early Eurasians. As is the case for other Eurasian individuals, the Neanderthal ancestry in the Salkhit individual is equally related to the two Neanderthals from Vindija Cave in Croatia and Chagyrskaya Cave in Siberia who are ~50,000 and 80,000 years old, respectively, and less related to the ~120,000-year-old Siberian “Altaï” Neanderthal from Denisova Cave

Using data from ~1.7 million SNPs where Neanderthal and/or Denisovan genomes differ from present-day African genomes, we detected 18 segments of Denisovan ancestry longer than 0.2 cM in the Salkhit genome (Fig. 3, table S18, and figs. S17 and S28) and 20 such segments in the Tianyuan genome (table S18 and figs. S19 and S28). We detected about one-third as many segments of Denisovan DNA in the genomes of the ancient Siberians Yana 1, Yana 2, and Mal’ta 1 (table S18, figs. S19 to S21, and fig. S28), consistent with the proportion of their East Asian ancestry. In contrast, no Denisovan ancestry was detected in the genome of the ~45,000-year-old Siberian individual from Ust’Ishim in West Siberia, nor in any European individual older than 20,000 years (table S18, figs. S22 to S25, and fig. S28). Thus, the Salkhit and Tianyuan genomes provide direct evidence that ancestors of modern humans who lived in East Asia 40,000 years ago had met and mixed with Denisovans.

Fig. 4 Overlap of Denisovan segments in the Salkhit genome and present-day non-African populations.
(A) Correlation coefficient of the overlap between the Denisovan segments larger than 0.2 cM in the Salkhit genome and Denisovan segments larger than 0.05 cM in 45 present-day Eurasian populations (see fig. S28 for the same with 111 present-day populations). Numbers above the bars give the number of overlapping segments and the number of segments in the present-day population. The range of correlation coefficients generated by 500 bootstraps is indicated. (B) Geographic locations of present-day populations for which Denisovan ancestry segments overlap significantly with the Salkhit individual (orange circles). Sizes of circles are proportional to the correlation coefficients.

the 34,000-year-old Salkhit individual carried more West Eurasian ancestry than the 40,000-year-old Tianyuan individual, indicating that after the major West/East Eurasia split, gene flow from West Eurasia to East Asia occurred earlier than 34,000 years ago, probably mediated by populations related to the Siberian Yana individuals. We also show that these early East Asians carried segments of Denisovan DNA that come from admixture events that also contributed Denisovan DNA to populations across mainland Asia today, but not to Papuans and Aboriginal Australians.

from Denisovan ancestry and population history of early East Asians | Science

Are the prominent brow ridges expected for an anatomically modern Homo sapiens of this timeframe?

Kale · 03-11-2024, 03:09 AM

Remarks were made before the DNA about it's 'archaic' features in that regard.
It seems like heavy brow ridges were more common back then, but it's not like it doesn't happen today.
Given Salkhit is from Mongolia, and we're talking about brow ridges, what automatically comes to mind as examples are Mongolian sumo wrestlers Hakuho (in his more recent years) and Terunofuji. They could both give Salkhit some competition.

tipirneni · 03-12-2024, 12:41 AM

(03-11-2024, 03:09 AM)Kale Wrote: Remarks were made before the DNA about it's 'archaic' features in that regard.
It seems like heavy brow ridges were more common back then, but it's not like it doesn't happen today.
Given Salkhit is from Mongolia, and we're talking about brow ridges, what automatically comes to mind as examples are Mongolian sumo wrestlers Hakuho (in his more recent years) and Terunofuji. They could both give Salkhit some competition.

Hakuho Me

TanTin · 03-25-2024, 08:42 AM

I did some F4 tests and I can't confirm such High Denisovan components in Salkhit.

16293 salkhit1_noUDG.SG salkhit1 Salkhit_skullcap Skull 2020

Test has been performed with V52.HO dataset.

Here are some F4-stats:

Show Content

On opposite, I see more Neanderthal (Vindija) markers than Denisovan. This result is only for a group of 76803 markers. The smaller number of snips could be the reason for such result and lower Z value.

TanTin · 03-25-2024, 08:51 AM

f4( prefix, left , "Russia_Ust_Ishim.DG" , "Chimp.REF" , "Denisova.DG" )
Another confirmation showing that Salkhit has more shared markers with Chimp, than Denisova.

Show Content

TanTin · 03-25-2024, 08:56 AM

The main reason to do such tests: was to show the high Denisova components in Ancient Greeks: Minoan and Mycenean.
I was looking where to share these results and found this topic as related to Denisova..

However the results for Salkhit are really disappointing. With Papuans and Micronesian there are no surprises as usual, because they are highly Denisovans. The big surprise for me are the Ancient Greeks. ( but not all of them).

tipirneni · 03-26-2024, 12:11 AM

(03-25-2024, 08:42 AM)TanTin Wrote: I did some F4 tests and I can't confirm such High Denisovan components in Salkhit.

16293 salkhit1_noUDG.SG salkhit1 Salkhit_skullcap Skull 2020

Test has been performed with V52.HO dataset.

Here are some F4-stats:

> R171
# A tibble: 19 x 9
pop1 pop2 pop3 pop4 est se z p n
<chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Turkey_N Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000655 0.000301 2.18 2.94e-2 560641
2 Iran_GanjDareh_N Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000750 0.000329 2.28 2.25e-2 533056
3 Georgia_Kotias.SG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000617 0.000374 1.65 9.95e-2 560142
4 Russia_Sidelkino_HG.SG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000288 0.000396 0.726 4.68e-1 476266
5 Tajikistan_BA_DashtiKozy Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000374 0.000319 1.17 2.41e-1 497289
6 Greece_Minoan_Lassithi Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000678 0.000320 2.12 3.38e-2 532747
7 Greece_Minoan_Kephala_Petras.SG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000788 0.000366 2.15 3.14e-2 551696
8 Greece_Minoan_Odigitria Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.0000352 0.000550 -0.0640 9.49e-1 144463
9 Italy_South_HG_Ostuni2 Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000925 0.00178 0.519 6.03e-1 11350
10 Russia_Ust_Ishim.DG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0 0 NaN NaN 561287
11 Denisova.DG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.0651 0.000617 106. 0 561287
12 Vindija_Neanderthal.DG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.0559 0.000597 -93.6 0 561287
13 Papuan.SDG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.00194 0.000352 5.53 3.26e-8 557761
14 Greece_BA_Mycenaean_Pylos Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000864 0.000489 1.77 7.73e-2 210959
15 Greece_BA_Mycenaean Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000774 0.000371 2.09 3.68e-2 346577
16 Micronesian Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000728 0.000320 2.27 2.31e-2 518559
17 Chimp.REF Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.0182 0.000467 38.9 0 549695
18 Japanese Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG 0.000329 0.000294 1.12 2.62e-1 561287
19 Mongolia_Salkhit_UP.SG Russia_Ust_Ishim.DG Denisova.DG Vindija_Neanderthal.DG -0.000173 0.000815 -0.212 8.32e-1 76803

On opposite, I see more Neanderthal (Vindija) markers than Denisovan. This result is only for a group of 76803 markers. The smaller number of snips could be the reason for such result and lower Z value.

May be you are not looking at the right file. The publication which introduced this sample clearly states there are significant Denisovan parts in it. There are diagrams in the paper I listed at the top which shows that and says it is the Mongolian Denisovan sample as opposite to the Oceanian Denisovan. maybe you are taking the Mongol denisovan parts to be Neaderthal. There are also Neanderthal parts in it. Or simply your file is probably a small open version of the full fileset which is available only to researchers

tipirneni · 03-26-2024, 12:17 AM

(03-25-2024, 08:56 AM)TanTin Wrote: The main reason to do such tests: was to show the high Denisova components in Ancient Greeks: Minoan and Mycenean.
I was looking where to share these results and found this topic as related to Denisova..

However the results for Salkhit are really disappointing. With Papuans and Micronesian there are no surprises as usual, because they are highly Denisovans. The big surprise for me are the Ancient Greeks. ( but not all of them).

Actually the full samples are not usually given to public other than for big publications papers like in Nature or science. Some time there are 2 versions of the samples as it happened to Otzi when there was a contaminated 2012 sample and the later 2020s sample which had significant differences due to precautions not followed in 2012 draw

TanTin · 03-26-2024, 04:31 AM

Salkhit sample is included in V52 HO version of Reich dataset. There is also a better version in the other dataset.
It is from the same publication in 2020.
Salkhit is very interesting one.
I am sure also it is Basal.
It is more basal compared to many other East asians.
By definition Basal are low on Neanderthal components.

TanTin · 03-26-2024, 05:12 AM

There is only 1 sample
Mongolia_Salkhit_UP.SG salkhit1_noUDG.SG
7310 salkhit1_noUDG.SG salkhit1 Salkhit_skullcap Skull 2020 MassilaniPaaboScience2020 Direct: IntCal20 34873 285 33458-32389 calBCE (30430±300, OxA-X-2717-25) .. Mongolia_Salkhit_UP.SG Khentii Province, Norovlin County, Salkhit Valley Mongolia

There are all the details provided for it in the .anno file.
I will redo the test with v52.2_1240K_public , but I don't expect big difference.

From the supplementary file in the original publication:

Show Content

Spoiler

The average coverage of the autosomes is similar to that of the X chromosome, indicating that despite the robust morphology of the skull, the Salkhit individual was female (table S8 and fig. S7). To determine to which major group of hominins she belonged, we estimated the percentage of derived alleles shared with the genomes of a present-day human (Mbuti, HGDP00982) (19), a Neanderthal (Denisova 5) (20), and a Denisovan (Denisova 3) (21). We found that 32% of informative positions covered by deaminated fragments carry alleles seen in the present-day human, whereas 5% and 7% carry alleles seen in the Neanderthal and Denisovan genomes, respectively. This falls within the range seen for present-day Eurasian individuals (table S9 and fig. S8), indicating that the Salkhit individual was a modern human, in agreement with more recent morphological analyses (13, 14).

....
We estimate the proportion of Neanderthal ancestry in the Salkhit genome to be ~1.7% (table S17 and fig. S15), similar to other early Eurasians. As is the case for other Eurasian individuals, the Neanderthal ancestry in the Salkhit individual is equally related to the two Neanderthals from Vindija Cave in Croatia and Chagyrskaya Cave in Siberia who are ~50,000 and 80,000 years old, respectively, and less related to the ~120,000-year-old Siberian “Altaï” Neanderthal from Denisova Cave (20, 26, 27) (fig. S16).

We detected about one-third as many segments of Denisovan DNA in the genomes of the ancient Siberians Yana 1, Yana 2, and Mal’ta 1 (table S18, figs. S19 to S21, and fig. S28), consistent with the proportion of their East Asian ancestry. In contrast, no Denisovan ancestry was detected in the genome of the ~45,000-year-old Siberian individual from Ust’Ishim in West Siberia, nor in any European individual older than 20,000 years (table S18, figs. S22 to S25, and fig. S28). Thus, the Salkhit and Tianyuan genomes provide direct evidence that ancestors of modern humans who lived in East Asia 40,000 years ago had met and mixed with Denisovans.

However, given their relatively short length (≤1.3 cM), the Denisovan introgression is likely to have happened at least 10,000 years before these individuals lived.

One of the risks of inferring ancestry fragments from ancient genomes is that genome quality may affect the ability to detect introgressed segments. Under the assumption that many of the factors that affect the detection of Denisovan DNA will similarly affect the detection of Neanderthal DNA, the ratio of Denisovan to Neanderthal ancestry segments may be a reasonably robust metric of the relative amount of Denisovan ancestry. In the Salkhit and Tianyuan genomes, these ratios are about 7.5% and 8.1%, respectively. For the genomes of the North Siberians Yana 1 and Yana 2, the ratios are about 3.9% and 4.7%. Because there is no substantial difference in the amounts of Neanderthal DNA in the two early East Asian genomes and the two Yana genomes (fig. S15), this observation indicates that the ancient Siberian individuals carry less Denisovan DNA than the Salkhit and Tianyuan individuals.

TanTin · 03-26-2024, 05:43 AM

If we read carefully in the original publication from Massilani:
[Image: Salkhit-Denisova.png]

Salkhit is very similar to Tianyuan.
The amount of Denisova ancestry in both Salkhit and Tianyuan is near 7% of the Neanderthal ancestry..
That means only a tiny part of their archaic markers came from Denisova.
Because generally Salkhit is a modern human.

The bigest chunk of Denisovan markers (whole segment) was found on Chr 4. You may see the orange zone on chr4 on the picture.
In total all these Denisovan segments are still very low, but they are higher compared to some other ancient samples.

Therefore in general Salkhit is not much different from Tianyuan . If we talk about the total percentage of Denisovan ancestry - it is still very low. May be near 0.1 - 0.2 % ..
In my F4 stats the Denisova components for Salkhit were calculated to be below these of Ust-Ishim.
That doesn't mean Ust-Ishim doesn't have any Denisovan . On opposite: all of them have some Denisovan.

In papuans we see up to 6% Denisovan markers. Let be more precise: If the amount of Neanderthal ancestry is about 2%, take only 7% of these 2%, then we see only 0.02 * 0.07 = 0.0014 . That means 0.14 % or 1.4/1000 ..

To confirm these numbers, here is a table from Massilani publication:

Show Content

Table S17. Proportion of Neandertal ancestry in some ancient and present-day human genomes estimated by f4-ratio statistics.

Altai Chimp Salkhit_all_deam Mbuti Altai Chimp Vindija33.19 Mbuti 1.73% 0.0048 3.63

So they estimate Neandertal ancestry (%) = 1.73% (near 2% ) .

The main conclusion: despite the age and some archaic features, Salkhit is a Modern Human with near 2% Neanderthal and 0.14 % Denisovan markers.

TanTin · 03-26-2024, 06:08 AM

I just reran the F4 stats for v52.2_1240K_public dataset.
As expected we see the same or near the same results as with HO panel.

Show Content

tipirneni · 03-27-2024, 02:12 AM

(03-26-2024, 05:43 AM)TanTin Wrote: If we read carefully in the original publication from Massilani:

Salkhit is very similar to Tianyuan.
The amount of Denisova ancestry in both Salkhit and Tianyuan is near 7% of the Neanderthal ancestry..
That means only a tiny part of their archaic markers came from Denisova.
Because generally Salkhit is a modern human.

The bigest chunk of Denisovan markers (whole segment) was found on Chr 4. You may see the orange zone on chr4 on the picture.
In total all these Denisovan segments are still very low, but they are higher compared to some other ancient samples.

Therefore in general Salkhit is not much different from Tianyuan . If we talk about the total percentage of Denisovan ancestry - it is still very low. May be near 0.1 - 0.2 % ..
In my F4 stats the Denisova components for   Salkhit were calculated to be below these of Ust-Ishim.
That doesn't mean Ust-Ishim doesn't have any Denisovan . On opposite: all of them have some Denisovan.

In papuans we see up to 6% Denisovan markers. Let be more precise: If the amount of Neanderthal ancestry is about 2%, take only 7% of these 2%, then we see only 0.02 * 0.07 = 0.0014 . That means 0.14 % or 1.4/1000 ..

To confirm these numbers, here is a table from Massilani publication:

Show Content

Spoiler
Neandertal 1 Outgroup1 Target - modern human Outgroup2 Neandertal 1 Outgroup1 Neandertal2 Outgroup2 Neandertal ancestry (%) std.err Z score Altai Chimp Ust’Ishim_snpAD Mbuti Altai Chimp Vindija33.19 Mbuti 2.11% 0.0041 5.18 Altai Chimp Yana1 Mbuti Altai Chimp Vindija33.19 Mbuti 2.34% 0.0041 5.74 Altai Chimp Yana2 Mbuti Altai Chimp Vindija33.19 Mbuti 2.72% 0.0039 6.92 Altai Chimp Kolyma1 Mbuti Altai Chimp Vindija33.19 Mbuti 1.97% 0.0037 5.23 Altai Chimp Salkhit_all_deam Mbuti Altai Chimp Vindija33.19 Mbuti 1.73% 0.0048 3.63 Altai Chimp Tianyuan Mbuti Altai Chimp Vindija33.19 Mbuti 1.71% 0.0043 3.99 Altai Chimp Oase1 Mbuti Altai Chimp Vindija33.19 Mbuti 6.36% 0.0077 8.20 Altai Chimp Kostenki14 Mbuti Altai Chimp Vindija33.19 Mbuti 1.75% 0.004 4.38 Altai Chimp GoyetQ116-1 Mbuti Altai Chimp Vindija33.19 Mbuti 2.60% 0.0046 5.64 Altai Chimp Muierii2 Mbuti Altai Chimp Vindija33.19 Mbuti 1.32% 0.0096 1.37 Altai Chimp KremsWA3 Mbuti Altai Chimp Vindija33.19 Mbuti 1.60% 0.0068 2.35 Altai Chimp Vestonice13 Mbuti Altai Chimp Vindija33.19 Mbuti 2.61% 0.008 3.27 Altai Chimp Vestonice16 Mbuti Altai Chimp Vindija33.19 Mbuti 1.45% 0.0045 3.26 Altai Chimp Malta1 Mbuti Altai Chimp Vindija33.19 Mbuti 2.24% 0.0041 5.45 Altai Chimp ElMiron Mbuti Altai Chimp Vindija33.19 Mbuti 1.87% 0.0046 4.04 Altai Chimp Dai Mbuti Altai Chimp Vindija33.19 Mbuti 1.90% 0.003 6.30 Altai Chimp Han Mbuti Altai Chimp Vindija33.19 Mbuti 1.96% 0.0031 6.23 Altai Chimp Papuan Mbuti Altai Chimp Vindija33.19 Mbuti 2.83% 0.0032 8.72 Altai Chimp French Mbuti Altai Chimp Vindija33.19 Mbuti 1.49% 0.0029 5.15 Altai Chimp Bougainville Mbuti Altai Chimp Vindija33.19 Mbuti 2.94% 0.0036 7.95

Table S17. Proportion of Neandertal ancestry in some ancient and present-day human genomes estimated by f4-ratio statistics.

Altai Chimp Salkhit_all_deam Mbuti Altai Chimp Vindija33.19 Mbuti 1.73% 0.0048 3.63

So they estimate Neandertal ancestry (%) =   1.73% (near 2% ) .

The main conclusion: despite the age and some archaic features,   Salkhit is a Modern Human with near 2% Neanderthal and 0.14 % Denisovan markers.

I see you are treating the single sample ancient culture Siberian Denisovan as a human admix. Unfortunately I don't get paid for educating such analysis. When I get paid to speak so I will definitely reach out to you seeking monetary compensation

Login
Username/Email:
Password:	Lost Password?
	Remember me