Check for new replies
Neanderthals data converted
#31
If we use the estimation from Mendez:

Quote:We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya).

Of course the estimation from Mendez is sending the  beginning of A00 in the zone where Neanderthals split from the common tree.

Therefore, the question is: are A00 more related to the Neanderthals or to the other humans (AMH) ?
If we use the time scale, the A00 haplogrup is exactly in the middle between the split of the Neanderthals and the formation of other AMH haplogroups. That why I think A00 is more related to the Neanderthal's side than the AMH. 
But also this opinion may change. We do our verifications on limited number of snips. 
If we add more and more snips for the verification: the position of A00 may vary in one direction or to the other.
It may happen that A00 are more  Neanderthal like.  And it may be the opposite:  the difference between A00/Neanderthals could be more significant than what we see from our current data. 
However as per our current data and several publications:  the time zone of A00 is in the middle between Neand. and the other AMH.
Reply
#32
Which one of the Neanderthals is sharing most variants with the Humans ?
There are many shared snips with Chimp / Denisova /Neanderthals.
We assume that shared snips: with Chimp, orang, Denisova / Neand are generally ancestral.
So let take the case where Chimp, orang, Denisova are the ancestral, Neanderthals are the derived .
How many of these derived snips are shared witht he humans ?
And which type of Neanderthal has the most shared snips with the humans ?

BTW, there are several ways for the humans to get Neanderthal type of variants.
Let me explain some of them:
1. Ancestral, shared origin from common ancestor. In general the Humans and the Neanderthals originated from common ancestor , which appeared many thousands years after the Denisovans separated from the tree..

2. Random mutation.. It is possible to have such weak DNA connection with high probability to mutate, so such mutations may appear independently in both Humans and Neand.

3. Mix ( admix).

To have such answers we need to have a good database with good coverage for the Neanderthals. Currently we have already many examples of Neand. DNA.
Another question in the same line: which one of the Neanderthals is most closely realted to Denisova ? We exclude Denisova 11, who is a direct mix between Denisovans and Neand.
So who is the next Neanderthal with highest amount of shared variants ?

I guess it is Chagirskaya, best sharing with Denisova.. But this could be also a question of DNA quality/ coverage, as the better coverage will provide higher number of shared variants.
Dispite the dificulties: Altai and Vnidija seems to share good amount of variants with the humans .
Reply
#33
From what I can see at least as far as f-stats go is that, among Neanderthals, AMH affinity is inversely correlated with Denisova affinity, which to me screams admixture (Neanderthals = Denisova + AMH)
Norfern-Ostrobothnian and TanTin like this post
Reply
#34
(01-28-2025, 03:18 PM)Kale Wrote: From what I can see at least as far as f-stats go is that, among Neanderthals, AMH affinity is inversely correlated with Denisova affinity, which to me screams admixture (Neanderthals = Denisova + AMH)

I don't know, I am not sure about this.
I think AMH are some complicated mixture of  Denisova and  Neanderthals.
It is interesting to see at specific snip positions that some AMH are carring Denisova snp. Other AMH carry Neand.
In addtition some Neanderthals have more shared snips with Denisova.  Therefore the ancestry of Neanderthals transferred to AMH is from the specific Neanderthal groups.
In general it is a total mess...
I don't think  Neanderthals = Denisova + AMH.. But definitely Neanderthals so far are from A00 Y haplogroup, the ancestral version of A00. AMH evolved a lot later.
Reply
#35
Sharing this diagram with some Altai variants, opposite of Chimp/Denisova. (Chr X, minor alleles  Build 37 position numbers)
AimSmall likes this post


Attached Files
.pdf   Rplot_display.pdf (Size: 33.33 KB / Downloads: 13)
Reply
#36
Are the humans more related to Neanderthals or to Denisovans ?
Denisovans were separated from MRCA earlier.
However the amount of shared variants between humans and Denisova is near the same as the variants shared with Neanderthals.
Is this because of admixture?

Next question: which populations are more related to Neanderthals and which populations are more related to Denisovans ?

The test that I am doing now:
1 . Select some variants , where Neanderthals are opposite of Denisovans.
2. Verify the distribution of such snips among humans to find who are more Neanderthal or Denisova related.

What is very weird in such results: I find more such Neanderthal variants among Africans. And there are more Denisovan variants among Eurasians.
What could be the explanation for such results ? Admixture ?
If all humans are coming from Africa, why those who left Africa lost their Neanderthal variants and obtain more Denisovan ?
Reply
#37
Because you can't just select variants like that when you're using an already biased SNP set like 1240k. Use outgroup f-stats, f4(Chimp, modern, Denisova, Neanderthal) will be highly positive for any modern human.
Reply
#38
This is an old publication from  2017.


IBD Sharing between Africans, Neandertals, and Denisovans
https://pmc.ncbi.nlm.nih.gov/articles/PMC5381509/

Quote:Abstract
Interbreeding between ancestors of humans and other hominins outside of Africa has been studied intensively, while their common history within Africa still lacks proper attention. However, shedding light on human evolution in this time period about which little is known, is essential for understanding subsequent events outside of Africa. We investigate the genetic relationships of humans, Neandertals, and Denisovans by identifying very short DNA segments in the 1000 Genomes Phase 3 data that these hominins share identical by descent (IBD). By focusing on low frequency and rare variants, we identify very short IBD segments with high confidence. These segments reveal events from a very distant past because shorter IBD segments are presumably older than longer ones. We extracted two types of very old IBD segments that are not only shared among humans, but also with Neandertals and/or Denisovans. The first type contains longer segments that are found primarily in Asians and Europeans where more segments are found in South Asians than in East Asians for both Neandertal and Denisovan. These longer segments indicate complex admixture events outside of Africa. The second type consists of shorter segments that are shared mainly by Africans and therefore may indicate events involving ancestors of humans and other ancient hominins within Africa. Our results from the autosomes are further supported by an analysis of chromosome X, on which segments that are shared by Africans and match the Neandertal and/or Denisovan genome were even more prominent. Our results indicate that interbreeding with other hominins was a common feature of human evolution starting already long before ancestors of modern humans left Africa.



Table 2
Number of Neandertal- and Denisovan-Matching IBD Segments Shared Exclusively by Africans that are Observed in a Particular Subpopulation
                            AFR ESN GWD LWK MSL YRI
Neandertal 1–22 9,607 2,987 3,135 2,994 3,191 3,133
Neandertal X 512 139 117 148 123 132
Denisovan 1–22 10,985 3,312 3,494 3,410 3,602 3,489
Denisovan X 563 167 154 187 163 166
Reply
#39
From this old publication we can see the number of shared IBD segments with Neandertals and Denisovans.
Surprisingly this number is the highest for the Africans.
The Africans share more short length IBD segments with the Denisovans.

For CHR X,  the shared segments with Denisovans is 10x times more than Neandertal shared IBD segm.


Attached Files Thumbnail(s)
   
Reply
#40
Discussion / Conclusions from the same publication:
https://pmc.ncbi.nlm.nih.gov/articles/PMC5381509/


There are different explanations for our results that concern the origin of segments that are shared between Africans and the Neandertal and/or Denisovan genome.

(1)
Quote:One interpretation of our results is that ancestors of humans and ancient hominins interbred within Africa. The hypothesis of ancient substructures in Africa with limited gene flow between subpopulations of hominins (Plagnol and Wall 2006; Slatkin 2008; Yang et al. 2012) does not contradict this interbreeding. Neandertals and Denisovans could be more closely related to Africans than to out-of-Africa populations because of more interactions between their ancestors. In this case, since the ancestors of Africans and Neandertals/Denisovans were not clearly separated, this could be considered “admixture” rather than “interbreeding”.


(2)
Quote: Another interpretation of the extensive IBD sharing between Africans and ancient genomes is that these shared IBD segments originate from a common ancestor of Neandertals/Denisovans and humans. They can only be found in modern Africans due to incomplete lineage sorting. According to this scenario, the detected IBD segments arose first in the population that existed prior to the ancient separation of Neandertals, Denisovans and modern humans, but were relatively rare. Consequently they survived in both archaic humans and in present-day Africans, while drifting to a very low frequency in non-Africans. On average, these IBD segments are tagged by more than 20 rare variants. Surprisingly the individuals analyzed possess either all of these variants or none of them while individuals with only some of these rare variants are missing. In our opinion, it is unlikely that, for thousands of IBD segments, only these extremes survived while all the intermediate cases died out completely.

Consequently, we assume that the source population was separated from all the other populations for a long time and, therefore, acquired such a high number of mutations. We do not know, whether the separated population was already a Neandertal, a Denisovan, their ancestor, or a different hominin. We cannot rule out, that the IBD segments also existed in ancestors of modern Eurasians and were lost due to strong genetic drift. However, our results suggest an interbreeding within Africa that involved a population that was isolated for an extended period of time. This early interbreeding can still be detected via IBD segments that are shared between Africans and Neandertals and/or Denisovans.

Another explanation without introgression in Africa is backto-Africa gene flow as suggested by Pru¨ fer et al. (2014), Wang et al. (2013), and Llorente et al. (2015) for Neandertal ancestry in Africans. However, (1) the large number of IBD segments shared exclusively between the ancient genomes and Africans, (2) their even distribution across all African populations analyzed, and (3) their short length contradict this hypothesis.

(3)
Quote:Besides the short IBD segments shared with Africans, the other interesting finding is, that there are more IBD segments shared between South Asians and Neandertals and/or Denisovans than between other non-African populations and these ancient genomes. Recent investigations found that South Asians share a surprisingly high amount of DNA with the Denisovan genome (Sankararaman et al. 2016). In our analysis the amount is even higher. Possible explanations for this finding are as follows:
(1) additional interbreeding events with ancestors of South Asians
,
(2) introduction of IBD segments from ancient genomes into other non-African populations via South Asians and not directly, and
(3) combinations of bottlenecks, genetic drift, and different selective pressures.
Reply
#41
... continue

Quote: As supplementary figure S7, Supplementary Material online, shows, the length distributions of IBD segments shared between Neandertals or Denisovans and different non-African populations are very similar. Thus, a separate interbreeding event at a different time point seems to be unlikely. However, based on the IBD segment length distributions, we cannot rule out multiple interbreeding events with different human populations in a relatively short time period. Because the IBD segment lengths are determined by the number of crossovers since the interbreeding, a single cannot be distinguishing from multiple events.


Quote:According to the second explanation, Denisovans and Neandertals interbred only with the ancestors of South Asians. In the following, South Asians introduced parts of the ancient genomes into the genomes of Europeans and East Asians via later admixture events. This explanation Povysil and Hochreiter GBE 3414 Genome Biol. Evol. 8(12):3406–3416. doi:10.1093/gbe/evw234 might account for the low number of Denisovan-matching segments found in Europeans. However, we think it is unlikely that it is the reason for the considerably larger number of IBD segments shared exclusively between Neandertals and Europeans/East Asians and between Denisovans and East Asians.

Quote:The third explanation is based on the idea that the interbreeding occurred between the ancient hominins and the common ancestors of Eurasians. Consequently, different populations went through different bottlenecks, experienced various selective pressures and admixtures with other human populations. Because of the aforementioned factors, ancient DNA that had entered the human gene pool survived in one population while it has been lost in another population, or has been diluted in the third population. This would explain why some of the detected IBD segments are present in all three non-African populations, some only in two out of three, and others are exclusively found in a single continental population. Previous results (Vernot and Akey 2014, 2015; Kim and Lohmueller 2015) showed that above factors probably are not the only reason for varying levels of Neandertal- and Denisovan-ancestry in different non-African populations, however, we assume that at least they affected IBD sharing between modern humans and ancient genomes.
Reply
#42
.. Conclusion

Quote:Since shorter IBD segments are presumably older than longer ones, the segments we extracted reveal events from the very distant past. We found short IBD segments that match the Neandertal and/or Denisovan genome and are shared mainly by Africans.

These segments may either stem from a common ancestor with subsequent incomplete lineage sorting or more likely from an interbreeding of ancestors of humans and other ancient hominins within Africa.
AimSmall likes this post


Attached Files Thumbnail(s)
   
Reply

Check for new replies

Forum Jump:


Users browsing this thread: 1 Guest(s)