Ancient DNA Reveals the First Known Neanderthal Family

[ilabv]

Genetic insights into the social organization of Neanderthals
https://www.nature.com/articles/s41586-022-05283-y

For the first time, researchers have identified a Neanderthal family: a father and his teenage daughter, as well as several others who were close relatives. They lived in Siberian caves around 54,000 years ago. A team of scientists, which included Svante Pääbo, winner of this year’s Nobel Prize for Physiology or Medicine, published the findings in Nature this week.

The researchers extracted ancient DNA from bones and teeth that once belonged to 11 Neanderthals living together at the Chagyrskaya Cave, as well as 2 others from a second cave nearby. Of the 13, eight were adults and five were children. Alongside these remains, the team also found stone tools and animal bones.

The researchers say that the individuals found at Chagyrskaya likely lived at the same time—an unusual finding at sites this old, where discoveries often span vast timelines.

https://www.smithsonianmag.com/smart-new...-180980979

I'm very interested in NeanderSovans.



I downloaded the BAMs of the Father & Daughter.  Extracted their RAW DNA and ran both K36 and K47 admixtures.  Using these I chose the K47 to simulate G25.  I also phased the daughter's DNA with her father's to get an approximation of her mother.  Since daughter's coverage is only 2% take the results with a grain of salt.

Code:

Chagyrskaya17_daughter_simulated,-0.572048,0.070008,0.029838,0.037892,0.004764,0.007103,0.238492,-0.180868,0.004763,0.015830,0.002041,-0.007484,0.013090,0.008618,0.006172,-0.010235,0.015320,0.099510,-0.032751,0.002134,-0.014175,-0.003029,0.001887,-0.002854,-0.000225
Chagyrskaya07_father_simulated,-0.593274,0.043454,0.022763,0.035508,0.000275,-0.004249,0.232132,-0.192279,0.009095,0.016493,0.002073,-0.010831,0.004770,0.003085,0.012715,-0.011554,0.017009,0.131002,-0.044379,0.001257,-0.015981,-0.001380,0.001245,-0.002460,0.000546
Chagyrskaya17_sim_phased_mother_simulated,-0.572563,0.069944,0.029780,0.037844,0.004724,0.007067,0.238627,-0.180997,0.004826,0.015816,0.002037,-0.007577,0.012987,0.008581,0.006245,-0.010275,0.015378,0.100182,-0.032983,0.002129,-0.014246,-0.003021,0.001886,-0.002859,-0.000216

Using Davidski Ancient Individuals

Target: Chagyrskaya07_father_simulated
Distance: 4.8066% / 0.04806567 | ADC: 0.25x RC
46.4 RUS_Neanderthal
46.0 MWI_Fingira
5.6 ZAF_2000BP
1.0 ARG_ArroyoSeco2_7700BP
1.0 TUR_SE_Cayonu_PPN

Target: Chagyrskaya17_daughter_simulated
Distance: 6.2702% / 0.06270189 | ADC: 0.25x RC
53.6 RUS_Denisova-Neanderthal
39.0 MWI_Fingira
4.2 DEU_MA_ACD_Baiuvaric
2.2 TUR_SE_Cayonu_PPN
1.0 CHE_FN_steppe_contam

Target: Chagyrskaya17_sim_phased_mother
Distance: 6.2449% / 0.06244851 | ADC: 0.25x RC
53.4 RUS_Denisova-Neanderthal
39.4 MWI_Fingira
4.0 DEU_MA_ACD_Baiuvaric
2.0 TUR_SE_Cayonu_PPN
1.2 CHE_FN_steppe_contam


Using Ajeje's ancient list

Target: Chagyrskaya07_father_simulated
Distance: 6.5497% / 0.06549660 | ADC: 0.25x RC
78.0 Malawi_Fingira_LSA_2500BP_noUDG
21.0 South_Africa_1900BP.SG
1.0 Bolivia_Totocachi_Tiwanaku

Target: Chagyrskaya17_daughter_simulated
Distance: 8.2930% / 0.08293019 | ADC: 0.25x RC
41.8 Malawi_Fingira_LSA_2500BP_noUDG
29.2 Cameroon_SMA
24.4 South_Africa_1900BP.SG
4.6 Germany_EarlyMedieval.SG

Target: Chagyrskaya17_sim_phased_mother
Distance: 8.2662% / 0.08266228 | ADC: 0.25x RC
41.2 Malawi_Fingira_LSA_2500BP_noUDG
29.4 Cameroon_SMA
24.8 South_Africa_1900BP.SG
4.6 Germany_EarlyMedieval.SG

The highest quality one was already converted to G25 right? It has the same label (I know they arent useful for G25, but just wondering)

[TanTin]

Checking the X-chromosome for Neanderthals:
- We have , Mezmaiskaya2_Neanderthal.SG 0.5253 - missingness . (we have 50% of the data)
For Spy, the missingness is 0.685, so we have 30 % of it.
So far I find them near the South Africans.

[Norfern-Ostrobothnian]

Note that in PCAs there's a danger of populations more distantly related to the bulk of the samples clustering together despite not having any relation to each other at all especially in the first few PCs.

[Norfern-Ostrobothnian]

Also because G25s SNPs probably don't cover much of derived Neanderthal alleles (and neither does 1240K by proxy as both are based on modern allele variation), Neanderthals will effectively be treated like the common ancestor of Humans and Neanderthals without many derived Neanderthal alleles, resulting in far shorter distances than one would expect. If one were to make a PCA with Neanderthal specific SNPs alongside modern Human variation, I bet that Neanderthals would appear to be far more distant from other populations than they are now.

[Kale]

To add some more snips in the list  (for SPY)

Why the poking with a handful of snps here and there? On Yfull A0-T is defined by 540 snps. How many of those are covered in Spy? (I'd assume about half that given the autosomal coverage). Of those, how many are ancestral and how many are derived?

[TanTin]

To add some more snips in the list  (for SPY)

Why the poking with a handful of snps here and there? On Yfull A0-T is defined by 540 snps. How many of those are covered in Spy? (I'd assume about half that given the autosomal coverage). Of those, how many are ancestral and how many are derived?

It should be something like that. (Using the diagram from the publication ).
5 snips of 540 is still near 1%.  I was expecting that we have a lot more.. But that's not the case. Still we may confirm that Spy and Mezmaiskaya are very closely positioned near A0.

[TanTin]

Technically, we have many 1000 of shared snips between these Neanderthals and A0 . I can give you a list with these many thousands .. However they are not counted for Yfull A0-T definition. Anyway, the exercise was very good ! Thanks !

[TanTin]

If we need to calculate the distance between these Neanderthals and A0, we need to count the total number of shared snips.
The distance is the ratio different snips / total number of snips

Distance = A0(different snips)/ ( A0(different snips) + total number of shared snips)

[kolompar]

It should be big news how close they are anyway, it was basically an earlier successful out of Africa migration (or Neanderthals giving their uniparentals to modern humans, but that's not very likely with how badly they fared in Eurasia). So when, where, how? It's interesting that the oldest Y-DNA splits are now found in West/Central Africa, and not the South/East. Is Jebel Irhoud in the right time and place?

[TanTin]

In connection to this discussions here is the publication from 2014:

An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree

https://www.cell.com/ajhg/fulltext/S0002...ryMaterial

Abstract
We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. 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). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Although the stochastic nature of the evolutionary process can explain the aforementioned incongruences, the extreme age and rarity of the A00 lineage point to the possibility of a highly structured ancestral population, consistent with recent work on the autosomes.40,  41,  43,  44 This could take the form of long-standing population structure among AMH populations45 or archaic introgression from an archaic form into the ancestors of AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ∼13 kya.47 Further surveys in sub-Saharan Africa and in the African Diaspora might uncover more diverged basal lineages, which will help to disentangle some of the complex evolutionary processes that shape patterns of Y chromosome diversity. Finally, the discovery of the A00 lineage demonstrates the power of public participation in the scientific process—a venture that is likely to continue in the current era of personal genomics.

[TanTin]

As we may expect, Mezmaiskaya and Spy Neanderthals are most closely related to some Gambia and Cameroon samples.
There are not so many of them in V52 dataset. I see only 10 from A0-A1 and 6 from A1b .
It seems we don't have any examples of A00 available in the current datasets.

[AimSmall]

Appreciate you sharing that article TanTin.

[kolompar]

Shum Laka are A00. But just because they are basal to other modern humans it doesn't mean they are more related to Neanderthals, they have the same TMRCA to them as anyone else.

[TanTin]

Shum Laka are A00. But just because they are basal to other modern humans it doesn't mean they are more related to Neanderthals, they have the same TMRCA to them as anyone else.

Thanks for correcting me.  I just confirmed  I10871 is A00 and we have 4 versions for the same individual. 

There is one more: mondal_BIR-14.SG which I haven't seen the exact Y position.

[TanTin]

During the test, that I was doing for A0 - A00 I've seen Oase , which is supposed to be A0 as well.
However on my data projection Oase came between T1 individuals.

In anno file Oase is described as: A0-T .
Despite the low coverage in my data Oase is clear hg T.