Ancient DNA Reveals the First Known Neanderthal Family

[AimSmall]

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

[Mitchell-Atkins]

Your post got me curious about Neaderthal Y-dna/haplogroups...so I googled and came across this link

https://www.science.org/content/article/...chromosome

The best scenario to explain the Y pattern is that early modern human men mated with Neanderthal women more than 100,000 but less than 370,000 years ago, according to the team's computational models. Their sons would have carried the modern human Y chromosome, which is paternally inherited. The modern Y then rapidly spread through their offspring to the small populations of Neanderthals in Europe and Asia, replacing the Neanderthal Y, the researchers report today in Science. Interestingly, the modern human mates were not ancestors to today's H. sapiens—but were likely part of a population that migrated early out of Africa and then went extinct. Traces of Neanderthal DNA in living humans were inherited from a separate mixing event between 50,000 and 70,000 years ago.

[TanTin]

Your post got me curious about Neaderthal Y-dna/haplogroups...so I googled and came across this link

https://www.science.org/content/article/...chromosome

The best scenario to explain the Y pattern is that early modern human men mated with Neanderthal women more than 100,000 but less than 370,000 years ago, according to the team's computational models. Their sons would have carried the modern human Y chromosome, which is paternally inherited. The modern Y then rapidly spread through their offspring to the small populations of Neanderthals in Europe and Asia, replacing the Neanderthal Y, the researchers report today in Science. Interestingly, the modern human mates were not ancestors to today's H. sapiens—but were likely part of a population that migrated early out of Africa and then went extinct. Traces of Neanderthal DNA in living humans were inherited from a separate mixing event between 50,000 and 70,000 years ago.

Spy Neanderthal is pretty much haplogroup A0 .  So he is an African haplogroup. And Spy is not the only one. We have also Mezmayskaya2 . Both of them are near the African haplogroups.  The story that tells us the Neanderthals mixed with HS outside of Africa and got some HS genes doesn't work.. It is the Africa where Neanderthals were together and mixed with HS.  I doubt if any mix happened outside of Africa.

[Horatio McCallister]

Your post got me curious about Neaderthal Y-dna/haplogroups...so I googled and came across this link

https://www.science.org/content/article/...chromosome

The best scenario to explain the Y pattern is that early modern human men mated with Neanderthal women more than 100,000 but less than 370,000 years ago, according to the team's computational models. Their sons would have carried the modern human Y chromosome, which is paternally inherited. The modern Y then rapidly spread through their offspring to the small populations of Neanderthals in Europe and Asia, replacing the Neanderthal Y, the researchers report today in Science. Interestingly, the modern human mates were not ancestors to today's H. sapiens—but were likely part of a population that migrated early out of Africa and then went extinct. Traces of Neanderthal DNA in living humans were inherited from a separate mixing event between 50,000 and 70,000 years ago.

Spy Neanderthal is pretty much haplogroup A0 .  So he is an African haplogroup. And Spy is not the only one. We have also Mezmayskaya2 . Both of them are near the African haplogroups.  The story that tells us the Neanderthals mixed with HS outside of Africa and got some HS genes doesn't work.. It is the Africa where Neanderthals were together and mixed with HS.  I doubt if any mix happened outside of Africa.

So then wouldn't it be more accurate to say that modern human y-DNA is actually Neanderthal derived instead of the other way around?

[TanTin]

Your post got me curious about Neaderthal Y-dna/haplogroups...so I googled and came across this link

https://www.science.org/content/article/...chromosome

The best scenario to explain the Y pattern is that early modern human men mated with Neanderthal women more than 100,000 but less than 370,000 years ago, according to the team's computational models. Their sons would have carried the modern human Y chromosome, which is paternally inherited. The modern Y then rapidly spread through their offspring to the small populations of Neanderthals in Europe and Asia, replacing the Neanderthal Y, the researchers report today in Science. Interestingly, the modern human mates were not ancestors to today's H. sapiens—but were likely part of a population that migrated early out of Africa and then went extinct. Traces of Neanderthal DNA in living humans were inherited from a separate mixing event between 50,000 and 70,000 years ago.

Spy Neanderthal is pretty much haplogroup A0 .  So he is an African haplogroup. And Spy is not the only one. We have also Mezmayskaya2 . Both of them are near the African haplogroups.  The story that tells us the Neanderthals mixed with HS outside of Africa and got some HS genes doesn't work.. It is the Africa where Neanderthals were together and mixed with HS.  I doubt if any mix happened outside of Africa.

So then wouldn't it be more accurate to say that modern human y-DNA is actually Neanderthal derived instead of the other way around?

Depending on your interpretation.. If you consider the Chimp as the common ancestor, then the  modern human y-DNA is should be Neanderthal  derived.  But that's not the whole story.  There are some other humans, not on the same branch. The real humans. So the Neanderthals took their Y dna from them.

[Megalophias]

The Spy Neanderthal paper says that Spy and Mezmaiskaya share a Y clade that falls outside of modern human variation, including A00 in the modern human clade. So why do you figure Spy has A0, TanTin?

[TanTin]

The Spy Neanderthal paper says that Spy and Mezmaiskaya share a Y clade that falls outside of modern human variation, including A00 in the modern human clade. So why do you figure Spy has A0, TanTin?

In general it is A0.

You may check also in the annotation file.  It is written there as A0.
v52.2_1240K_public.anno

10138 Spy_noUDG.SG Spy_final Spy 94a
A0
It is on the same line with some other african humans. So as I remember they justify this coincident as if he received its Y chromosome from humans.  And Mezmayskaya is near the same situation. Another A.

(if you compare with other Y-chromosomes, the A-chromosome of Spy is very much closer to the african A, compared to any other non-A human chromosomes. )

[Capsian20]

The Spy Neanderthal paper says that Spy and Mezmaiskaya share a Y clade that falls outside of modern human variation, including A00 in the modern human clade. So why do you figure Spy has A0, TanTin?

In general it is A0.

You may check also in the annotation file.  It is written there as A0.
v52.2_1240K_public.anno

10138 Spy_noUDG.SG Spy_final Spy 94a
A0
It is on the same line with some other african humans. So as I remember they justify this coincident as if he received its Y chromosome from humans.  And Mezmayskaya is near the same situation. Another A.

(if you compare with other Y-chromosomes,  the A-chromosome of Spy is very much closer to the african A, compared to any other non-A human chromosomes. )

very interesting i think Tree china (TheYtree) are was added Y-DNA and maybe mtDNA Neanderthal (im not sure about mtDNA) ,anway i wish YFULL also added Y-DNA Neanderthal like mtdna https://www.yfull.com/mtree/NA/

[Capsian20]

Nothing about mtDNA in TheYtree
https://www.theytree.com/tree/Neanderthals

[Kaltmeister]

Your post got me curious about Neaderthal Y-dna/haplogroups...so I googled and came across this link

https://www.science.org/content/article/...chromosome

The best scenario to explain the Y pattern is that early modern human men mated with Neanderthal women more than 100,000 but less than 370,000 years ago, according to the team's computational models. Their sons would have carried the modern human Y chromosome, which is paternally inherited. The modern Y then rapidly spread through their offspring to the small populations of Neanderthals in Europe and Asia, replacing the Neanderthal Y, the researchers report today in Science. Interestingly, the modern human mates were not ancestors to today's H. sapiens—but were likely part of a population that migrated early out of Africa and then went extinct. Traces of Neanderthal DNA in living humans were inherited from a separate mixing event between 50,000 and 70,000 years ago.

As "modern Humans" and Neandertals share the same haplogroups - would it be possible that the Neandertals became the ancestors of at least a part of the Eurasian Homo Sapiens living today? The oldest Homo Sapiens genome we have is Ust-Ishim (45k years), but most genomes we are dealing with are much younger. The Neandertal finds from Chagyrskaya and Okladnikov described here are between 44k and 60k years old. So could the genetic difference be the result of evolution? Or, would it be possible that these Neandertal Y-chromosomes evolved into one of the modern haplogroups we observe today, making them at least the ancestors of certain male lines?

The French archaeologist Ludovic Slimak has stated that the Palaeolithic sites of Byzovaya and Mamontova Kurya in northern Europe, west of the Ural mountains, are "clearly Mousterian" and for that of Neandertal origin. They are about 28.000 years old. This would mean that the Neandertals survived in this area much longer than actually assumed.

[Kale]

The Spy Neanderthal paper says that Spy and Mezmaiskaya share a Y clade that falls outside of modern human variation, including A00 in the modern human clade. So why do you figure Spy has A0, TanTin?

In general it is A0.

You may check also in the annotation file.  It is written there as A0.
v52.2_1240K_public.anno

10138 Spy_noUDG.SG Spy_final Spy 94a
A0
It is on the same line with some other african humans. So as I remember they justify this coincident as if he received its Y chromosome from humans.  And Mezmayskaya is near the same situation. Another A.

(if you compare with other Y-chromosomes,  the A-chromosome of Spy is very much closer to the african A, compared to any other non-A human chromosomes. )

Don't pay much mind to the Neanderthal haplogroup calls in anno sheet. I believe they used an automated system to fill the haplogroup columns, and with anything automated, there are bugs. For example, two samples 'with H2a2a1' (CRS)
CAO031_3.2Mall 603-655 calCE Cuba_CanimarAbajo_Archaic
I2966.SG 7131-6775 calBCE Malawi_Hora_LSA_8500BP.SG
Really?

[TanTin]

The Spy Neanderthal paper says that Spy and Mezmaiskaya share a Y clade that falls outside of modern human variation, including A00 in the modern human clade. So why do you figure Spy has A0, TanTin?

In general it is A0.

You may check also in the annotation file.  It is written there as A0.
v52.2_1240K_public.anno

10138 Spy_noUDG.SG Spy_final Spy 94a
A0
It is on the same line with some other african humans. So as I remember they justify this coincident as if he received its Y chromosome from humans.  And Mezmayskaya is near the same situation. Another A.

(if you compare with other Y-chromosomes,  the A-chromosome of Spy is very much closer to the african A, compared to any other non-A human chromosomes. )

Don't pay much mind to the Neanderthal haplogroup calls in anno sheet. I believe they used an automated system to fill the haplogroup columns, and with anything automated, there are bugs. For example, two samples 'with H2a2a1' (CRS)
CAO031_3.2Mall 603-655 calCE Cuba_CanimarAbajo_Archaic
I2966.SG 7131-6775 calBCE Malawi_Hora_LSA_8500BP.SG
Really?

Regarding Spy and Mezmayskaya - I found they have human Y chr by myself. I was playing to project Ychr on PCA and both these Neanderthal projected in between African and non-Africans.  Then I found that Spy has many common markers with other A chr individuals.  So there are no doubts these 2 Neanderthals are A.  I can also give you the list of snips if you need.  But you can find them easy, as they are in the file.

[Woz]

It is the Africa where Neanderthals were together and mixed with HS.  I doubt if any mix happened outside of Africa.

Why not? There's modern human presence in the Levant dating to more than 120 kya (Skhul and Qafzeh hominins):

A more recent hypothesis is that Skhul/Qafzeh hominids represent the first exodus of modern humans from Africa around 125,000 years ago, probably via the Sinai Peninsula, and that the robust features exhibited by the Skhul/Qafzeh hominids represent archaic sapiens features rather than Neanderthal features.[7] The discovery of modern human made tools from about 125,000 years ago at Jebel Faya, United Arab Emirates, in the Arabian Peninsula, may be from an even earlier exit of modern humans from Africa. In January 2018 it was announced that modern human finds at the Mount Carmel cave of Misliya, discovered in 2002, had been dated to around 185,000 years ago, giving an even earlier date for an out-of-Africa migration.[9][10][11][12] .

Plenty of opportunities for Neanderthals and modern humans to mix in SW Asia in that time period.

[Kale]

Regarding Spy and Mezmayskaya - I found they have human Y chr by myself. I was playing to project Ychr on PCA and both these Neanderthal projected in between African and non-Africans.  Then I found that Spy has many common markers with other A chr individuals.  So there are no doubts these 2 Neanderthals are A.  I can also give you the list of snips if you need.  But you can find them easy, as they are in the file.

You understand that would be huge news, and thus something that would likely have been publicized yes? Consequently skepticism is the reasonable approach. Can you give a list of positive and negative calls for A0-T for example?

[TanTin]

It is the Africa where Neanderthals were together and mixed with HS.  I doubt if any mix happened outside of Africa.

Why not? There's modern human presence in the Levant dating to more than 120 kya (Skhul and Qafzeh hominins):

A more recent hypothesis is that Skhul/Qafzeh hominids represent the first exodus of modern humans from Africa around 125,000 years ago, probably via the Sinai Peninsula, and that the robust features exhibited by the Skhul/Qafzeh hominids represent archaic sapiens features rather than Neanderthal features.[7] The discovery of modern human made tools from about 125,000 years ago at Jebel Faya, United Arab Emirates, in the Arabian Peninsula, may be from an even earlier exit of modern humans from Africa. In January 2018 it was announced that modern human finds at the Mount Carmel cave of Misliya, discovered in 2002, had been dated to around 185,000 years ago, giving an even earlier date for an out-of-Africa migration.[9][10][11][12] .

Plenty of opportunities for Neanderthals and modern humans to mix in SW Asia in that time period.

The first major admix between humans and Neanderthals happened clearly in Africa. Then there was a smaller secondary admix, which could be in North Africa or Arabian Peninsula . This secondary admix  is what we see in Oase, Bacho Kiro  and in Papuans.