# Population Genetics > Paleogenetics > Paleolithic & Mesolithic >  Neanderthal Ydna

## Angela

*The Divergence of Neandertal and Modern Human Y Chromosomes*http://www.cell.com/ajhg/abstract/S0...2816%2930033-7

"Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured *Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain.* We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. *We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages.* This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. *The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct*. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to _PCDH11Y_, _TMSB4Y_, _USP9Y,_ and _KDM5D_. *Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from* *KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups."
*
So, they're proposing, that offspring of a Homo Sapiens, Sapiens, mother and Neanderthal father would have died in utero, yes? 
Again, Reich seems to have been correct...this is just about at the limit of biological compatibility.

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## Yetos

> This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes.


thank you, I was always wondering about that,
but this means that a mtDNA must have comed from Neantherthal right?

I think now the interesting questions have changed,
No common link among Neantherthal and sapiens? they can have offsprings, but not same origin as species? or I missunderstood?

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## Maciamo

> *The Divergence of Neandertal and Modern Human Y Chromosomes*
> 
> 
> http://www.cell.com/ajhg/abstract/S0...2816%2930033-7
> 
> "Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured *Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain.* We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. *We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages.* This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. *The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct*. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to _PCDH11Y_, _TMSB4Y_, _USP9Y,_ and _KDM5D_. *Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from* *KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups."
> *
> So, they're proposing, that offspring of a Homo Sapiens, Sapiens, mother and Neanderthal father would have died in utero, yes? 
> Again, Reich seems to have been correct...this is just about at the limit of biological compatibility.



Very interesting, but I have serious doubts about antigens eliciting a maternal immune response during gestation. Half a million year of divergent evolution is not enough to bring to related sub-species to the limit of biological compatibility. The evidence for that is that lions and tigers can procreate and give birth to both male and female fertile offspring (tigons or ligers, depending if the father is a tiger or a lion), even though their common ancestors lived *3.5 million years ago*. The same is true for dogs, wolves, coyotes, jackals and perhaps also foxes (see canine hybrids, e.g. the coywolf), and canidae branched off from one another even longer ago, approximately *12 million years ago* (7.5 million if we exclude foxes). 

The only reason that a mule is infertile is that horses and donkeys don't have the same number of chromosomes (like humans and chimpanzees). So far all evidence suggest that Neanderthals and Denisovans had 23 pairs of chromosomes like Homo sapiens, and indeed if they didn't we wouldn't carry traces of their DNA today (as hybrids would have been infertile).

Additionally, the severe population bottleneck in the genus Homo caused Y-chromosomes to be very similar to one another compared to chimpanzee Y-chromosomes. In other terms, when compared to two chimpanzees belong to very distant Y-haplogroups, Homo sapiens and Neanderthal Y-DNA look very similar. There is no rational reason to believe that this would have caused an immune reaction leading to miscarriage.

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## Angela

> thank you, I was always wondering about that,
> but this means that a mtDNA must have comed from Neantherthal right?
> 
> I think now the interesting questions have changed,
> No common link among Neantherthal and sapiens? they can have offsprings, but not same origin as species? or I missunderstood?


We do descend from a common ancestor, but that was about 590,000 years ago according to these researchers. When the two groups met again about 50,000 years ago, they interbred to some extent, which is why Eurasians have on average about 3% Neanderthal dna. 

However, many researchers now believe that the two groups were now different enough that the offspring were sometimes not very viable. If these researchers are onto something, one of the reasons is that Homo Sapiens Sapiens mothers would have suffered miscarriages because of histo-incompatibility if they carried an offspring with Neanderthal y dna. They speculate that's why no Neanderthal yDna has yet been found in modern Homo Sapiens Sapiens males. The offspring of Neanderthal women and Homo Sapiens Sapiens males must have been slightly more viable or we wouldn't have that 3% autosomal inheritance, but they don't discuss the possibility of finding Neanderthal mtDna in modern humans. 

Still, even without this supposed incompatibility, there were other things that might have disadvantaged Neanderthals. There are a number of papers discussing them; just use the search engine. In this paper, this is what they say:

*"*I*n comparing the Neandertal lineage to those of modern humans, we identified four coding differences with predicted functional impacts, three missense and one nonsense (**Table 1**).* Three mutations—within _PCDH11Y_, _USP9Y_, and _TMSB4Y_—are unique to the Neandertal lineage, and one, within _KMD5D_, is fixed in modern human sequences. *The first gene,**PCDH11Y, resides in the X-transposed region of the Y chromosome. Together with its X-chromosome homolog PCDH11X, it might play a role in brain lateralization and language development.*25 *The second gene,* *USP9Y, has been linked to ubiquitin-specific protease activity26 and might influence spermatogenesis.*27 *Expression of the third gene,* *TMSB4Y, might reduce cell proliferation in tumor cells, suggesting tumor suppressor function.28* Finally, the fourth gene,*KDM5D, encodes a lysine-specific demethylase whose activity suppresses the invasiveness of some cancers.29"


*The fourth one is unique to humans, but the first two are unique to Neanderthals and aren't very advantageous.

The researchers also state the following:
"*Polypeptides from several Y-chromosome genes act as male-specific minor histocompatibility (H-Y) antigens that can elicit a maternal immune response* during gestation. *Such effects could be important drivers of secondary recurrent miscarriages30 and might play a role in the fraternal birth order effect of male sexual orientation.31* Interestingly, all three genes with potentially functional missense differences between the Neandertal and modern humans sequences are H-Y genes, including _KDM5D_, the first H-Y gene characterized.32 It is tempting to speculate that some of these mutations might have led to genetic incompatibilities between modern humans and Neandertals and to the consequent loss of Neandertal Y chromosomes in modern human populations. Indeed, reduced fertility or viability of hybrid offspring with Neandertal Y chromosomes is fully consistent with Haldane’s rule, which states that “when in the [first generation] offspring of two different animal races one sex is absent, rare, or sterile, that sex is the [heterogametic] sex.”

Secondary recurrent miscarriages are defined as situations where the first offspring survives but the immune response kicks in with subsequent births and there are then a series of miscarriages. Nowadays, fertility specialists prescribe the kind of anti-rejection drugs given for transplants. I don't understand what this has to do with homosexuality. Perhaps someone more knowledgeable can chime in.
I

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## Angela

> We do descend from a common ancestor, but that was about 590,000 years ago according to these researchers. When the two groups met again about 50,000 years ago, they interbred to some extent, which is why Eurasians have on average about 3% Neanderthal dna. 
> 
> However, many researchers now believe that the two groups were now different enough that the offspring were sometimes not very viable. If these researchers are onto something, one of the reasons is that Homo Sapiens Sapiens mothers would have suffered miscarriages because of histo-incompatibility if they carried an offspring with Neanderthal y dna. They speculate that's why no Neanderthal yDna has yet been found in modern Homo Sapiens Sapiens males. The offspring of Neanderthal women and Homo Sapiens Sapiens males must have been slightly more viable or we wouldn't have that 3% autosomal inheritance, but they don't discuss the possibility of finding Neanderthal mtDna in modern humans. 
> 
> Still, even without this supposed incompatibility, there were other things that might have disadvantaged Neanderthals. There are a number of papers discussing them; just use the search engine. In this paper, this is what they say:
> 
> *"*I*n comparing the Neandertal lineage to those of modern humans, we identified four coding differences with predicted functional impacts, three missense and one nonsense (**Table 1**).* Three mutations—within _PCDH11Y_, _USP9Y_, and _TMSB4Y_—are unique to the Neandertal lineage, and one, within _KMD5D_, is fixed in modern human sequences. *The first gene,**PCDH11Y, resides in the X-transposed region of the Y chromosome. Together with its X-chromosome homolog PCDH11X, it might play a role in brain lateralization and language development.*25 *The second gene,* *USP9Y, has been linked to ubiquitin-specific protease activity26 and might influence spermatogenesis.*27 *Expression of the third gene,* *TMSB4Y, might reduce cell proliferation in tumor cells, suggesting tumor suppressor function.28* Finally, the fourth gene,*KDM5D, encodes a lysine-specific demethylase whose activity suppresses the invasiveness of some cancers.29"
> 
> 
> ...


This article gives potential causes for recurrent miscarriages. An immune response by the mother is one of them. As I said, when no other cause is found some women are given steroids. I've seen it work, but I always thought the parents were taking quite a risk and it might have been better to get artificially inseminated if it was so important .

https://en.wikipedia.org/wiki/Recurrent_miscarriage

"A common feature of immune factors in causing recurrent pregnancy loss appears to be a decreased maternal immune tolerance towards the fetus.[7]

"
*Male-specific minor histocompatibility*Immunization of mothers against male-specific minor histocompatibility (H-Y) antigens has a pathogenic role in many cases of _secondary recurrent miscarriage_, that is, recurrent miscarriage in pregnancies succeeding a previous live birth. An example of this effect is that the male:female ratio of children born prior and subsequent to secondary recurrent miscarriage is 1.49 and 0.76 respectively.[11]"

Further down in the article they say immunotherapy doesn't work, but I know of women who were treated that way and kept the babies.

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## Fire Haired14

@Maciamo,

Walrus's are bears? :)

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## Maciamo

> @Maciamo,
> 
> Walrus's are bears? :)


Don't be stupid. The phylogenetic tree just shows a selection of distantly related carnivorous mammalian species.

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## Maciamo

> This article gives potential causes for recurrent miscarriages. An immune response by the mother is one of them. As I said, when no other cause is found some women are given steroids. I've seen it work, but I always thought the parents were taking quite a risk and it might have been better to get artificially inseminated if it was so important .
> 
> https://en.wikipedia.org/wiki/Recurrent_miscarriage
> 
> "A common feature of immune factors in causing recurrent pregnancy loss appears to be a decreased maternal immune tolerance towards the fetus.[7]
> 
> "
> *Male-specific minor histocompatibility*
> 
> ...


Yes, but that also happens between modern humans, even within the same ethnic group and within small country communities where all individuals are related within 5 to 10 generations. MHC compatibility issues have little to do with Neanderthals. Actually, as you know and we have discussed before, quite a few HLA types today were inherited from Neanderthals, including HLA-A2, which is found in 25% to 30% of people of European descent.

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## Fire Haired14

> Don't be stupid. The phylogenetic tree just shows a selection of distantly related carnivorous mammalian species.


At least they're canines, and Bear's closest relatives. That in itself is a surprise. It's similar to how, humans are apes, but we look so differnt from other apes. Chimps look more similar to Gorillas than to humans, but are more related to humans. Just like how bears look more similar to wolves than to Walrus's, but are more related to Walrus's.

EDIT: Can you post a link where you got those phylogenetic trees from?

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## Maciamo

> At least they're canines, and Bear's closest relatives.


I meant: It's a _canine_ phylogenetic tree showing _also_ a selection of distantly related carnivorous mammalian species.




> EDIT: Can you post a link where you got those phylogenetic trees from?


It's from Nature: Genome sequence, comparative analysis and haplotype structure of the domestic dog, by Lindblad-Toh et al (2005).

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## Goga

The whole thing between Neandertal and Homo Sapiens species doesn't make any sense, but it's fascinating nerveless.

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## Moi-même

> We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages.


Which leave the door open for Homo Antecessor (dated between 700k and 1.2m years old) to be the commun ancestor between Sapiens and Neandertal.

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## berun

Someone must say it: maybe the case against the male Neandertal lines is cultural instead of genetic.

After the apparition of homo sapiens sapiens the major mammals dissapear, romans and ancient empires used to get slaves in their wars (human slaves...), even two centuries ago the europeans were trafficking with African slaves (negroes had not soul...), half century ago the Soviet empire was deporting entire nations, when the nazis were killing jews and conquering territories of inferior races... by simple empirism applied to the situation human / neandertal, those spared could be slavized by sapiens bands (females even as sexual slaves); a 3% of autosomal DNA is a lot if it only comes from female neandertals that surely were not in a relation one to one with human females...

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## bicicleur

> Someone must say it: maybe the case against the male Neandertal lines is cultural instead of genetic.
> 
> After the apparition of homo sapiens sapiens the major mammals dissapear, romans and ancient empires used to get slaves in their wars (human slaves...), even two centuries ago the europeans were trafficking with African slaves (negroes had not soul...), half century ago the Soviet empire was deporting entire nations, when the nazis were killing jews and conquering territories of inferior races... by simple empirism applied to the situation human / neandertal, those spared could be slavized by sapiens bands (females even as sexual slaves); a 3% of autosomal DNA is a lot if it only comes from female neandertals that surely were not in a relation one to one with human females...


well, that is not what this study is about, but I agree with your first line, 
but I can't imagine slavery among nomadic HG tribes, it would not be practical

but there was a frontier in SW Asia of 75000 years (125-50 ka) between Neanderthals and homo sapiens, and they didn't merge, I think that says enough

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## Tomenable

> there was a frontier in SW Asia of 75000 years (125-50 ka) between Neanderthals and homo sapiens, and they didn't merge


Maybe some Neanderthal carved a good CV and got admitted to some human tribe?:  :Grin: 




^ There was no question about Y-DNA haplogroup during that tribal admission process.

*BTW:*

It seems that vast majority of uniparental lineages (subclades) from Upper Paleolithic times are extinct by now. Our present-day Y-DNA haplogroups come from only several dozen out of many thousands of men who lived at that time. So it is possible that some Neanderthal Y-DNA lineages existed among AMHs in Upper Paleolithic era, but got extinct between that era and present-day, as great majority of all Upper Paleolithic lineages (both mtDNA and especially Y-DNA) did. Ancient DNA will provide answers.

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## berun

Bicicleur your point is right, i was thinking after posting which kind of works could do slaves among paleolithic bands and i had no ideas... only could be used female neandertals as sexual slaves by men and as "cave maidens" by human women itself (i suppose it would be the use thought by a mean modafaka)

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## Moi-même

> well, that is not what this study is about, but I agree with your first line, 
> but I can't imagine slavery among nomadic HG tribes, it would not be practical


North American Indians didn't find it impractical.




> In Canada, the majority of slaves were not of African, but rather of Aboriginal origin. *Native populations customarily subjugated war captives before the arrival of the French*, but this practice acquired new meanings and unprecedented proportions in the context of western expansion. Beginning in the 1670s, the French began to receive captives from their Aboriginal partners as tokens of friendship during commercial and diplomatic exchanges. *The Illinois were notorious for the raids which they led against nations to the southeast and from which they brought back captives.* By the early eighteenth century, the practice of buying and selling these captives like merchandise was established. 
> 
> The ethnic origin of Aboriginal slaves is occasionally specified in period documents. They included Foxes and Sioux from the western Great Lakes, Inuit from Labrador, Chickasaws from the Mississippi valley, Apaches from the American southeast, and especially “Panis”. The latter designation can be misleading. In its strictest sense it referred to the Pawnees, a nation which inhabited the basin of the Missouri River and which was heavily targeted by the allies of the French. Amongst colonists, however, their name rapidly became a generic way of referring to any Aboriginal slave. Many an “esclave panis” (Panis slave) who show up in the records, thus, was not Pawnee at all.


historymuseum.ca/virtual-museum-of-new-france/population/slavery/

Originally, it was the losers of a war who has to replace losts the winners endured, replacing, say, 10 dead warriors.

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## berun

Well, slavery was not usual among hunter-gatherers as their economy is purely autonomous, but there are other case of hunter-gatherers with slavery as a byproduct of their economy: fishing (it's necessary to make canoes, nets, drying fish...)

https://en.wikipedia.org/wiki/Coast_Salish_peoples




> With earlier access to European guns through the fur trade, they raided for slaves and loot.
> 
> There existed no formal political institutions. ... No formal political office existed. Warfare for the southern Coast Salish was primarily defensive, with occasional raiding into territory where there were no relatives. No institutions existed for mobilizing or maintaining a standing force.
> 
> Society was divided into upper class, lower class and slaves, all largely hereditary. ... Unlike hunter-gatherer societies widespread in North America, but similar to other Pacific Northwest coastal cultures, Coast Salish society was complex, hierarchical and oriented toward property and status.
> 
> Slavery was widespread. The Coast Salish held slaves as simple property and not as members of the tribe. The children of slaves were born into slavery.


It seems that slavery could be promoted if the economy "stands" for it (working force to make fishing instruments and conserve fish) or if there is a big unbalance among tribes (the use of guns), even so, it is the economy / working force necessary that "justifies" the use of slaves and not having guns, even more, the slavery would hinder the evolution to a productive economy as is agriculture. 

Taking this exemple to Europe... with their big mammals roaming free... how would it transform the economy of the first modern humans getting there?

https://en.wikipedia.org/wiki/Pleistocene_megafauna

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## Yetos

what about the 'hobbit'
do we have his DNA?

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## Greying Wanderer

@Angela




> So, they're proposing, that offspring of a Homo Sapiens, Sapiens, mother and Neanderthal father would have died in utero, yes?


I think they're saying there would have been a higher probability of immune system driven miscarriage so over hundreds of generations you get a gradual winnowing effect only leaving those Neanderthal genes that were very beneficial.

Makes sense imo.

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## Greying Wanderer

> well, that is not what this study is about, but I agree with your first line, 
> but I can't imagine slavery among nomadic HG tribes, it would not be practical
> 
> but there was a frontier in SW Asia of 75000 years (125-50 ka) between Neanderthals and homo sapiens, and they didn't merge, I think that says enough


The paper shows they could have merged but the end result would be the same.

Three assumptions.
1) Neanderthal were cold adapted
2) the earth warmed up gradually created a rolling series of warmer latitude bands over time from the south to the north
3) the AMH coming from the warmer south always had larger numbers along the border

Then if
- Neanderthal and AMH females randomly troupe swapped along the border like chimps 
- the population ratio each time was say 2:1
then the Neanderthal along the border would become 50% AMH in the first wave while the AMH along the border would only become 25% Neanderthal - repeated over time I think it stabilizes somewhere around both being c. 75% AMH just due to larger AMH starting population.

So if both populations select against the minority component (except for the most beneficial genes) then they'd both end up with the same final percentage.

Repeat for each latitude band as warming continues.

The only differences would be the *last* populations to go through the process might still have a higher percentage of Neanderthal DNA or more recently (less anciently) had a larger percentage.

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## Greying Wanderer

not really on topic but Neanderthal related

http://www.theatlantic.com/science/a...n-site/484070/

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## LeBrok

> not really on topic but Neanderthal related
> 
> http://www.theatlantic.com/science/a...n-site/484070/


Cool find. They were going 360 meters with fire, and dragged tons of wood to maintain fire, to play with stalactites. Dudes with fantazy, a human nature, lol. I bet many died of CO poisoning, unless there is a draft in this cave.

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## epoch

> not really on topic but Neanderthal related
> 
> http://www.theatlantic.com/science/a...n-site/484070/


175.000 years ago is a good find. It is far better than the 40.000 years old hand paintings in the El Castillo cave, which were attributed to Neanderthals due to age rather than pushing back evidence for the earliest modern humans.

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## Greying Wanderer

> Cool find. They were going 360 meters with fire, and dragged tons of wood to maintain fire, to play with stalactites. Dudes with fantazy, a human nature, lol. I bet many died of CO poisoning, unless there is a draft in this cave.


neanderthal d&d group

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## LeBrok

> neanderthal d&d group


I don't know d&d, maybe R&D, research and development. :)

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## epoch

> Very interesting, but I have serious doubts about antigens eliciting a maternal immune response during gestation. Half a million year of divergent evolution is not enough to bring to related sub-species to the limit of biological compatibility. The evidence for that is that lions and tigers can procreate and give birth to both male and female fertile offspring (tigons or ligers, depending if the father is a tiger or a lion), even though their common ancestors lived *3.5 million years ago*. The same is true for dogs, wolves, coyotes, jackals and perhaps also foxes (see canine hybrids, e.g. the coywolf), and canidae branched off from one another even longer ago, approximately *12 million years ago* (7.5 million if we exclude foxes).



Tiger-lion hybrids suffer fertility issues.

https://en.wikipedia.org/wiki/Tigon#Fertility

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## I1a3_Young

Has Neanderthal mtDNA ever been identified?

Sent from my XT1080 using Eupedia Forum mobile app

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## t50

I know this thread is a bit old, but it seems like a good place for this curiosity:

reddit.com/r/genetics/comments/2gt9d2/denisova_cave_neanderthal_was_ydna_haplogroup_r/

Anyone care to repeat his finding and comment?

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## jose luis

The first attempt to find out if we had interbreed with Neanderthals was directed to the mitochondrial dna because it is usually the one that passes most easily from the replaced population to the successor population and none were found. I don't know if they already found it. Homo sapiens should find Neanderthal women, grotesque nightmare characters, Neanderthals should find all homo sapiens homosexuals couturiers and treacherous in the perverse intelligence of their traps, and adore the femina sapiens (women) beautifully decorated and sensual in their tropical dances.

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## jose luis

Unlike neanderthal mtDNA in humans, human mtDNA in neanderthal was easy to find. Although people like to fantasize about these things, Neanderthals could easily kidnap human women, for example when they drove away from camp for food, and have a big party with them and their daughters. In a few generations Neanderthal mitochondria disappeared from their pack. A few more kidnappings, and the pack gradually became anatomically indistinguishable from a homo sapiens band just continuing under the orders of the Neanderthal boss chromosome (y chromosome). The elements of these flocks easily integrated into the pure homosapiens flocks giving rise to such approximately 2% Neanderthals who came to us and thus the Neanderthals would have been defeated by love and not by war.

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## Gnarl

An interesting thing about interbreeding with Neanderthals is, though, that mostly we didn't. Even in places where we overlapped with them for thousands of years. We clearly did have several successful successful matings with Neanderthals over a period of time, perhaps thousands of years. But all those snippets of Neanderthal DNA in our genome come from a single line of Neanderthals that separated from the rest of them about 70 000 years ago. The rest of them didn't pass on any DNA, even the gracile Croatian ones with their wide-ranging mating networks.

This is very different from how human-human interactions normally go. When we look at even very old DNA we find it made up of the genes of many previous groups. Total replacement is very rare.

To me at least, this indicates some kind of biological barrier to hybridization. Lack of male-specific DNA is a bit of circumstantial evidence for that as well. Haldanes rule etc. 

Its outside my expertise, but I don't think there are firm rules on how many generations it takes to build barriers to reproduction. I would speculate that changes in diet, sustenance patterns, climate etc along with random chance all contribute to the accumulation of factors that can be barriers to reproduction. If there was some biochemical issue that was recently evolved it could be that one tribe of Neanderthals didn't have it fixated in the population yet.

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## Ownstyler

> An interesting thing about interbreeding with Neanderthals is, though, that mostly we didn't. Even in places where we overlapped with them for thousands of years.


While the two groups did overlap for a long time in some areas, we have to consider the possibility that there were matings that not produced successful offspring who just don't happen to be ancestors. In that case the issue would not be inter-group incompatibility, but the failure of the sapiens group to re-enter the broader sapiens pool. If I remember correctly, the very first Europeans, who are the ones who interacted with Neanderthals for thousands of years, only left a tiny genetic imprint on the subsequent European populations.

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## jose luis

Contribution to explaining that we inherited only the Neanderthal genetics absorbed by the homo sapiens flocks that crossed the Sinai Desert approximately 60 000 years ago: Although Europe is neighboring Africa, homo sapiens only began to penetrate it 25 000 years after reaching the other side of the planet (Austalia and western Pacific), certainly due to the resistance of the Neanderthals. We had been in Morocco for over 300,000 years and more than 270,000 years later had not yet dislodged the Neanderthals of Gibraltar, the same thing in the near east, we started to move forward and back there, more than 100,000 years ago but we also just came in eastern Europe approximately 35 000 years ago and perhaps from the northern steppe/tundra. There yes, we had a decisive advantage. Neanderthals would at most drill holes in skins where animal tendons were crudely passed, for their sporadic steppe/tundra expeditions in the few weeks of the Arctic summer, while we explored deeply their huge mammoth herds, and other herbivores, thanks to our clothes hermetically sewn with the eyed needle that protected us from the cold. For these pioneer sapiens flocks, coming from the steppe/tundra rather than populating, the priority would be to know the territories: By the amount of migrating birds measure the size of the territories from which they come, by the flow of the rivers at the mouth the size of their watershed ... .They must have lived closely together, even having children in common, with the Neanderthals to extract the millenary information they have accumulated about Europe, otherwise impossible to obtain: Location of - silex, obsidian, and other stones to make tools; rock salt and other useful minerals; gold nuggets to hang around the neck; animal cliffs, big game and migratory birds passages, river rapids and other fishing grounds; edible, medicinal and useful plants; water points in dry areas; caves... and in the end magical places and who are their spiritual entities. I see them crouching around the fire, in great complicity, the Neanderthals with the trapeze of their shoulders almost higher than their heads. When the terrain recognition phase was over the settler phase begun (the gravetense and their statuettes of large women or goddesses) which will extreminate earlier pioneer populations because they have accumulated obvious Neanderthal characteristics. As southern sapiens never had high hopes of progressing on the ground, they did not mix with Neanderthals, as there was no point in extracting information ,and so, the little genetics we received would be that of southern sapiens.

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## jose luis

This process of gathering information was certainly accelerated with the help of some crazy mushrooms, such as those brought from the tundra still today, or further south with other plants used to get enebriated before widespread use of wine and distilled beverages (mandragora, henbane, ephedra, cannabis, white poppy ...). So we mixed our dances and songs (epics, odes, hymns, litanies ...), our legends and beliefs would be more difficult, but mixing the configuration of our constellations was simple .... Of course I doesn't included the most obvious information such as the location of mountains, plains, rivers and lakes, the seas and their shells, but also harmful winds such as sirocco, rocky recesses ... All of this a bit like the process of early colonization of North America (Daniel boone, Davy Crockett ...), which gave rise to the isolated groups of melangeons and diffuse Indian DNA in the populations on the east coast, which did not occur in the post-pioneer settlement. In the previous post where I wrote silex I should have written flint and instead of large women statuettes I meant overly procreative women statuettes.

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## jose luis

*The evolutionary history of Neandertal and Denisovan Y chromosomes

*I still can't get the links to work:


https://www.biorxiv.org/content/10.1...03.09.983445v1

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## Gnarl

> An interesting thing about interbreeding with Neanderthals is, though, that mostly we didn't.
> 
> Its outside my expertise, but I don't think there are firm rules on how many generations it takes to build barriers to reproduction. I would speculate that changes in diet, sustenance patterns, climate etc along with random chance all contribute to the accumulation of factors that can be barriers to reproduction. If there was some biochemical issue that was recently evolved it could be that one tribe of Neanderthals didn't have it fixated in the population yet.


I've recently come across a paper that has an interesting and plausible-sounding explanation for why we have DNA in us from only one line of Neanderthals. 
_"Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals" :

_From the paper:_





Once the interaction front was destabilized, presumably around 45–50 kya, other processes, previously overshadowed by disease burden, would then have been responsible for the replacement of Neanderthals by Moderns, although it has been suggested that disease transmission dynamics could also have played a prominent role in the replacement process. Our model supports this possibility. Conditions relating to disease dynamics need not have been symmetric between Moderns and Neanderthals—for example, the Moderns’ tropical pathogen package may have been more burdensome to the Neanderthals than the Neanderthals’ temperate pathogen package was to Moderns, following the pattern of decreasing pathogen burden with latitude. Hence, Moderns may have overcome the disease burden from contact sooner than Neanderthals. This asymmetry would have eventually allowed bands of Moderns to migrate into the Neanderthal regions unhindered by novel transmissible diseases, while carrying contagious diseases to which the Neanderthals were not yet immune. Moreover, after the historical front of interaction was crossed and migration reached deeper into Eurasia, this relative Modern advantage would have increased further, as Neanderthal bands encountered far from the initial contact zone would have been intolerant to the entirety of the novel pathogen package spread by the Moderns.


_

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## jose luis

https://en.wikipedia.org/wiki/Neanderthal_extinction

the links still don't work

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## jose luis

In the previous post ,In the last chapter of the Wikipedia article that I sent the link , I would like to draw your attention to the Campanian Ignimbrite Eruption - 


https://en.wikipedia.org/wiki/Campan...brite_eruption

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## firetown

I am still suggesting that all Neanderthal males were likely killed over thousands of years. They lived in small groups, around 30 each. If there were 30,000 of them alive at one point, that would mean having around 1,000 villages spread all over Europe. This means those small groups were isolated. What were the numbers of Homo sapiens entering Europe? Were they mostly males? Were they in large groups?
I have a tough time imagining that if there were large numbers of males, the encounters with Neanderthals were friendly.
They likely killed the males and mated with the females.

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## anishakapoor11

Thanks for the post.

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## Doggerland

Neatherhal/Denisova/Heildebergensis Y-Data Output from BAM Analysis Kit:


*DenisovaCave Child*


#Mutation	ISOGG-Y-Haplogroup
CTS3662/M5671/PF704= CT
CTS3837= T
CTS12478/PF6529= R1b1a2
FGC5628/Y4010= R1b1a2a1a2c1f2a1a
L2/S139= R1b1a2a1a2b1
L16/M522/PF3493/S138= IJK
L268= P/(Investigation)
L467/KL2= O3a1
L471/PF5989= P/(Investigation)
L611= E/(Investigation)
L721/PF6020= P/(Investigation)
L1004= A1
L1136= A0-T
M251/M9122/PF699= BT
M294= CT
M522/L16/PF3493/S138= IJK
M3581/PF3047= G2
M5585/PF1414/V9= CT
M5588/PF210= CT
M5607= CT
M5609= CT
M5613= CT
M5671/CTS3662/PF704= CT
M5786/PF1061= CT
M8967= BT
M8977= BT
M8994= BT
M9046/PF324= BT
M9083= BT
M9094/PF671= BT
M9097/PF672= BT
M9122/M251/PF699= BT
M9138= BT
M9187= BT
M9258= BT
M9295/PF1000= BT
M9310= BT
M9331/PF1057= BT
M9338/PF1064= BT
M9378= BT
P158/PF2706= F
P225= R1
P310/PF6546/S129= R1b1a2a1a
PF79= BT
PF210/M5588= CT
PF324/M9046= BT
PF626= BT
PF672/M9097= BT
PF699/M251/M9122= BT
PF704/CTS3662/M5671= CT
PF1000/M9295= BT
PF1057/M9331= BT
PF1061/M5786= CT
PF1064/M9338= BT
PF1414/M5585/V9= CT
PF2706/P158= F
PF3047/M3581= G2
PF3493/L16/M522/S138= IJK
PF5989/L471= P/(Investigation)
PF6020/L721= P/(Investigation)
PF6497/YSC0000219= R1b1a2
PF6529/CTS12478= R1b1a2
PF6546/P310/S129= R1b1a2a1a
S129/P310/PF6546= R1b1a2a1a
S138/L16/M522/PF3493= IJK
S139/L2= R1b1a2a1a2b1
V9/M5585/PF1414= CT
V84= B/(Investigation)
Y1480= CT
Y1531= CT
Y1791= CT
Y4010/FGC5628= R1b1a2a1a2c1f2a1a
YSC0000219/PF6497= R1b1a2
Z1357/CTS7128= C1a1a2
Z11933= BT
Z11979= BT
Z12110= BT
Z13341= H3a
Z15165= E1a2
Z17357= BT
Z17378= BT
Z17385= BT
Z17457= E1a1
Z17710= CT


*Simade los Huesos (2 samples had Y-data)*


#Mutation	ISOGG-Y-Haplogroup
M9039= BT
M9156/PF764= BT
PF764/M9156= BT


#Mutation	ISOGG-Y-Haplogroup
M9359= BT


*ForbesQuarry*


#Mutation	ISOGG-Y-Haplogroup
PF620= BT
Z12005= BT
Z14904= E1a2b1a1a1


*Mezmaiskaya*


#Mutation	ISOGG-Y-Haplogroup
50f2(P)= B2b1
CTS484= T1a1
CTS7482/M5720= CT
CTS8591= R1b1a2
CTS8608/M5745= CT
CTS12019= E1b1b1a1a1
CTS12440/M3629/PF3126= G
FGC756= G2a1a1a1a1a1b1
FGC1920/Y2754= Q1b1a1a1a1b
L1129= A0-T
M141= A1b1a1
M734/PF6057/S4/YSC0000201= R
M3629/CTS12440/PF3126= G
M5630= CT
M5720/CTS7482= CT
M5738= CT
M5745/CTS8608= CT
M5786/PF1061= CT
M5811/PF1238= CT
M8980/PF229= BT
M9005= BT
M9086/PF648= BT
M9192= BT
M9227= BT
M9254= BT
M9266/PF946= BT
PF229/M8980= BT
PF648/M9086= BT
PF946/M9266= BT
PF1061/M5786= CT
PF1238/M5811= CT
PF3126/CTS12440/M3629= G
PF6057/M734/S4/YSC0000201= R
S4/M734/PF6057/YSC0000201= R
S355/Z196= R1b1a2a1a2a1
S484/Z48= R/(Investigation)
Y1521= CT
Y1580= CT
Y2754/FGC1920= Q1b1a1a1a1b
YSC0000201/M734/PF6057/S4= R
Z47= R/(Investigation)
Z48/S484= R/(Investigation)
Z848= E1b1b1b2a1
Z930/CTS3045= E1a
Z1842= J1a3a
Z6106= G
Z6107= G
Z12477= C1b1a1a
Z13364= H3a
Z13439= H3a
Z13616= H3
Z14907= E1a2b1a1a1
Z14926= E1a2b1a1a1
Z15557= E1a
Z16208= E1b1a1a1c2c3c
Z16986= I
Z17342= BT
Z17897= A1b

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## Jeremy Sun

It is much more probably, in my opinion, the reason for incompatibility between humans and Neanderthals has to do with chromosomal differences rather than to Y chromosome itself. The genes may not have aligned the way lions and tigers do not even though the numbers are the same.

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## gandalf

Neandertal had a bigger head than Sapiens , so it could lead to impossibility for women Sapiens to give birth to a Neandertal child . For a Neandertal woman no problem to have one or the other . This could partly explain the decrease of male Neandertal genes ?

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## Salento

> Neandertal had a bigger head than Sapiens , so it could lead to impossibility for women Sapiens to give birth to a Neandertal child . For a Neandertal woman no problem to have one or the other . This could partly explain the decrease of male Neandertal genes ?


Modern Human infants have soft spots on top of their heads to facilitate the skull to change shape during birth, … I guess it would have been the same for Neanderthal newborns.

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## Salento

… Obviously the newborn was half Sapiens and half Neanderthal, and in addition to the skull soft spots, the head would have been smaller than a Neanderthal infant.

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## Diictodon

Jebel Irhoud + Qafzeh and Skhul DNA need be sequenced imo. Would give wonderful insight t the origins of Hss and their interaction with Near East Neanderthals

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## firetown

> While the two groups did overlap for a long time in some areas, we have to consider the possibility that there were matings that not produced successful offspring who just don't happen to be ancestors. In that case the issue would not be inter-group incompatibility, but the failure of the sapiens group to re-enter the broader sapiens pool. If I remember correctly, the very first Europeans, who are the ones who interacted with Neanderthals for thousands of years, only left a tiny genetic imprint on the subsequent European populations.


How do we know that Neanderthal males and Sapiens females ever mated?

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## gandalf

> How do we know that Neanderthal males and Sapiens females ever mated?


Because you are here mate !

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