Neanderthal Ydna

Angela

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[h=1]The Divergence of Neandertal and Modern Human Y Chromosomes[/h]
http://www.cell.com/ajhg/abstract/S0002-9297(16)30033-7

"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.
 
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?
 
The Divergence of Neandertal and Modern Human Y Chromosomes


http://www.cell.com/ajhg/abstract/S0002-9297(16)30033-7

"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.

o'brien_evolution.png


nature04338-f10.2.jpg
 
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:

"In 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
 
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:

"In 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

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]

"

[h=4]Male-specific minor histocompatibility[/h]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.
 
@Maciamo,

Walrus's are bears? :)
 
@Maciamo,

Walrus's are bears? :)

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

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.
 
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?
 
The whole thing between Neandertal and Homo Sapiens species doesn't make any sense, but it's fascinating nerveless.
 
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.
 
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...
 
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
 
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.
 
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)
 
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.
 
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
 
what about the 'hobbit'
do we have his DNA?
 
@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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