Modern men lack Y chromosome genes from Neanderthals, researchers say

April 7, 2016, Stanford University Medical Center

Although it's widely known that modern humans carry traces of Neanderthal DNA, a new international study led by researchers at the Stanford University School of Medicine suggests that Neanderthal Y-chromosome genes disappeared from the human genome long ago.

The study will be published April 7 in The American Journal of Human Genetics, in English and in Spanish, and will be available to view for free. The senior author is Carlos Bustamante, PhD, professor of biomedical data science and of genetics at the School of Medicine, and the lead author is Fernando Mendez, PhD, a postdoctoral scholar at Stanford.

The Y chromosome is one of two human sex . Unlike the X chromosome, the Y chromosome is passed exclusively from father to son. This is the first study to examine a Neanderthal Y chromosome, Mendez said. Previous studies sequenced DNA from the fossils of Neanderthal women or from mitochondrial DNA, which is passed to children of either sex from their mother.

Other research has shown that the DNA of is from 2.5 to 4 percent Neanderthal DNA, a legacy of breeding between modern humans and Neanderthals 50,000 years ago. As a result, the team was excited to find that, unlike other kinds of DNA, the Neanderthal Y chromosome DNA was apparently not passed to modern humans during this time.

"We've never observed the Neanderthal Y chromosome DNA in any human sample ever tested," Bustamante said. "That doesn't prove it's totally extinct, but it likely is."

Why no Neanderthal DNA?

Why is not yet clear. The Neanderthal Y chromosome genes could have simply drifted out of the human gene pool by chance over the millennia. Another possibility, said Mendez, is that Neanderthal Y chromosomes include genes that are incompatible with other , and he and his colleagues have found evidence supporting this idea. Indeed, one of the Y chromosome genes that differ in Neanderthals has previously been implicated in transplant rejection when males donate organs to women.

"The functional nature of the mutations we found," said Bustamante, "suggests to us that Neanderthal Y chromosome sequences may have played a role in barriers to gene flow, but we need to do experiments to demonstrate this and are working to plan these now."

Several Neanderthal Y chromosome genes that differ from those in humans function as part of the immune system. Three are "minor histocompatibility antigens," or H-Y genes, which resemble the HLA antigens that transplant surgeons check to make sure that organ donors and organ recipients have similar immune profiles. Because these Neanderthal antigen genes are on the Y chromosome, they are specific to males.

Theoretically, said Mendez, a woman's immune system might attack a male fetus carrying Neanderthal H-Y genes. If women consistently miscarried male babies carrying Neanderthal Y chromosomes, that would explain its absence in modern humans. So far this is just a hypothesis, but the immune systems of modern women are known to sometimes react to male offspring when there's genetic incompatibility.

When did we part ways?

The Y chromosome data also shed new light on the timeline for the divergence of humans and Neanderthals. The human lineage diverged from other apes over several million years, ending as late as 4 million years ago. After the final split from other apes, the human lineage branched into a series of different types of humans, including separate lineages for Neanderthals and what are now modern humans.

Previous estimates based on mitochondrial DNA put the divergence of the human and Neanderthal lineages at between 400,000 and 800,000 years ago. The last common ancestor of Neanderthals and humans—based on the Y chromosome DNA sequenced in the study—is about 550,000 years ago.

Sequencing the Neanderthal Y chromosome may shed further light on the relationship between humans and Neanderthals. One challenge for the research team is to find out whether the Y chromosome Neanderthal gene variants identified were indeed incompatible with human genes.

The data for the study came from public gene sequencing databases. "We did not collect any data for this work," said Mendez. "It was all public data."

Explore further: A world map of Neanderthal and Denisovan ancestry in modern humans

More information: American Journal of Human Genetics, Mendez et al.: "The divergence of Neanderthal and modern human Y chromosomes" dx.doi.org/10.1016/j.ajhg.2016.02.023

Related Stories

Recommended for you

Chinese Cretaceous fossil highlights avian evolution

September 24, 2018

A newly identified extinct bird species from a 127 million-year-old fossil deposit in northeastern China provides new information about avian development during the early evolution of flight.

Ancient mice discovered by climate cavers

September 24, 2018

The fossils of two extinct mice species have been discovered in caves in tropical Queensland by University of Queensland scientists tracking environment changes.

The first predators and their self-repairing teeth

September 24, 2018

The earliest predators appeared on Earth 480 million years ago—and they even had teeth capable of repairing themselves. A team of palaeontologists led by Bryan Shirley and Madleen Grohganz from the Chair for Palaeoenviromental ...

Fat from 558 million years ago reveals earliest known animal

September 20, 2018

Scientists from The Australian National University (ANU) and overseas have discovered molecules of fat in an ancient fossil to reveal the earliest confirmed animal in the geological record that lived on Earth 558 million ...

26 comments

Adjust slider to filter visible comments by rank

Display comments: newest first

neilmurray203
3.5 / 5 (2) Apr 07, 2016
As females carry xx and males xy, perhaps neanderthal males never bred with human females, but the more aggressive human males did breed with neanderthal females?
SoylentGrin
3.7 / 5 (6) Apr 07, 2016
perhaps neanderthal males never bred with human females, but the more aggressive human males did breed with neanderthal females?

Likely, breeding went both ways. The gender of the offspring has nothing to do with the gender of either parent. 50% of the sperm would be carrying an X, 50% would be carrying a Y, no matter if the father was neanderthal or homo sapien.
The article gives a likely hypothesis, that neanderthal Y chromosomes were incompatible with certain gene flows, resulting in the fetus being rejected if it was neanderthal Y.
crusher
1.8 / 5 (5) Apr 07, 2016
wow the mystery of disappearing Neanderthals is solved!
SoylentGrin
4.3 / 5 (6) Apr 07, 2016
wow the mystery of disappearing Neanderthals is solved!


Um... no.
antigoracle
3 / 5 (5) Apr 07, 2016
As females carry xx and males xy, perhaps neanderthal males never bred with human females, but the more aggressive human males did breed with neanderthal females?

Or Neanderthals being physically larger, resulted in larger babies that human females had difficulty with.
antigoracle
1 / 5 (2) Apr 07, 2016
[deleted]
Jeffhans1
5 / 5 (4) Apr 07, 2016
As females carry xx and males xy, perhaps neanderthal males never bred with human females, but the more aggressive human males did breed with neanderthal females?

Or Neanderthals being physically larger, resulted in larger babies that human females had difficulty with.


We see the variations possible in the extreme example of the Ligers versus Tigons. If something similar was happening with neanderthal hybrids, we may have only seen fertile females. Infertile males may have existed, but would not have left contributions in the gene pool obviously.
crusher
not rated yet Apr 07, 2016
I like your nickname- soylent grin!
compose
Apr 07, 2016
This comment has been removed by a moderator.
crusher
5 / 5 (1) Apr 07, 2016
As females carry xx and males xy, perhaps neanderthal males never bred with human females, but the more aggressive human males did breed with neanderthal females?

Or Neanderthals being physically larger, resulted in larger babies that human females had difficulty with.


A very likely hypothesis.
compose
Apr 07, 2016
This comment has been removed by a moderator.
Solon
1.7 / 5 (6) Apr 07, 2016
Likely the Gods just made some design changes.
compose
Apr 07, 2016
This comment has been removed by a moderator.
antigoracle
2.6 / 5 (5) Apr 07, 2016
I don't get it - how is it supposed to work?..................

OK. Calm down and read the following from this study.. "If women consistently miscarried male babies carrying Neanderthal Y chromosomes, that would explain its absence in modern humans."

So, instead of miscarriage, I'm saying human females being smaller had difficulty giving birth to a larger Neanderthal baby. This would have been even more pronounced with male offspring since they are generally bigger than females.
Uncle Ira
3.3 / 5 (7) Apr 07, 2016
Maybe the Neanderthal-Skippys were so ugly the Modern-Skippettes did not want to have anything to do with them.
ParaFunkt
1.8 / 5 (5) Apr 07, 2016
Or maybe the Neanderthal were a hermaphroditic species....

Must be propaganda if its allowed to be published in a scientific journal backed by institution and industry.
antigoracle
1 / 5 (3) Apr 07, 2016
I wonder if they haven't stumbled upon the reason for Neanderthal extinction. Perhaps the Neanderthal male took a hankering for the human female, whose inability to produce male offspring sealed their fate.
torbjorn_b_g_larsson
4.2 / 5 (5) Apr 09, 2016
As females carry xx and males xy, perhaps neanderthal males never bred with human females, but the more aggressive human males did breed with neanderthal females
Yes, this is the most probable explanation: the Neanderthal females were raped and all males killed for to prohibit their offspring. After all, such a behavior emerged during most genocides documented in the human past.


Um, no. Paleoanthropologist John Hawks has shown conclusively that the data contradicts a cultural explanation.

"So, instead of miscarriage, I'm saying human females being smaller had difficulty giving birth to a larger Neanderthal baby. This would have been even more pronounced with male offspring since they are generally bigger than females."

The genetic data supports an immune system compatibility. There is scant data on fetus sizes, and no reason to think the sizes were different.
Captain Stumpy
2.6 / 5 (5) Apr 09, 2016
Must be propaganda if its allowed to be published in a scientific journal backed by institution and industry
@ParaFunkt
you mean like QM? GR? SR? physics? medicine? engineering?

are you being sarcastic or ....????
Befe
1 / 5 (1) Apr 10, 2016
These findings point to that our predecessors who lived ~60-40K years ago did not ONLY raid and usurp (murder) their Neanderthal cousins but to a significant extent they also carried out bride-stealing (in the same genocidal "process").

They (mainly our male ancestors) successfully took or exploited this (naturally environmentally presented) evolutionary opportunity to keep their genetic lineage going thanks to their superior language-function-related AEVASIVE capacity to 'behave successfully' in this nasty way; A way manifested not only, but currently most notably, by Islamists.
Think "fanatic goal-mindedness coupled with neurotic channeling="sublimation" that amplify instinctive aggressive motivation.
The results of our AEVASIVEness are exemplified by our 'fine and nice' as well as by our 'ugly and nasty' behavior/"expressions of culture". Religious believing is but one type of such results.
crusher
not rated yet Apr 10, 2016
they are invasive but they are the same species
cantdrive85
2 / 5 (4) Apr 10, 2016
Obviously, they never tested Cap'n Stoopid's DNA....
cantdrive85
1 / 5 (3) Apr 10, 2016
A way manifested not only, but currently most notably, by Islamists.

There is another Asiatic "race" that is even more notable and successful in that nasty way. Their tally exceeds a couple hundred million in the 20th century alone, including twelve million or so of their own (at least that's the claim).
crusher
5 / 5 (1) Apr 11, 2016
are you calling the Jews orientals? Nazi racial mythology? What are you talking about/
baudrunner
1 / 5 (1) Apr 11, 2016
It's possible that Neanderthals could not integrate by reasons related to racism. Face it, Neanderthals are very different. Over time, as the dominant race grew to vastly outnumber the Neanderthal population, who would have trouble keeping up with cultural, social, and technological changes, they would simply disappear from the radar, due to rejection, genocide, etc.

All of which doesn't really answer the question, where did they come from, or for that matter, where did WE come from?
compose
Apr 11, 2016
This comment has been removed by a moderator.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.