Mutations in Y Chromosome made us separate species from Neanderthals | Hacker News Reader

Mutations in Y Chromosome made us separate species from Neanderthals

newscientist.com

42 pointstechnotony33 comments

A little dark hypothesis:

I've seen some (intertwined) hypotheses in the news lately of why there's no neanderthal Y chromosomes: the mixed-race-neanderthal-Y boys didn't do so well for some reason, the human Y chromosome had advantages, or the neanderthal-Y wasn't compatible genetically.

How about the more obvious guess: homo sapiens invaded and conquered neanderthals, killing all the males (and their Y chromosomes with them). It's speculative, but it would definitely not be the first time in history that such a thing has happened. And the neaderthals live for hundreds of thousands of years, then disappear just tens of thousands of years after homo sapiens show up in their neighborhood. So it's likely one group wiped out the other. And it's not hard to imagine keeping the women when you decide to kill a whole neighboring tribe.

I actually came up with the hypothesis about how the two groups most likely interbred just a few days before I found out in the news that the neanderthal Y-chromosome disappeared. I don't know if I should be excited or disgusted that the evidence might support my hypothesis.

Human history is unfortunately littered with stories like this, but we know the Neanderthal genetic flow came in from the males. The reason why we know this is we are missing all Neanderthal mitochondrial DNA sequences which are only inherited down the female line. If your theory was correct then we would see modern humans with Neanderthal mitochondrial genomes.

It appears what happened is much more interesting - Neanderthal males mated with female humans of African origin, but the male offspring were infertile.

Thank you for the insight. I wonder, how do we know the males were infertile?

We don't - all we know is that the Neanderthal Y chromosome is missing from the modern human population. This could have occurred by chance (genetic drift), lethal genetic incompatibility (all males died), or infertility. Given the data we have it is hard to know which of these is the real cause.

Is it not equally likely the other way around - that the Neanderthal mitochondria disappeared because of unsuccessful mixed females or other genetic drift?

No because of the way genetics works it is much more likely to be the Y chromosome that is lost. First the Y chromosome is under stronger indirect selection than the mitochondria due to asymmetric mating. Second in mammals when two different species have a genetic incompatibility this incompatibility manifests in the male offspring. Both of theses point towards male Neanderthal female African as the way this hybridization happened.

Edit. I should add the scientific paper behind this New Scientist article proposes a precise genetic mechanism for how the Neanderthal Y chromosome is lost which is further evidence the loss is due Y Chromosome incompatibility.

Yeah, given the symmetrical evidence: no Neanderthal Y chromosome DNA, and no Neanderthal mitochondrial DNA - it seems most gendered hypotheses you could come up with should also work with the genders switched?

The title on NS is: "Missing Y chromosome kept us apart from Neanderthals" and that is importantly different from the title here on HN.

Only males have Y chromosomes so if only "Mutations in Y Chromosome made us separate species from Neanderthals" then female Homo Sapiens and Neanderthals would be genetically the same. I know I'm being a bit pedantic about the use of the word 'made' in the title but it seems important to me.

It is not that Africans females and Neanderthals are genetically the same, just that the genetic incompatibility between the two species appears to be sex specific. This is pretty common when different species hybridise.

Haldane's rule covers why this occurs [1].

1. https://en.m.wikipedia.org/wiki/Haldane%27s_rule

Actual study (open access!): http://www.cell.com/ajhg/abstract/S0002-9297(16)30033-7

Many of the shortcuts taken in TFA seem to lead to confusion rather than understanding, so this might be worth a read.

I think someone needs to tell New Scientist that many of us are part Neanderthal.

Given that much of the definition of speciation these days is the inability to produce fertile offspring with high likelihood, it sounds like they're right on the nose.

Something like one mule (horse-donkey hybrid) in tens of thousands is fertile, having by chance received just the right combination of chromosomes to be able to reproduce. But the rest are sterile. The rare successful interbreeding doesn't make horses and donkeys the same species either, despite being closely related. (In their case, IIRC, the infertility of hybrids has to do with differing chromosome counts between horses and donkeys.)

So we can have some Neanderthal genes (whether from prior to y-chromosome differentiation or from the rare successful interbreeding or from successful and fertile but rare female offspring) but still be separate species.

Besides, it's oft cited that we share 98% of our DNA with chimps, and nobody's claiming that we're the same species.

The definition of a species is not the inability to produce fertile offspring. Certainly if you can't produce fertile offspring then you are a different species, but having fertile offspring does not mean you are the same species.

Many humans (all non Africans) are a hybrid between two different species - all this result is telling us is that Africans and Neanderthals really are two different species.

You've made this claim before. It's so extraordinary that either we all would have learned it in school or Nature would have published it and in addition it would have been in all the major media.

Claiming that blacks are a different species, not even a different race, is some next level Hitler / KKK / etc. shit.

But basically, I just think you don't know what you're talking about. For example, I just typed "species" into my search box and Google handily provided the following from Wikipedia:

> A species is often defined as the largest group of organisms in which two individuals are capable of reproducing fertile offspring, typically using sexual reproduction.

Go try and fix Wikipedia if you wish to spread nonsense.

> Claiming that blacks are a different species, not even a different race, is some next level Hitler / KKK / etc. shit.

I may be missing something, but the claim I've read around the Internet is that "Africans" are the only pure Human group, and are a different species from Neanderthals, while other Human groups have a small percentage of Neanderthal genes.

Whether that's true or not, it seems like a far less problematic claim than the one you mention.

I think you missed the “often" in your quote from wiki.

This study is telling us that Africans and Neanderthals are not able to produce fertile male offspring when a male Neanderthal reproduces with a African female. This is a common occurrence when two different species breed.

I do agree that it is extraordinary that the meaning of this discovery is not recognised more widely, but please do not place words in my mouth as to what this means.

"male fetuses conceived through sex with Neanderthal males would have miscarried"

Actually we don't know this - it may just be that the male offspring were infertile, not that the genetic incompatibility was lethal.

So easy a caveman can do it...

I am reading about this story for a while now and still do not get what is so surprising about it. While people of caucasian descent all share about 2% of their DNA with the Neanderthals, thats all random bits and not a single larger fragment or even chromosome. The latter would need to happen for the Y Chromosome. All Chromosomes but Y (and Mitochondria) can exchange fragments with their homologs but as there is always just one Y chromosome in any given cell, thats is not going to happen there. Therefore, if we should find it, we would find a whole Y Chromosome. But that is not going to happen. And that is honestly not very surprising...

> While people of caucasian descent all share about 2% of their DNA with the Neanderthals

That number is shockingly low to me, which probably means I misunderstand some subtlety of what you're saying. Could you expand/explain? (I'd have expected a figure starting with at least two 9s [99+%])

Modern Europeans share about 2% of their alleles with Neanderthals might be a more correct way to put it. But to understand that sentence, you have to understand what's an allele (and I'm not completely sure I'm using the term correctly).

This is pretty close. A simpler way of describing this is 2% of the average genetic heritage of a European is able to be traced back to Neanderthals. This is a lower bound and it may be higher.

The more interesting observation is that the 2% is not the same 2% in everyone of a European genetic background. Overall at least 25% of the Neanderthal genome is present across the whole population.

Perhaps it's only counting 2% of the DNA that we didn't already share with Neanderthals prior to cross-breeding. As in, 2% of what had diverged from a common ancestor. So, you could look at DNA of neanderthals and humans prior to cross-breeding events, and then eliminate everything in common, which would probably be the 99+% you would expect. Then take what's left and look at how much we picked up after cross breeding.

The context of the comment is - Humans share 40% of DNA with a lot of plants.

Perhaps GP means that 2% of the "DNA" can't be traced to recent African ancestors, so it "must have" come from Neanderthals?

Ah, nice, that meets my steelmanning quota for this week.

IIRC from some long-ago bio courses, the Y chromosome also shares fragments via copying mistakes, but what tends to happen over time is that they "migrate" off the Y chromosome entirely, further shrinking it.

Form my own memories of long-ago courses, the Y chromosome is partially homologous to X and exchanges alleles with it during meiosis.

It has its own, non-homologous region too that doesn't trade DNA.

Reading about things like this, I wonder about the fertility between groups of modern humans that split the farthest back. Admittedly it isn't 600,000 years ago, but I suppose there would have to be some problems.

Apparently is it common for there to be issues with teeth when individuals from different genetic lineages have children. The genes that control teeth size and location have some level of incompatibility that manifests itself in orthodontist’s vacation homes.

Took me a few seconds and some stares to my dutch friend until I realized I read "Netherlanders" and not "Neanderthals"

This is fucking dumb. Drift is far more likely by orders of magnitude. New Scientist is like the Gawker of science journalism.

Overstated. The article just says the genetic change is "linked to increased risk of miscarriages ".

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