Traces of two unknown archaic human species turn up in modern DNA | Hacker News Reader

Traces of two unknown archaic human species turn up in modern DNA

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52 pointssahin31 comments

> We knew the story out of Africa wasn't a simple one, but it seems to be far more complex than we have contemplated

Things are always going to be much more complex than the evidence shows, simply because the evidence we have is always going to be incomplete.

I realize the concept of species is hard to pin down, but I thought one first-order approximation was that if two animals can reliably breed and form fertile offspring, then they are the same species. There are weird cases like ring species, and there is often a period of time during speciation where two lineages could functionally breed fine but don't because of some kind of ecological or behavioral barrier.

But if all these different human lineages apparently bred successfully and had fertile offspring (enough to leave a few percent of their DNA in modern humans), what is to say they were different species?

In the end the concept of a species is a man-made construct that tries to shoehorn the evolutionary diversity into pigeonholes.

For example, your definition of breeding might work okayish for higher eukaryotes, but is unusable for prokaryotes. There people might be using some kind of definition based on the sequence identity of genomes. It's a bit like looking at a color gradient from black to white and then trying to classify each pixel to either black or white.

The first approximation is an approximation only. The closer you look, the fuzzier it gets.

There are many pairs of species which can interbreed, and sometimes be fertile, and as a result genes can get from one to the other. But for the most part they don't interbreed, even when they share a territory. An example today is tigers and lions. (They no longer overlap in the wild, but they used to before humans shrank both their territories.)

Similarly homo sapiens and neanderthals coexisted for tens of thousands of years. And yet we only have evidence for a handful of successful interbreeding events. That's pretty good evidence that they were separate species.

For these new ones, whether they were fertile or not is subject to dispute. However we can estimate how far back the last common ancestor of their chromosomes and ours is. And from that gap, we have reason to believe that they are similarly distant from homo sapiens as Neanderthals were. And so they likely were a different species, even though some interbreeding was possible.

> Similarly homo sapiens and neanderthals coexisted for tens of thousands of years. And yet we only have evidence for a handful of successful interbreeding events. That's pretty good evidence that they were separate species.

I don't think it's as simple as what you're saying. We have evidence that 2-4% of the entire modern genome of non-Africans came in from Neanderthals, and an even larger amount of genetics coming in from Denisovans for many in modern Asia and beyond into Australia.

As I understand it, all Neanderthal genetics that modern man has came in through the X chromosome. This could indicate that male offspring of Neanderthals and Homosapiens were infertile, which would be a cut-and-dry indicator that they're two separate species.

It's also worth mentioning that if we assume that interbreeding didn't occur somewhat frequently then that means that non-African humans evolved from the same ancestors that the Neanderthals' and Denisovans evolved from, while most people in Africa evolved from another group or groups.

The earliest modern human remains found outside Africa date to about 200,000 years ago, yet almost all people born outside Africa are descendants of people migrating from Africa about 70,000-50,000 years ago. We don't really know what happened to the first waves of emigrants but we do know they didn't leave many traces. The traces we have found don't indicate hostility so the easiest explanation is that they simply lived alongside the Neanderthals and Denisovans and that the Neanderthals and Denisovans were more successful. Since we know there were interbreeding I find it very likely that those were isolated incicents, considering the human sexual drive. :)

People do have sex with other species. And if there were other human species, it'd probably be even more common. There's some non-human prostitution, and that does include other primates.

Precisely. We do have a handful of cases where it is known to have happened, and I can't see how it could be a few isolated incidents only.

I can imagine that first-generation hybrids were slaves. Maybe with males being castrated.

This was in hunter gatherer times. There weren't any slaves. There much formal hierarchy as we'd understand it. Some people were known to be wiser and/or tougher but that wasn't a formal role. And if you didn't like how things were run you could always try to convince people to go somewhere else with you and split the tribe.

Also, where are you getting castration from? We know these people existed from the genetic traces of their descendants, and people who are castrated don't have kids.

And you know that, how?

The Cree, for example, raided for slaves.

So, you bring up Cree slavery and at first I was really surprised because the Cree lived in hunter-gatherer bands of exactly the sort that I thought never took slaves. But I did some quick research on the internet and the only thing I could find about Cree slaves was them taking slaves in raids and then immediately turning around and selling the slaves to other, settled groups. So they took slaves but didn't keep them.

Or perhaps you meant the Creek instead of the Cree? They certainly took and kept slaves but they were a settled agricultural group of the sort you'd expect could have slavery.

No, I just happened to remember reading about Slavey Lake.

But it is my impression that some Native American groups did engage in slavery. As did many in Africa, even before they started dealing with Arabs and Europeans.

So it's arguably not a stretch that early humans engaged in slavery. Indeed, I recall reading that the male breeding population was substantially smaller than the female breeding population for a while. I can't find the source, but it was maybe 10-50 kyr BP.

Parent said:

> As I understand it, all Neanderthal genetics that modern man has came in through the X chromosome. This could indicate that male offspring of Neanderthals and Homosapiens were infertile, which would be a cut-and-dry indicator that they're two separate species.

Castration is an alternative (or additional) explanation.

> We have evidence that 2-4% of the entire modern genome of non-Africans came in from Neanderthals

The actual evidence is pretty weak (Pattersons D-statistic is a rather crude method), and crucially doesn't infer a direction. It's equally possible that 2-4% of the Neanderthals' genomes come from humans, and I think it's more believable that a few percent of the Denisovan's (there is only one!) genome come from (relatives of the ancestors of present day) Melanesians.

I'm not sure I understand. In your last scenario, where would the Melanesians have gotten significant differences from most other humans, to then pass on to Denisovans?

The Melanesians didn't pass anything on, that's chronologically impossible. They are the descendants of a migration wave out of Africa, through Asia, to Australia. If some interbreeding with the Denisovan (there is only one!) happened, the Melanesians are the closest extant relatives of whoever did the interbreeding. Outside Melanesia, that branch of humanity was later replaced by the expansion of another migration wave, and the again by the Han expansion.

Yes, their ancestors is what I meant. I get it now, thanks.

https://www.nationalgeographic.com/science/2019/03/ancient-i... during the bronze age it's speculated that all the native men were replaced by men from the steppes. so since all the neanderthal genetics came from the X chromosome, then that means the original european inhabitants were decedents of neanderthals. however, isn't it so that east asians have more neanderthal dna than europeans? is the notion that neanderthal dna is only express in the X chromosome true for east asians as well? if that's the case, maybe a similar event occurred there but at a much earlier date. or were the original european women captured and brought back to east asia?

the notion that a hybrid offspring maybe infertile is imo dominating these discussions too much.

what I find lacking in these discussions is the real possibility that genocide and slavery (the sexual and work kind) would explain so much.

The concept of a species is historic and has no equivalent in molecular biology. It was established in its basic form more or less 250 years ago when evolution wasn't even a real concept yet. Sure, it has been adapted in so many ways but in the end is mostly kept nowadays for legacy reasons. I mean there are so many inconsistencies to begin with like are house animals their own species, the interbreeding you mention, when does one archaic species becomes modern etc.

In the comments you have already gotten, the neanderthal people are referred to as a species, even though very often they are only considered a subspecies of modern humans. There have been successful interbreeding events while at the same time every child can distinguish a neaderthal skull from a modern human one. Svante Pääbo and his team intentionally declared Denisovans only as a genomic type but neither as a subspecies nor species.

I think, Dr. Teixera simply misspoke. Neanderthals have never been considered a distinct species from humans, nor should they, because humans and Neanderthals probably had fertile offspring.

The moment you talk about extinct species, the terminology falls apart. At some point (about 6.5Ma ago), the ancestors of humans and chimpanzees were one species. Humans and chimps are clearly distinct species. With extant difficult cases (ring species), you take the transitive closure; do that for all extinct species, and there are no species anymore.

So what can you do? Apply an arbitrary cutoff and argue endlessly whether Neanderthals were a subspecies of humans but homo erectus wasn't? Or just give up, use the terms species, subspecies, clade and population interchangeably. Population genetics apparently decided to give up and picked "population" as a neutral term.

Whether they were Homo neanderthalensis or Homo sapiens neanderthalensis is actually a matter of debate. It looks like the first generation human/neanderthal hybrids were significantly less fertile than either alone given the sections of the neanderthal genome that have been systematically selected against, like all of the neanderthal mDNA. But still fertile enough to leave descendants, some of which were more fertile.

It is interesting that we only seem to be descendants of pairing of male neanderthals and female homo sapiens - as there is no neanderthal mitochondrial in modern humans.

Were there offspring from female neanderthals/human fathers? Did they survive, were they fertile?

Or were there so few pairing that our lineage goes back to just a few individuals (similar to the compression in cheetah ancestors?)

http://humanorigins.si.edu/evidence/genetics/ancient-dna-and...

http://fire.biol.wwu.edu/hooper/204_06microevo.pdf

(I always have a real interested in neanderthal 'history', after finding that I have approx 4% neanderthal dna - more than 99% of people in the world).

It's possible that only male neanderthal/female sapiens pairings produced offspring but that's probably not what happened. First generation descendants of a male sapiens and female neanderthal are going to have N mDNA and both complete N and S chromosomes so they'll have genes to code for proteins that'll form nice tight respiratory chains with the protiens from the mDNA. But in the third generation if you have another pairing with a sapiens you're likely to be missing N respiratory chain nuclear genes in half the offspring meaning half the fertilized eggs will have mitochondria that leak free radicals like seives and will go straight into apoptosis and never result in pregnencies. So in the third generation and onwards in a population that's mostly sapiens you're going to be having many more sons than daughters to mixed children and the mDNA will asymptotically die out. If it was a sapiens woman joining a neanderthal population it would be the sapiens mDNA that would die out. At least if I'm getting this right, I'm just a dilettante here. Plus generally neanderthals have bigger heads so I'd expect male sapiens / female neanderthals pairing to have less trouble with childbirth.

If ability to breed meant same species, you'd end up with awkward results upon taking the transitive closure. I can't breed with a rabbit, but there exists a historical path of millions of organisms, starting with me and ending with a rabbit, such that any two steps along the path can breed with each other. So therefore am I the same species as the rabbit?

>For example, all present-day populations show about two percent of Neanderthal ancestry which means that Neanderthal mixing with the ancestors of modern humans occurred soon after they left Africa, probably around 50,000 to 55,000 years ago somewhere in the Middle East.

I thought subsaharans lacked Neanderthal admixture?

According to https://genographic.nationalgeographic.com/neanderthal/ and the chart on top of https://en.wikipedia.org/wiki/Interbreeding_between_archaic_..., that seems correct.

There are many fascinating relics and bizarre ancient remnants in human DNA. Endogenous Viral Elements are a great example of this. Referred to as “horizontal evolution”, there are a variety of organisms that have the ability to literally transfer their DNA to other species. Something like 5-8% of the Human Genome is the result of “injections” from these paleoviruses.

Part of that percentage is junk / redundant DNA strands humans evolved over time to make it more difficult for viruses to navigate and compromise our DNA.

There is also evidence of admixture with archaic species within Africa. The picture within Africa is probably even more complex, and analysis is made more difficult by the absence of ancient DNA due to the warm climate.

"Outstanding questions in the study of archaic hominin admixture" - https://journals.plos.org/plosgenetics/article?id=10.1371/jo...

What humans have in common is that we are descended from the most aggressive, fastest breeding population that killed off all our close competitors.

> What humans have in common is that we are descended from the most aggressive, fastest breeding population that killed off all our close competitors.

We didn't necessarily kill 100% of all our individual close competitors. We might've won the majority of resources and protected them from outsiders.

We also could've been the most adaptable and naturally curious group that was more clever at over coming hardships and willing to travel long distances to discover new resources even if the risk level was high.

Also the existing (extinct) populations could have become diluted within the larger immigrant population, until their mating opportunities went to zero?

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