Thanks to interbreeding, just 7% of our DNA is unique to modern humans: study(latimes.com)
latimes.com
Thanks to interbreeding, just 7% of our DNA is unique to modern humans: study
https://www.latimes.com/science/story/2021-07-16/thanks-to-interbreeding-just-7-of-our-dna-is-unique-to-modern-humans-study-shows
87 comments
https://archive.is/Rs62D
It does raise the question of "us" versus "them". But who was "them" really?
It's clear there were some stupid humans:
homo habilis
home erectus
homo naledi
It's clear there are some smart humans:
homo neanderthal
homo denisovan
homo sapien
And it's clear there are some that we are not yet sure about, in particular:
homo heidelbergensis
But what about:
homo antecessor
If you could wave a magic wand, and summon them now, it's likely that Sapiens, Neanderthals, and Denisovans could learn each other's language and have a conversation. But would we be able to have a conversation with Heidelbergensis?
So the question comes up again, as strong as ever, who was the first smart human? We used to think they were Sapiens, now it is seems likely the first really smart humans came before Sapiens, and we are just one of several smart humans.
There was a species of humans that was unique to southern easter Africa, they had the largest skulls of any known human species, a recent article in the New York Times quoted one scientist saying they all would have been as smart as Albert Einstein. (I just searched for the article on Google and NYT but could not find it, it was an article that ran within the last 2 years.)
In an ideal world we could find more DNA samples, and eventually figure out what the DNA is trying to tell us, but DNA doesn't last 2 million years, so we will never have the full DNA story of humans, going all the way back to homo habilis.
So we are left looking at the clues and wondering, "When did us begin?"
It's clear there were some stupid humans:
homo habilis
home erectus
homo naledi
It's clear there are some smart humans:
homo neanderthal
homo denisovan
homo sapien
And it's clear there are some that we are not yet sure about, in particular:
homo heidelbergensis
But what about:
homo antecessor
If you could wave a magic wand, and summon them now, it's likely that Sapiens, Neanderthals, and Denisovans could learn each other's language and have a conversation. But would we be able to have a conversation with Heidelbergensis?
So the question comes up again, as strong as ever, who was the first smart human? We used to think they were Sapiens, now it is seems likely the first really smart humans came before Sapiens, and we are just one of several smart humans.
There was a species of humans that was unique to southern easter Africa, they had the largest skulls of any known human species, a recent article in the New York Times quoted one scientist saying they all would have been as smart as Albert Einstein. (I just searched for the article on Google and NYT but could not find it, it was an article that ran within the last 2 years.)
In an ideal world we could find more DNA samples, and eventually figure out what the DNA is trying to tell us, but DNA doesn't last 2 million years, so we will never have the full DNA story of humans, going all the way back to homo habilis.
So we are left looking at the clues and wondering, "When did us begin?"
What makes you assume homo erectus was stupid? The neanderthals, denisovans, and sapiens are identified as separate evolutions from erectus because they evolved separate features which are considered markers of "anatomical modernity", but that seems to be a sapien-centric attitude that needlessly assumes appearance similar to sapiens corresponds to higher intelligence. The archeological evidence doesn't really suggest any one group from homo was smarter - all seemed to develop the same lower paleolithic and then middle paleolithic technology. The only difference archeologically happened when sapiens outbred and assimiliated the other groups ~50,000-80,000 years ago and then developed upper paleolithic technology.
We can put homo erectus in the ambiguous category, if you know of some argument to do so, but the early homo erectus (what splitters would simply call actual homo erectus) had a brain size of 900 cc, so you'd need to explain how modern intelligence works in that dramatically smaller brain.
Lumpers include later humans in the category of "homo erectus" when brain size is 1200cc. If you yourself are a lumper, you should say so, as that would resolve some confusion. I'm personally with the splitters, having been won over by the arguments that Ian Tattersall advanced, so when I say that homo erectus is stupid, I'm referring to people whose brains were 900cc.
Here is an article written from the lumper point of view, so perhaps this is what you were thinking of:
https://www.shorthistory.org/prehistory/brain-size-of-the-pr...
"Homo habilis, who lived approximately 2 million years ago, was 750 cc. Homo erectus shows this transition most dramatically, indicating that most of the evolutionary increase in brain size took place during the life of this species. Early Homo erectus in Africa (from about 1.7 to 1 million years ago) averaged 900 cc in brain size, but later Homo erectus specimens from .5 million years ago average 1100-1200 cc, which falls within the range of the brain size of modern humans. The earliest or archaic forms of Homo sapiens, the species to which we belong, dates to 300,000-400,000 years ago and averages over 1200 cc. The Neanderthal skull has a brain size of 1500 cc, which is actually larger than the brains of most modern humans. The average for ourselves, Homo sapiens, is around 1400 cc."
That is not the story I was working with when I wrote the above comment. Here is an article that suggests the splitter story:
https://www.discovermagazine.com/planet-earth/homo-heidelber...
"Between H. erectus and H. sapiens, intermediate species existed, variably named Homo heidelbergensis, Homo rhodesiensis or Homo antecessor, depending on a researcher’s views. Many anthropologists just call the whole bunch Middle Pleistocene hominins, after the geologic time period 130,000 to 780,000 years ago. One spectacular site, Sima de los Huesos in Spain, has yielded the most Mid-Pleistocene hominin remains. Excavations there since the 1980s have unearthed more than 7,000 fossils representing at least 28 individuals dated to 430,000 years ago."
In that story, homo heidelbergensis is in between homo erectus and homo sapien.
Lumpers include later humans in the category of "homo erectus" when brain size is 1200cc. If you yourself are a lumper, you should say so, as that would resolve some confusion. I'm personally with the splitters, having been won over by the arguments that Ian Tattersall advanced, so when I say that homo erectus is stupid, I'm referring to people whose brains were 900cc.
Here is an article written from the lumper point of view, so perhaps this is what you were thinking of:
https://www.shorthistory.org/prehistory/brain-size-of-the-pr...
"Homo habilis, who lived approximately 2 million years ago, was 750 cc. Homo erectus shows this transition most dramatically, indicating that most of the evolutionary increase in brain size took place during the life of this species. Early Homo erectus in Africa (from about 1.7 to 1 million years ago) averaged 900 cc in brain size, but later Homo erectus specimens from .5 million years ago average 1100-1200 cc, which falls within the range of the brain size of modern humans. The earliest or archaic forms of Homo sapiens, the species to which we belong, dates to 300,000-400,000 years ago and averages over 1200 cc. The Neanderthal skull has a brain size of 1500 cc, which is actually larger than the brains of most modern humans. The average for ourselves, Homo sapiens, is around 1400 cc."
That is not the story I was working with when I wrote the above comment. Here is an article that suggests the splitter story:
https://www.discovermagazine.com/planet-earth/homo-heidelber...
"Between H. erectus and H. sapiens, intermediate species existed, variably named Homo heidelbergensis, Homo rhodesiensis or Homo antecessor, depending on a researcher’s views. Many anthropologists just call the whole bunch Middle Pleistocene hominins, after the geologic time period 130,000 to 780,000 years ago. One spectacular site, Sima de los Huesos in Spain, has yielded the most Mid-Pleistocene hominin remains. Excavations there since the 1980s have unearthed more than 7,000 fossils representing at least 28 individuals dated to 430,000 years ago."
In that story, homo heidelbergensis is in between homo erectus and homo sapien.
The evolution of ‘anatomically modern humans’ was almost certainly a continuous change over many tens of thousands of generations. The assignment of arbitrary cutoffs and categories doesn’t really map onto reality well, as you’ve shown.
Of course it’s difficult to accept that for every generation prior they were simply less ‘human’ and more ‘ape like’ all the way back to the first bipedal generation in sub-Saharan Africa. Because the implication is that our 10000th great grand parents were less human than we are, and their 10000th great grand parents were even less so, and so on until they were literally apes, or proto-apes to be more precise.
Of course it’s difficult to accept that for every generation prior they were simply less ‘human’ and more ‘ape like’ all the way back to the first bipedal generation in sub-Saharan Africa. Because the implication is that our 10000th great grand parents were less human than we are, and their 10000th great grand parents were even less so, and so on until they were literally apes, or proto-apes to be more precise.
Can you have continuous change when you have isolated populations who are facing different environmental pressures, which are pushing them in different directions?
"Continuous change" suggests a story with a narrative, an outcome that grew naturally from the initial trends, rather than being frequently convulsed by contrary trends in a world that saw multiple reverses of global climate trends during various periods of glaciation interrupted by inter glacial periods.
"Continuous change" suggests a story with a narrative, an outcome that grew naturally from the initial trends, rather than being frequently convulsed by contrary trends in a world that saw multiple reverses of global climate trends during various periods of glaciation interrupted by inter glacial periods.
So it’s true?!!
http://www.youtube.com/watch?v=vUEN1ZuDSMg
http://www.youtube.com/watch?v=vUEN1ZuDSMg
I wasn't expecting to see this here...
Is this for some subset of our DNA? Quick skim of the article didn't tell me. But there is a popular factoid that human dna is 98.8% similar to chimpanzee dna on average. Is that factoid false?
The popular factoid is correct, but the confusion here is that these are different measurements. Humans and chimps' genomes are similar in that if you align all the bases [A,C,T,G] that can be unambiguously aligned between the two genomes, 98.8% of the bases are identical. For modern humans to Neanderthals, that number is 99.7%, and between two random modern humans, it would be ~99.9% on average.
This paper is asking a subtly different question - how much of the modern human genome is strictly human, not by simply lining up bases and running a diff, but looking at the inheritance of chunks of DNA ("haplotype blocks", size determined by processes of recombination, etc.) to try to understand how much and which regions of the modern human genome came from interbreeding with Neanderthals or Denisovans. There was variation in the pre-human population before the human/Neanderthal split, which means that if you compare just a single human to a single neanderthal, you'll find unique variants to each. However, most of those variants will have existed in both the human and neanderthal populations, so they should count neither as uniquely human nor neanderthal (knows as Incomplete Lineage Sorting, or ILS).
The chunks in modern humans that derive from Neanderthals or Denisovans are different in different people and broadly across population groups (e.g. highest percent introgressed in Melanesians, lowest in Africans). But across all the modern humans in the study, there are regions where Neanderthal/Denisovan inheritance or shared variation (ILS) was never seen - that's 7% of the genome ("deserts"). And just 1.5% of the genome was in chunks where moderns human commonly have a unique mutation compared to Denisovans/Neanderthals.
This paper is asking a subtly different question - how much of the modern human genome is strictly human, not by simply lining up bases and running a diff, but looking at the inheritance of chunks of DNA ("haplotype blocks", size determined by processes of recombination, etc.) to try to understand how much and which regions of the modern human genome came from interbreeding with Neanderthals or Denisovans. There was variation in the pre-human population before the human/Neanderthal split, which means that if you compare just a single human to a single neanderthal, you'll find unique variants to each. However, most of those variants will have existed in both the human and neanderthal populations, so they should count neither as uniquely human nor neanderthal (knows as Incomplete Lineage Sorting, or ILS).
The chunks in modern humans that derive from Neanderthals or Denisovans are different in different people and broadly across population groups (e.g. highest percent introgressed in Melanesians, lowest in Africans). But across all the modern humans in the study, there are regions where Neanderthal/Denisovan inheritance or shared variation (ILS) was never seen - that's 7% of the genome ("deserts"). And just 1.5% of the genome was in chunks where moderns human commonly have a unique mutation compared to Denisovans/Neanderthals.
This comment is better quality content than the article. I just wish I understood more of it.
human genetics/genomics papers assume you understand an enormous amount of details of human genetics, the knowledge of which has been hard-won over a century. I worked in this field for decades, know a ton, and still have to read every sentence in this paper carefully, multiple ttimes, and check various sources to remind myself of technical concepts. There's a reason I switched to working on computing full time- a lot of these state of the art arguments can only be contributed to by people who are, well, state of the art, thick-skinned, and well-funded.
If you’re a layperson wrt genetics, check out ‘The Gene’ by Siddartha Mukherjee - it’s not too dense, interspersed with personal stories he relates to genetics and a great read. His book on cancer is also amazing, ‘Emperor of all maladies’
In my limited experience, these are two of the best non fiction books I’ve read. The author makes these subjects utterly fascinating. If he released a book about watching paint dry, I’d buy it in a heart beat and read it.
1.5% of the genome sounds like a crazy big number. If that much of genome went the wrong way, we could be dragons.
Would it be safe to say it's not the percentage of difference that matters, but the role of DNA that's different?
The point being, not all DNA is equal so to speak. That a couple of changes can have massive impact?
The point being, not all DNA is equal so to speak. That a couple of changes can have massive impact?
Yes, a single base change can give you a disease, cause intellectual disability or make you never be born.. There are mutations we never see in adults, as they are embryonically lethal.
Generally, you can tell what matters by seeing if it's been under selection - ie the frequency of that version in the population changes more than randomly.
Generally, you can tell what matters by seeing if it's been under selection - ie the frequency of that version in the population changes more than randomly.
Thanks, your comment makes the basic differences clear to me.
> However, most of those variants will have existed in both the human and neanderthal populations, so they should count neither as uniquely human nor neanderthal (known as Incomplete Lineage Sorting, or ILS)
This makes a hash of the headline "Thanks to interbreeding, just 7% of our DNA is unique to modern humans" -- this would be just as true if there had never been any interbreeding between "modern humans" and their various sister lineages.
This makes a hash of the headline "Thanks to interbreeding, just 7% of our DNA is unique to modern humans" -- this would be just as true if there had never been any interbreeding between "modern humans" and their various sister lineages.
From the paper [0] they say in the abstract that the differences are 1.5% - 7%.
So the lower end of that lines up with the 98.x% similarity.
Then in the paper there is this paragraph:
> Our ARG strategy allows us to bin the human genome into regions containing archaic admixture in at least some humans, regions of ILS, and regions free of both archaic admixture and ILS in all humans (hereafter archaic “deserts”). We find that approximately 7% of the human autosomal genome is human-unique and free of both admixture and ILS. Roughly 50% of the human genome contains regions where one or more humans has archaic ancestry obtained through admixture. If deserts are further restricted to regions that contain a high-frequency, human-specific derived allele, i.e., a substitution that can be assigned to the human lineage (hereafter “human-specific regions”), then these comprise only 1.5% of the assayed genome (Fig. 4A).
Maybe someone here understands what these words mean and can clarify?
[0]: https://advances.sciencemag.org/content/7/29/eabc0776
Then in the paper there is this paragraph:
> Our ARG strategy allows us to bin the human genome into regions containing archaic admixture in at least some humans, regions of ILS, and regions free of both archaic admixture and ILS in all humans (hereafter archaic “deserts”). We find that approximately 7% of the human autosomal genome is human-unique and free of both admixture and ILS. Roughly 50% of the human genome contains regions where one or more humans has archaic ancestry obtained through admixture. If deserts are further restricted to regions that contain a high-frequency, human-specific derived allele, i.e., a substitution that can be assigned to the human lineage (hereafter “human-specific regions”), then these comprise only 1.5% of the assayed genome (Fig. 4A).
Maybe someone here understands what these words mean and can clarify?
[0]: https://advances.sciencemag.org/content/7/29/eabc0776
I asked the author (I was a postdoc at the lab he was a grad student in about 20 years ago).
My question: """Are these differences evaluated/inferred using data from all regions of the genome (intergenic, viral repeats, etc) or just genes? I recall that the early reports that compared primates to humans just used genes (or maybe just the easily aligned regions, but out of order) which seemed like a big omission."""
His answer: """We used the Simons Genome Diversity panel (full phased genomes for ~300 people), along with Neanderthal and Denisovan genomes to make an ancestral recombination graph (ARG). The ARG is a sequence of trees describing relationships between everyone all along the genome. It's really just a sequence of trees at each variable site. Then, you can look at these trees and find segments where the archaics fall outside the variation of the humans. These are regions where no human shares ancestry with archaic either by recent admixture or by incomplete-lineage sorting. Turns out that's about 7% of the genome. What's in that 7%? It's a lot of genes and specifically a lot of genes involved in neural development and neural function! The method itself is blind to what is genic or nongenic. But this method is about the genealogy of genes across the genome, i.e., from whom they were inherited and not necessarily how different the versions were. In other words, it's about the topology of the trees across the genome, not their branch lengths."""
Beyond that things start to get really complicated, you need to understand concepts like haptotype blocks, how new genes arise, etc.
My question: """Are these differences evaluated/inferred using data from all regions of the genome (intergenic, viral repeats, etc) or just genes? I recall that the early reports that compared primates to humans just used genes (or maybe just the easily aligned regions, but out of order) which seemed like a big omission."""
His answer: """We used the Simons Genome Diversity panel (full phased genomes for ~300 people), along with Neanderthal and Denisovan genomes to make an ancestral recombination graph (ARG). The ARG is a sequence of trees describing relationships between everyone all along the genome. It's really just a sequence of trees at each variable site. Then, you can look at these trees and find segments where the archaics fall outside the variation of the humans. These are regions where no human shares ancestry with archaic either by recent admixture or by incomplete-lineage sorting. Turns out that's about 7% of the genome. What's in that 7%? It's a lot of genes and specifically a lot of genes involved in neural development and neural function! The method itself is blind to what is genic or nongenic. But this method is about the genealogy of genes across the genome, i.e., from whom they were inherited and not necessarily how different the versions were. In other words, it's about the topology of the trees across the genome, not their branch lengths."""
Beyond that things start to get really complicated, you need to understand concepts like haptotype blocks, how new genes arise, etc.
the chimpanzee factoid was distorted in a way that made the number look much larger than it really was. It only compared highly conserved regions in common between both organisms.
I’d heard that as well and thought that 7% unique seemed extraordinarily high compared to the factoids I’d integrated over time.
I just spent some time looking for the source, but I seem to have lost it, so take this all with a grain of salt, but based on some article I read:
My understanding of the "shared DNA" factoids is that they are based on a very rudimentary analysis of DNA sequences. The human-chimp 98.8% thing is "true" in that 98.8% of sequences that appear in the human genome also appear in the chimp genome. But this ignores other axes of differences: Humans may have multiple copies of certain sequences, while chimps only have one. Or certain sequences may appear in completely different parts of the genome in one or the other. And all of these differences are relevant.
TL;DR: 98.8% is true, but not really relevant for determining how "different" we are from chimps.
My understanding of the "shared DNA" factoids is that they are based on a very rudimentary analysis of DNA sequences. The human-chimp 98.8% thing is "true" in that 98.8% of sequences that appear in the human genome also appear in the chimp genome. But this ignores other axes of differences: Humans may have multiple copies of certain sequences, while chimps only have one. Or certain sequences may appear in completely different parts of the genome in one or the other. And all of these differences are relevant.
TL;DR: 98.8% is true, but not really relevant for determining how "different" we are from chimps.
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I wonder if we knew the Neanderthals were a different species. It seems weird that we would have chosen to breed with them if they were obviously not the same species as us.
> I wonder if we knew the Neanderthals were a different species.
Whether Neanderthals are a different species in genus Homo (H. neanderthalensis) or a different subspecies of H. sapiens (H. sapiens neanderthalensis) doesn't even seem to be completely a matter of consensus today (similar is true of Denisovans, for instance.)
And, honestly, the more evidence of ongoing, successful, fertile interbreeding we find, the less strong the “separate species” argument is, though its ultimately unresolvable because there's not a clearcut objective definition of what constitutes a “species”. Taxonomy isn't (well, the decision as to which taxonomic level a division is, at least, isn’t; the phylogenetic organization is) science so much as a necessary tool to have names for things to use when doing science.
Whether Neanderthals are a different species in genus Homo (H. neanderthalensis) or a different subspecies of H. sapiens (H. sapiens neanderthalensis) doesn't even seem to be completely a matter of consensus today (similar is true of Denisovans, for instance.)
And, honestly, the more evidence of ongoing, successful, fertile interbreeding we find, the less strong the “separate species” argument is, though its ultimately unresolvable because there's not a clearcut objective definition of what constitutes a “species”. Taxonomy isn't (well, the decision as to which taxonomic level a division is, at least, isn’t; the phylogenetic organization is) science so much as a necessary tool to have names for things to use when doing science.
A ‘species’ is a human categorization, it is not some objective thing. They likely didn’t have a concept like we do about species.
No, generally within science 'species' has a loose definition that roughly correlates with the actual underlying physical events occurring in the wild (the true population of the gene pool).
For example, if pressed, about as much as you could get from an evo biologist is that what distinguishes difference between species is their inability to interbreed.
Humans probably could tell neanderthal were "different" but not in a way where they thought they were truly "other".
For example, if pressed, about as much as you could get from an evo biologist is that what distinguishes difference between species is their inability to interbreed.
Humans probably could tell neanderthal were "different" but not in a way where they thought they were truly "other".
Right, but any human could tell that a chimpanzee is not the same thing as themselves. Could they tell that with neanderthals?
Sure they did. Not so long ago, a lot of people thought that black humans were a different specie, or at least a subspecie.
If anything, humans tend to be more prone to look for differences than assume equality.
If anything, humans tend to be more prone to look for differences than assume equality.
thaumasiotes(1)
They(we?) were more related to each other. I guess that like chimpanzee[1] and bonobos[2], perhaps closer, but my biology knowledge is not strong enough to choose the perfect example.
Note the humans and chimpanzees diverged like 5 million years ago. Neanderthal is very close to us and it's reclassified as it's own specie or as the same specie from time to time.
There is a nice graphic in https://en.wikipedia.org/wiki/Chimpanzee%E2%80%93human_last_... Neanderthal is not in the graphic, but if you want to add it, you should put in near the top left, between us and H. Erectus, probably closer to us.
[1] https://en.wikipedia.org/wiki/Chimpanzee
[2] https://en.wikipedia.org/wiki/Bonobo
Note the humans and chimpanzees diverged like 5 million years ago. Neanderthal is very close to us and it's reclassified as it's own specie or as the same specie from time to time.
There is a nice graphic in https://en.wikipedia.org/wiki/Chimpanzee%E2%80%93human_last_... Neanderthal is not in the graphic, but if you want to add it, you should put in near the top left, between us and H. Erectus, probably closer to us.
[1] https://en.wikipedia.org/wiki/Chimpanzee
[2] https://en.wikipedia.org/wiki/Bonobo
Having just seen a comparison of human and Neanderthal skeletons in person, it seems rather far fetched that they couldn’t tell each other were different.
Forensic scientists can also tell what race you are from your skeleton. It's not necessarily a determining factor.
"Same thing" obviously has blurry boundaries. Neanderthals might have seemed to be a different race or the like.
Yeah, and any human can tell that you are not the same thing as me. We can form all sorts of groups… people with dark hair and light hair, skin color, eye color, nose shape, etc. Which differences determine that another person is too ‘other’?
I always recommend one of my favorite essays for this topic: “The categories were made for man, not man for the categories”
https://slatestarcodex.com/2014/11/21/the-categories-were-ma...
I always recommend one of my favorite essays for this topic: “The categories were made for man, not man for the categories”
https://slatestarcodex.com/2014/11/21/the-categories-were-ma...
You will have to ask them
If Neanderthals were attractive and the offspring was viable, that's all they needed to know. I think people have an instinct for enriching their genome, that's why we're attracted to features our own group lacks, like different skin/hair color, facial structure, etc.
> I think people have an instinct for enriching their genome, that's why we're attracted to features our own group lacks, like different skin/hair color, facial structure, etc.
This is simply false. We know for a fact that humans have an in-group bias. Studies have shown that even infants and toddlers are biased toward their own in-group.
https://phys.org/news/2017-04-infants-racial-bias-members.ht...
https://time.com/67092/baby-racists-survival-strategy/
If what you claim is true, we would never have had miscegnation laws. Most people in the world wouldn't encourage marrying their own kind.
Just think about it. If people naturally favored the out-group ( people who look different ), racial/ethnic groups and diversity wouldn't exist. Blue eyes and blonde hair wouldn't exist because they are recessive traits. We wouldn't have any diversity because ethnic/racial groups require in-group bias to exist. The fact that we have black people, white people, indian people, chinese people, etc shows that in-group bias is the norm.
People naturally find their own kind and traits to be attractive. We know it's innate since it exists in babies. To find out-group features to be desirable requires external pressure - media, education, etc.
Edit: Since so many here are downvoting science because of their political agenda...
"We Choose Friends Who Are Genetically Similar to Us"
https://www.smithsonianmag.com/smart-news/we-choose-friends-...
"I like your genes: People more likely to choose a spouse with similar DNA"
https://www.sciencedaily.com/releases/2014/05/140519160716.h...
This is simply false. We know for a fact that humans have an in-group bias. Studies have shown that even infants and toddlers are biased toward their own in-group.
https://phys.org/news/2017-04-infants-racial-bias-members.ht...
https://time.com/67092/baby-racists-survival-strategy/
If what you claim is true, we would never have had miscegnation laws. Most people in the world wouldn't encourage marrying their own kind.
Just think about it. If people naturally favored the out-group ( people who look different ), racial/ethnic groups and diversity wouldn't exist. Blue eyes and blonde hair wouldn't exist because they are recessive traits. We wouldn't have any diversity because ethnic/racial groups require in-group bias to exist. The fact that we have black people, white people, indian people, chinese people, etc shows that in-group bias is the norm.
People naturally find their own kind and traits to be attractive. We know it's innate since it exists in babies. To find out-group features to be desirable requires external pressure - media, education, etc.
Edit: Since so many here are downvoting science because of their political agenda...
"We Choose Friends Who Are Genetically Similar to Us"
https://www.smithsonianmag.com/smart-news/we-choose-friends-...
"I like your genes: People more likely to choose a spouse with similar DNA"
https://www.sciencedaily.com/releases/2014/05/140519160716.h...
You're reaching. Early bias exists, but that doesn't remove culture from the equation. Culture is much more powerful.
Also, the difficulty of travel until quite recently would still lead to a lot of variety in different locations.
Also, that's not how recessive genes work.
> To find out-group features to be desirable requires external pressure - media, education, etc.
This is a massive mistake, of looking at an overall average and trying to apply it to individual situations. It's like expecting every man to be taller than every woman.
Also, the difficulty of travel until quite recently would still lead to a lot of variety in different locations.
Also, that's not how recessive genes work.
> To find out-group features to be desirable requires external pressure - media, education, etc.
This is a massive mistake, of looking at an overall average and trying to apply it to individual situations. It's like expecting every man to be taller than every woman.
> You're reaching. Early bias exists, but that doesn't remove culture from the equation.
I'm not "reaching". I didn't do the research. Scientists did. The research was on 3 month old infants. Before they are conscious. Before they know how to speak.
> Also, the difficulty of travel until quite recently would still lead to a lot of variety in different locations.
Right because miscegnation laws existed in the US because one simply couldn't travel from one town in alabama to another town in alabama.
> Culture is much more powerful.
I agree. Hence why I wrote: "To find out-group features to be desirable requires external pressure - media, education, etc.". Government/media/propaganda can easily undo our natural programming. But that doesn't mean that underlying natural programming doesn't exist.
> Also, that's not how recessive genes work.
No. That's exactly how it works.
To show how powerful culture is, you are denying science because it goes against your "programming". Also, just because I'm pointing out science doesn't mean I'm for miscegnation laws or against people marrying outside their group. I'm for people marrying who they like. Also, ever notice that it's people with an agenda who always downvote science?
I'm not "reaching". I didn't do the research. Scientists did. The research was on 3 month old infants. Before they are conscious. Before they know how to speak.
> Also, the difficulty of travel until quite recently would still lead to a lot of variety in different locations.
Right because miscegnation laws existed in the US because one simply couldn't travel from one town in alabama to another town in alabama.
> Culture is much more powerful.
I agree. Hence why I wrote: "To find out-group features to be desirable requires external pressure - media, education, etc.". Government/media/propaganda can easily undo our natural programming. But that doesn't mean that underlying natural programming doesn't exist.
> Also, that's not how recessive genes work.
No. That's exactly how it works.
To show how powerful culture is, you are denying science because it goes against your "programming". Also, just because I'm pointing out science doesn't mean I'm for miscegnation laws or against people marrying outside their group. I'm for people marrying who they like. Also, ever notice that it's people with an agenda who always downvote science?
> I didn't do the research. Scientists did.
The reach is in how far you're applying it.
> I agree. Hence why I wrote: "To find out-group features to be desirable requires external pressure - media, education, etc.". Government/media/propaganda can easily undo our natural programming. But that doesn't mean that underlying natural programming doesn't exist.
But then you can't say the natural programming is the reason. It's one factor and not one of the bigger factors.
> No. That's exactly how it works.
> To show how powerful culture is, you are denying science because it goes against your "programming".
It's not how it works, and I didn't deny any science.
Do I seriously need to pull out a genetics textbook? If you keep a steady population and have people marry at random, the number of copies of any particular recessive gene will stay the same. Mix up everyone's eye genes and you'll have a billion people with at least one copy of the gene for blue eyes. If two people with one copy have children, about a quarter of them will have blue eyes.
Even if you were making a strawman of ultra-extreme outgroup preference, where couples want to pair brown and blue eyes above all else, you'll still have carriers marrying people with blue eyes and having blue-eyed children. Even if you remove all of those, once you have a single generation of kids that all have one brown gene and one blue gene, they'll mix back up to give you kids with blue eyes.
The reach is in how far you're applying it.
> I agree. Hence why I wrote: "To find out-group features to be desirable requires external pressure - media, education, etc.". Government/media/propaganda can easily undo our natural programming. But that doesn't mean that underlying natural programming doesn't exist.
But then you can't say the natural programming is the reason. It's one factor and not one of the bigger factors.
> No. That's exactly how it works.
> To show how powerful culture is, you are denying science because it goes against your "programming".
It's not how it works, and I didn't deny any science.
Do I seriously need to pull out a genetics textbook? If you keep a steady population and have people marry at random, the number of copies of any particular recessive gene will stay the same. Mix up everyone's eye genes and you'll have a billion people with at least one copy of the gene for blue eyes. If two people with one copy have children, about a quarter of them will have blue eyes.
Even if you were making a strawman of ultra-extreme outgroup preference, where couples want to pair brown and blue eyes above all else, you'll still have carriers marrying people with blue eyes and having blue-eyed children. Even if you remove all of those, once you have a single generation of kids that all have one brown gene and one blue gene, they'll mix back up to give you kids with blue eyes.
> The reach is in how far you're applying it.
I'm not "applying it". I'm stating what it is.
> But then you can't say the natural programming is the reason.
Sure you can. Because as I said, infants do it. It's why the researchers chose infants and toddlers. Nobody TAUGHT an infant to prefer their own kind over others.
> It's one factor and not one of the bigger factors.
You are simply not getting it. We are NATURALLY programmed to prefer our in-group. But we can be programmed via propaganda ( government, media, education, etc ) to go AGAINST our programming.
> Do I seriously need to pull out a genetics textbook? If you keep a steady population
Not only do you fail at genetics, you fail at statistics.
> If two people with one copy have children, about a quarter of them will have blue eyes.
Right and 3/4th will have non-blue eyes. Just think about it. Breeding at random, the blue eyed population will simply diminish generation after generation.
> and have people marry at random
Also, who is talking about "random". The original commenter wrote : "I think people have an instinct for enriching their genome, that's why we're attracted to features our own group lacks, like different skin/hair color, facial structure, etc."
He was saying that people have an "instinct" and preference for out-group. I proved this was false with many sources. Science says that people have an "instinct" to prefer their in-group. The only way to counter it is with societal programming/propaganda. As I said.
I provided the sources. You aren't arguing against me, you are fighting against science. I'll end the "debate" here as it gets tiring repeating science over and over again.
I'm not "applying it". I'm stating what it is.
> But then you can't say the natural programming is the reason.
Sure you can. Because as I said, infants do it. It's why the researchers chose infants and toddlers. Nobody TAUGHT an infant to prefer their own kind over others.
> It's one factor and not one of the bigger factors.
You are simply not getting it. We are NATURALLY programmed to prefer our in-group. But we can be programmed via propaganda ( government, media, education, etc ) to go AGAINST our programming.
> Do I seriously need to pull out a genetics textbook? If you keep a steady population
Not only do you fail at genetics, you fail at statistics.
> If two people with one copy have children, about a quarter of them will have blue eyes.
Right and 3/4th will have non-blue eyes. Just think about it. Breeding at random, the blue eyed population will simply diminish generation after generation.
> and have people marry at random
Also, who is talking about "random". The original commenter wrote : "I think people have an instinct for enriching their genome, that's why we're attracted to features our own group lacks, like different skin/hair color, facial structure, etc."
He was saying that people have an "instinct" and preference for out-group. I proved this was false with many sources. Science says that people have an "instinct" to prefer their in-group. The only way to counter it is with societal programming/propaganda. As I said.
I provided the sources. You aren't arguing against me, you are fighting against science. I'll end the "debate" here as it gets tiring repeating science over and over again.
> Sure you can. Because as I said, infants do it. It's why the researchers chose infants and toddlers. Nobody TAUGHT an infant to prefer their own kind over others.
But I'm not talking about infants. I'm talking about people in general. By the time you're an adult, it's 90% culture.
If culture and instincts were opposites, culture would win. Which you agree with!
So when you say "If people naturally favored the out-group ( people who look different ), racial/ethnic groups and diversity wouldn't exist." that's not true. If you flipped the instinctual switch, people would still be clique-y.
> Breeding at random, the blue eyed population will simply diminish generation after generation.
No it won't. Oh my god. The more the blue-eyed population shrinks this way, the more brown-eyed carriers you have. The more carriers you have, the more often two brown-eyed people have a blue-eyed baby. This hits a steady state very quickly. We don't run out of people with a recessive trait.
And if people suddenly preferred to hook up with opposite-eyed people, the number of blue-eyed kids would actually drop down for a generation before rising over time to the steady state!
> Also, who is talking about "random".
I laid out the random scenario and the extreme out-group scenario. Neither one causes recessive traits to stop showing up en masse.
> He was saying that people have an "instinct" and preference for out-group. I proved this was false with many sources.
Yeah he was wrong about that. But you overcorrected.
Edit:
Let me put this by itself. Really simple logic.
> Right and 3/4th will have non-blue eyes. Just think about it.
These sentences were discussing parents that have one of each gene, right?
So all the parents under discussion here have brown eyes.
But only 75% of their children have brown eyes.
That sure doesn't sound like blue eyes disappearing to me!
But I'm not talking about infants. I'm talking about people in general. By the time you're an adult, it's 90% culture.
If culture and instincts were opposites, culture would win. Which you agree with!
So when you say "If people naturally favored the out-group ( people who look different ), racial/ethnic groups and diversity wouldn't exist." that's not true. If you flipped the instinctual switch, people would still be clique-y.
> Breeding at random, the blue eyed population will simply diminish generation after generation.
No it won't. Oh my god. The more the blue-eyed population shrinks this way, the more brown-eyed carriers you have. The more carriers you have, the more often two brown-eyed people have a blue-eyed baby. This hits a steady state very quickly. We don't run out of people with a recessive trait.
And if people suddenly preferred to hook up with opposite-eyed people, the number of blue-eyed kids would actually drop down for a generation before rising over time to the steady state!
> Also, who is talking about "random".
I laid out the random scenario and the extreme out-group scenario. Neither one causes recessive traits to stop showing up en masse.
> He was saying that people have an "instinct" and preference for out-group. I proved this was false with many sources.
Yeah he was wrong about that. But you overcorrected.
Edit:
Let me put this by itself. Really simple logic.
> Right and 3/4th will have non-blue eyes. Just think about it.
These sentences were discussing parents that have one of each gene, right?
So all the parents under discussion here have brown eyes.
But only 75% of their children have brown eyes.
That sure doesn't sound like blue eyes disappearing to me!
> But I'm not talking about infants. I'm talking about people in general.
You specifically responded to my comment which was a response to "I think people have an instinct for enriching their genome...". INSTINCT. Something that's INBORN, not cultural. That's what I specifically responded to. You are being dishonest here.
> Yeah he was wrong about that. But you overcorrected.
Overcorrected? Oh give me a break.
> Let me put this by itself. Really simple logic... But only 75% of their children have brown eyes.
I'm so glad you caught on. So you do know a little bit about statistics. So now I know all your misleading replies are not based on ignorance but agenda. Now ask yourself, in your non-biased random world, which produces 75% brown eyes and 25% blue eyes, how some countries have nearly 90% blue eyes or over 50% blue eyes? Your logic proves that in the real world, there was a bias. I won't even bother with how a recessive mutation in a 99.99% brown-eyed world ( 8000 years or so ago ) can survive without some selection bias to begin with.
https://www.livescience.com/9578-common-ancestor-blue-eyes.h...
For fun, put your two browned eyed people with recessive blue eyed genes with 98 other people without any blue eye recessive genes. And see how things work out without any bias. Randomly breed that population without bias and see how things turn out. But then again, you already know the answer right? Oh yeah, make it "real" and don't create exactly 4 offsprings either. And see how things really turn out.
I just don't understand why people like you intentionally lie about such mundane stuff. I know that you know better since you "caught" my statistical "mistake". If you weren't wasting my and other people's time with lies, I wouldn't care. Heck, you are wasting your own time. I don't get it.
I'll end it here. For reals this time. Have a nice day.
You specifically responded to my comment which was a response to "I think people have an instinct for enriching their genome...". INSTINCT. Something that's INBORN, not cultural. That's what I specifically responded to. You are being dishonest here.
> Yeah he was wrong about that. But you overcorrected.
Overcorrected? Oh give me a break.
> Let me put this by itself. Really simple logic... But only 75% of their children have brown eyes.
I'm so glad you caught on. So you do know a little bit about statistics. So now I know all your misleading replies are not based on ignorance but agenda. Now ask yourself, in your non-biased random world, which produces 75% brown eyes and 25% blue eyes, how some countries have nearly 90% blue eyes or over 50% blue eyes? Your logic proves that in the real world, there was a bias. I won't even bother with how a recessive mutation in a 99.99% brown-eyed world ( 8000 years or so ago ) can survive without some selection bias to begin with.
https://www.livescience.com/9578-common-ancestor-blue-eyes.h...
For fun, put your two browned eyed people with recessive blue eyed genes with 98 other people without any blue eye recessive genes. And see how things work out without any bias. Randomly breed that population without bias and see how things turn out. But then again, you already know the answer right? Oh yeah, make it "real" and don't create exactly 4 offsprings either. And see how things really turn out.
I just don't understand why people like you intentionally lie about such mundane stuff. I know that you know better since you "caught" my statistical "mistake". If you weren't wasting my and other people's time with lies, I wouldn't care. Heck, you are wasting your own time. I don't get it.
I'll end it here. For reals this time. Have a nice day.
> Now ask yourself, in your non-biased random world, which produces 75% brown eyes and 25% blue eyes, how some countries have nearly 90% blue eyes or over 50% blue eyes? Your logic proves that in the real world, there was a bias.
I never said there was no bias. Why do you spend so long arguing against things I didn't say?
> For fun, put your two browned eyed people with recessive blue eyed genes with 98 other people without any blue eye recessive genes. And see how things work out without any bias. Randomly breed that population without bias and see how things turn out.
But in the real world, those genes are in a pretty big fraction of people. No matter how you shuffle them around, you'll end up with tens of millions of people with blue eyes.
> I just don't understand why people like you intentionally lie about such mundane stuff.
What the fuck are you talking about?
...I got flagged for saying 'fuck', great.
I never said there was no bias. Why do you spend so long arguing against things I didn't say?
> For fun, put your two browned eyed people with recessive blue eyed genes with 98 other people without any blue eye recessive genes. And see how things work out without any bias. Randomly breed that population without bias and see how things turn out.
But in the real world, those genes are in a pretty big fraction of people. No matter how you shuffle them around, you'll end up with tens of millions of people with blue eyes.
> I just don't understand why people like you intentionally lie about such mundane stuff.
What the fuck are you talking about?
...I got flagged for saying 'fuck', great.
You shouldn't accuse anyone of lies if you fail to understand how genetics work.
Recessive alleles are not "in danger", their number would not decrease over time if there is no bias. That's basics.
https://en.wikipedia.org/wiki/Hardy–Weinberg_principle
Also anti-miscegenation laws is not a universal thing, but rather a specific facet of an Enlightenment-era Western culture, along with slavery.
https://en.wikipedia.org/wiki/Hardy–Weinberg_principle
Also anti-miscegenation laws is not a universal thing, but rather a specific facet of an Enlightenment-era Western culture, along with slavery.
Different people can have different views. You can easily have some people wanting to mate with outgroup members and other people not wanting the former people to mate with outgroup members and trying to prevent it. This is not a contradiction.
> Since so many here are downvoting science because of their political agenda
It doesn't have to be an all-or-nothing situation. If your posture was true, only Asians would find Asian girls attractive, for example. The fact that mixed people exist is proof that a subset of the population finds variance attractive, and another subset doesn't or doesn't care.
We don't have to differentiate instinct from culture from nurture, just look at the final effect. Politics has no place in this discussion.
It doesn't have to be an all-or-nothing situation. If your posture was true, only Asians would find Asian girls attractive, for example. The fact that mixed people exist is proof that a subset of the population finds variance attractive, and another subset doesn't or doesn't care.
We don't have to differentiate instinct from culture from nurture, just look at the final effect. Politics has no place in this discussion.
Preferences evolve during the lifetime of humans. Preferences in infants is usually different from preferences in sexual partners. Don't have the source handy, but it has been shown that females look for people with different genes (at least in regards to antibody-encoding) for mating, but once pregnant, seek people with similar genes (e.g. family).
In general, most studies saying people prefer sexual partners with different genes refer to the genes encoding antibodies, not the genome in general.
Do you really think we had a concise definition of "species" that was generally recognized back then? Do you think they pondered whether Neanderthals were a different race, a subspecies, or actually a different species?
And do you think that their societal mores regarding inter-species sex were identical to those of typical humans today?
Also, our current definition of species takes into account whether there is significant interbreeding in the wild. So that makes your question rather circular.
And do you think that their societal mores regarding inter-species sex were identical to those of typical humans today?
Also, our current definition of species takes into account whether there is significant interbreeding in the wild. So that makes your question rather circular.
I think it's a valid question. I often wonder what the cutoff is for how something determines whether another entity is of the same species (ie, something I have sex with vs something I eat). For instance, you could go off of looks, but then why would a german shepherd try to have sex with a pug? There seems to be some sort of ingrained biological threshold for what is a compatible mate and what isn't. Determining that threshold for various species is interesting to me.
> There seems to be some sort of ingrained biological threshold for what is a compatible mate and what isn't.
Clearly, Neanderthals were very much within the acceptable mate boundary, the question was whether that occurred despite recognizing them as “other” or not.
Clearly, Neanderthals were very much within the acceptable mate boundary, the question was whether that occurred despite recognizing them as “other” or not.
Ok but the question is assuming they have a concept of species, presumably with a bright line, and then are using that to determine whether or not to have sex. Which is circular (as well as absurd on so many levels).
That said, I'm sure they had some concept of "differentness," which would lie on a spectrum, rather than the black and white way the above poster described it.
Humans may, for instance, find people of different races to be less attractive in general. But exceptions can be made. I imagine if you are desperate enough, you widen the pool of acceptable candidates. I have no reason to think it was very different back then.
That said, I'm sure they had some concept of "differentness," which would lie on a spectrum, rather than the black and white way the above poster described it.
Humans may, for instance, find people of different races to be less attractive in general. But exceptions can be made. I imagine if you are desperate enough, you widen the pool of acceptable candidates. I have no reason to think it was very different back then.
> There seems to be some sort of ingrained biological threshold for what is a compatible mate and what isn't.
Perhaps in a general sense yes, but across millions of people across tens of thousands of years, there will always be outliers who'll mate with anything with two legs.
Perhaps in a general sense yes, but across millions of people across tens of thousands of years, there will always be outliers who'll mate with anything with two legs.
The old definition of biological species was exactly that animals of the same species are able to breed and get fertile offspring.
So I suppose they made a point, by definition, by doing so.
So I suppose they made a point, by definition, by doing so.
laws all over the land that say it is illegal to have sex with animals demonstrate the fact that we, as humans, will breed with literally anything
That's bestiality, not breeding as it doesn't produce offspring. It's like saying "i breed with my hand"
Well we have no way of knowing if the couplings that produced human-neanderthal hybrids were done with the intention of producing offspring. If you stick your dick in what you think is a bull but is actually the queen of Crete in a bull costume, your bestiality may very well result in a child.
"Species" is a rather arbitrary concept. Sometimes we divide species by whether they can produce fertile offspring, but many times we divide them by much fuzzier criteria such as where they live, how they behave, or what they look like. If there was an offshoot of humanity that found themselves facing a plague and only those with trisomy 21 survived it, we might well have regarded that population as a different species.
Neanderthals, denisovans, homo erectus, etc. were likely just members of the shared human species together with surviving homo sapiens.
You could say they were separate subspecies, but it's not clear that such a designation is reasonable without likewise considering various groups of bushmen and pygmies (e.g. khoi, san, hadza, mbuti) separate subspecies from each other and from the rest of humans as well.
You could say they were separate subspecies, but it's not clear that such a designation is reasonable without likewise considering various groups of bushmen and pygmies (e.g. khoi, san, hadza, mbuti) separate subspecies from each other and from the rest of humans as well.
Why not? We willingly breed with people who have extremely different physical characteristics than us all the time. Would a human and neanderthal from the same region back in the day be as different as, say, people of different races from the opposite sides of the world today?
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Genetically and physically yes, you would be way closer to a H. Sapien from the other side of the world than you would be to a Neanderthal who lived a cave over.
Perhaps culturally a geographically close Neanderthal would be easier to relate with than a more distant modern human, but that's pure speculation.
Perhaps culturally a geographically close Neanderthal would be easier to relate with than a more distant modern human, but that's pure speculation.
Looking around, I’d say humans will have sex with anybody and anything, given the opportunity. Doesn’t seem weird to me at all.
Rumours always swirl about the disgusting things people from $X_NEARBY_CITY do to animals even today...
i think that also can be interpreted as "it is the modern human and Neandertals hybrid which happened to be the winning combination that took over the planet" or "interbreeding with Neanderthals is what saved modern humans after the genetic bottleneck of 70K year ago" or "the modern humans who didn't bred with Neandertals got selected out".
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How does that compare to other species
This seems to explain the technique they're using to study this:
Ancestral recombination graph (ARG) inference (2) is a powerful starting point for such an analysis. An ARG can be conceptualized as a series of trees, mapped to individual sites, over phased haplotypes (chromosomes) in a panel of genomes. Ancestral recombination events, or sites at which chromosome segments with different histories were joined together by historical recombination, form boundaries between trees. Each ancestral recombination event manifests as a clade of haplotypes, all of which descend from the first ancestral haplotype to have it, moving from one position in the tree upstream of the event to a new position in the downstream tree (3). ARGs are complete descriptions of phylogenomic datasets and present for recombining genomes what single trees present for nonrecombining genomes, i.e., a complete description of their genetic relationships.
We run [our ARG] SARGE on a panel of 279 modern human genomes, two high-coverage Neanderthal genomes, and one high-coverage Denisovan genome. Using the resulting ARG, we map Neanderthal and Denisovan ancestry, ILS, and the absence of both across modern human genomes.
We find that approximately 7% of the human autosomal genome is human-unique and free of both admixture and ILS. Roughly 50% of the human genome contains regions where *one or more humans* has archaic ancestry obtained through admixture. If deserts are further restricted to regions that contain a high-frequency, human-specific derived allele, i.e., a substitution that can be assigned to the human lineage (hereafter “human-specific regions”), then these comprise only 1.5% of the assayed genome.
It sounds like a fancy graph-based Venn diagram of the genome overlap between different groups comprising sets of individual genomes. I'm still not 100% clear on their definition of "human-unique" - i.e. are these regions where all 279 sample human genomes are identical, or maybe all 279 had one or more modern versions of the allele vs. any of the samples still having an ancestral version?
They go into detail on some specific genes:
Several patterns emerge when considering genes with high-scoring human-specific mutations, and we highlight some of these key findings. Gene ontology terms related to mRNA splicing, processing, and export are enriched in genes with high-scoring mutations (table S7). Of these, we find a regulatory mutation affecting one—LUC7L3—that is somewhat tissue specific (tau, a measure of tissue specificity scaled from 0 to 1 = 0.713), most highly expressed in cerebellar tissue, and annotated to be involved in splice site selection. Its paralog LUC7L and the gene KHDC4, both of which also have high-scoring (top 50th percentile) regulatory mutations, are involved in the same process. In addition, the gene NOVA1, which harbors a nonsynonymous mutation in the top 95th percentile of our score distribution (Fig. 5C), is a neuronal splicing factor that regulates splicing of genes involved in synapse formation within the brain (43).
Which makes it sound like maybe yes, all modern humans have the "new and (hopefully) improved" version of these genes while no ancestral samples did.
https://advances.sciencemag.org/content/7/29/eabc0776
Ancestral recombination graph (ARG) inference (2) is a powerful starting point for such an analysis. An ARG can be conceptualized as a series of trees, mapped to individual sites, over phased haplotypes (chromosomes) in a panel of genomes. Ancestral recombination events, or sites at which chromosome segments with different histories were joined together by historical recombination, form boundaries between trees. Each ancestral recombination event manifests as a clade of haplotypes, all of which descend from the first ancestral haplotype to have it, moving from one position in the tree upstream of the event to a new position in the downstream tree (3). ARGs are complete descriptions of phylogenomic datasets and present for recombining genomes what single trees present for nonrecombining genomes, i.e., a complete description of their genetic relationships.
We run [our ARG] SARGE on a panel of 279 modern human genomes, two high-coverage Neanderthal genomes, and one high-coverage Denisovan genome. Using the resulting ARG, we map Neanderthal and Denisovan ancestry, ILS, and the absence of both across modern human genomes.
We find that approximately 7% of the human autosomal genome is human-unique and free of both admixture and ILS. Roughly 50% of the human genome contains regions where *one or more humans* has archaic ancestry obtained through admixture. If deserts are further restricted to regions that contain a high-frequency, human-specific derived allele, i.e., a substitution that can be assigned to the human lineage (hereafter “human-specific regions”), then these comprise only 1.5% of the assayed genome.
It sounds like a fancy graph-based Venn diagram of the genome overlap between different groups comprising sets of individual genomes. I'm still not 100% clear on their definition of "human-unique" - i.e. are these regions where all 279 sample human genomes are identical, or maybe all 279 had one or more modern versions of the allele vs. any of the samples still having an ancestral version?
They go into detail on some specific genes:
Several patterns emerge when considering genes with high-scoring human-specific mutations, and we highlight some of these key findings. Gene ontology terms related to mRNA splicing, processing, and export are enriched in genes with high-scoring mutations (table S7). Of these, we find a regulatory mutation affecting one—LUC7L3—that is somewhat tissue specific (tau, a measure of tissue specificity scaled from 0 to 1 = 0.713), most highly expressed in cerebellar tissue, and annotated to be involved in splice site selection. Its paralog LUC7L and the gene KHDC4, both of which also have high-scoring (top 50th percentile) regulatory mutations, are involved in the same process. In addition, the gene NOVA1, which harbors a nonsynonymous mutation in the top 95th percentile of our score distribution (Fig. 5C), is a neuronal splicing factor that regulates splicing of genes involved in synapse formation within the brain (43).
Which makes it sound like maybe yes, all modern humans have the "new and (hopefully) improved" version of these genes while no ancestral samples did.
https://advances.sciencemag.org/content/7/29/eabc0776