neanderthal dna in homosapiens

[mattrix]

This has been asked before but not adequately answered.

"It's indicated online that 1–4% of the genetic material of modern non-African humans is Neanderthal DNA but this doesn't make sense when both Neanderthals and earlier-Sapiens both evolved from a common ancestor."

I just don't know what "4%" this is referring to.

Neanderthals and modern humans share a plethora of features; bilateral symmetry 2 eyes, 2 ears, 2 kidneys, 2 hands each with 4 fingers and a thumb; complex organs kidney, liver, lung, brain; and the chemicals and hormones that support them; and a million other things.

Am I to believe that all of this is encoded in less than 1% of our coding DNA?

I think I heard somewhere that something like 90% of a butterflies (or your favorite genus) DNA is found in humans.

Are we more related to a butterfly than we are to neanderthals?

So the reason for my not understanding, "4%" of what?

 

 

[mattrix]

I missed the edit window.

Above I said "coding DNA", but I meant "functional DNA".

[exchemist]

1 hour ago, mattrix said:

This has been asked before but not adequately answered.

"It's indicated online that 1–4% of the genetic material of modern non-African humans is Neanderthal DNA but this doesn't make sense when both Neanderthals and earlier-Sapiens both evolved from a common ancestor."

I just don't know what "4%" this is referring to.

Neanderthals and modern humans share a plethora of features; bilateral symmetry 2 eyes, 2 ears, 2 kidneys, 2 hands each with 4 fingers and a thumb; complex organs kidney, liver, lung, brain; and the chemicals and hormones that support them; and a million other things.

Am I to believe that all of this is encoded in less than 1% of our coding DNA?

I think I heard somewhere that something like 90% of a butterflies (or your favorite genus) DNA is found in humans.

Are we more related to a butterfly than we are to neanderthals?

So the reason for my not understanding, "4%" of what?

 

 

All the features you list are common to a vast range of creatures, so would not be part of this 1-4% you are enquiring about. So we share DNA all of these, even though we are not directly descended from any of them. It is often said we share 50% of our DNA with a banana, even. 

But my understanding is the 1-4% relates to DNA features found in homo sapiens neanderthalensis but NOT found in homo sapiens sapiens of African origin. As for where it comes from, one needs to keep in mind that H sapiens sapiens and H sapiens neanderthalensis appear to have interbred. So they are not fully separate species. Therefore, if, like me, you are of N European ancestry, it is likely you have some ancestors who were Neanderthals, rather in the way that I have one Welsh great-grandmother.       

 

[Genady]

Should not this percentage depend on the length of DNA chunks that are compared? In the extreme case, if we compare pieces of one nucleotide long, any organism on Earth shares 100% of its DNS with any other organism on Earth; they all are AT and CG.

[mattrix]

Thanks exchemist,

I have no problem sharing genes with neanderthals or bananas for that matter.

I wonder how much difference there is between neanderthal and african sapiens, if as you say, it is 1-4% of this difference. Your take at least makes sense.

^^ to rephrase that, I wonder how much DNA they have in common? The split was not that long ago, geologically speaking.

[Genady]

2 hours ago, exchemist said:

But my understanding is the 1-4% relates to DNA features found in homo sapiens neanderthalensis but NOT found in homo sapiens sapiens of African origin.

However,

Quote

We all likely have a bit of Neanderthal in our DNA – including Africans who had been thought to have no genetic link to our extinct human relative, a new study finds.

(All modern humans have Neanderthal DNA, new research finds | CNN)

2 hours ago, exchemist said:

it is likely you have some ancestors who were Neanderthals, rather in the way that I have one Welsh great-grandmother.

It is not clear to me how DNA acquired by a direct descent differs from DNA shared because of a common ancestry.

Another question regarding direct descent is about the amount, 1-4%. We have this amount of DNA directly from our grandparents of 5-6 generations back, which is too recent for neanderthals.

Edited December 17, 2023 by Genady

[exchemist]

2 hours ago, Genady said:

However,

(All modern humans have Neanderthal DNA, new research finds | CNN)

It is not clear to me how DNA acquired by a direct descent differs from DNA shared because of a common ancestry.

Another question regarding direct descent is about the amount, 1-4%. We have this amount of DNA directly from our grandparents of 5-6 generations back, which is too recent for neanderthals.

Not if all our grandparents had it, surely?

[Genady]

55 minutes ago, exchemist said:

Not if all our grandparents had it, surely?

Sure, this is right. 

Then the question is, how much interbreeding would create a stable inherited set throughout the entire population.

The OP question is still open, I think. 1-4% of what? Do we have on average 1 neanderthal gene? 5? 100? Are they genes that we share with neanderthal but with nothing else? Are they "genes" or long chunks of DNA? How long?

Is this just a pop-science number?

Edited December 17, 2023 by Genady

[mattrix]

Thanks Genady for expressing those questions.

I've had a chance to think about this. What is to say that European sapiens didn't diverge from African sapiens before they interbred with neanderthals. Then the genetic material in question, could be sapien DNA that was introduced into neanderthal DNA.

We talk about populations, but as far as I can find we only have 1 or very few reliable sources of neanderthal DNA.

Totally confused!!

 

 

[CharonY]

8 hours ago, Genady said:

Sure, this is right. 

Then the question is, how much interbreeding would create a stable inherited set throughout the entire population.

The OP question is still open, I think. 1-4% of what? Do we have on average 1 neanderthal gene? 5? 100? Are they genes that we share with neanderthal but with nothing else? Are they "genes" or long chunks of DNA? How long?

Is this just a pop-science number?

I think I might have addressed it here somewhere (or potentially elsewhere, I cannot really recall) but the 1-4% were based on earlier studies and hinges on comparison with sequences obtained from Neanderthal samples. Also, these are not genes (generally speaking, we all have the same genes, but what is relevant are Neanderthal specific variants, or alleles). These numbers, however are not exact calculations but rather rely on identification of matches with the Altai Neanderthal genome and then using existing modern human sequences to estimate the rate of introgression (i.e. how much genetic material was introduced). The 1-4% therefore represent the level of ancestry calculated by these comparative analyses. 

 

57 minutes ago, mattrix said:

We talk about populations, but as far as I can find we only have 1 or very few reliable sources of neanderthal DNA.

This is an interesting point and indeed having insufficient Neanderthal reference can lead to wrong calls in the process. I.e. sequences might be tagged as likely Neanderthal, while they actually aren't or vice versa. This is actually what some folks think what happened. Based on a fairly recent paper the assumption is now that the Altai Neanderthal might have picked up DNA form modern humans based on a failed migration from Africa to the middle yeast and this might have led to a misattribution of signals as Neanderthal, although they were actually from modern humans. This would explain the mystery that East Asian population were showing a higher Neanderthal signal, despite the fact that no fossils were found there. However, if those signals were actually modern human to begin with, that would perfectly explain the distribution.

[mattrix]

4 hours ago, CharonY said:

what is relevant are Neanderthal specific variants, or alleles). These numbers, however are not exact calculations but rather rely on identification of matches with the Altai Neanderthal genome and then using existing modern human sequences to estimate the rate of introgression

That actually, for me, muddies the waters. As far as I know, nearly every loci in current humans shows some form of polymorphism. ( I hope I used the terminology correctly). I doubt that we know all  of these alleles for current humans, let alone all possible allelomorphs in archaic sapiens.

That a sequence occurs in the Altai neanderthal does not mean it did not arise independently in sapiens, or is not a hanger on from a common ancestor, no matter how rare.

I think I'm pondering around: How do we know the direction the allele took between neanderthal and archaic sapiens? At least without us having an awful lot more exemplars.

 

4 hours ago, CharonY said:

The 1-4% therefore represent the level of ancestry calculated by these comparative analyses

I'm not sure how to interpret this. Whilst on the face of it, it seems reasonable, I would have difficulty explaining it.

It is not so much the words but how one formulates it into their understanding. I'll think on it.

Edited December 18, 2023 by mattrix

[CharonY]

I think you might overthink it. What folks basically do is look at a locus I.e. a given stretch of DNA and check what variability is there in a population. These variations are not entirely random and by having sufficiently distant members of a species, we can infer or estimate what their ancestors might had.

Of course there is always the chance that we miss variations that somehow have vanished from extant populations or misjudge the gene flow. But you are correct that limited data might impact interpretation and an lead to false assumptions.

 

 

[sethoflagos]

11 hours ago, mattrix said:

I'm not sure how to interpret this. Whilst on the face of it, it seems reasonable, I would have difficulty explaining it.

It is not so much the words but how one formulates it into their understanding. I'll think on it.

A clue can be found be looking at where introgressive Neanderthal alleles are found in the modern human genome.

They are strongly represented in areas associated with climate adaptation (skin and hair type) and immune response, areas that would be particularly useful for a newly migrating population to acquire from a sitting population that had adapted to that environment over a long period.

They are to all intents and purposes absent from large areas (known as 'Neanderthal deserts') where our post split ancestors, underwent significant genetic change such as in FOXP2 (language development etc) and the X chromosome - the areas that make us most distinctly, who we are.

The distribution therefore seems to be based not on how many times introgression occurred, but on whether that introgression was beneficial or not. The % DNA contribution doesn't therefore correlate with the number of Neanderthals in our family tree, but merely indicates that there was at least one.

[sethoflagos]

Apparently I could have added 'morningness' to the assistance given by Neanderthals to climate adaptation:

Published last week:

Archaic Introgression Shaped Human Circadian Traits

... with a fair amount of interest.

Neanderthal DNA May Help Explain Why Some People Are Early Risers

[CharonY]

Yeah, I used that paper to tell my wife that she is more Neanderthal than me. Did not go over well at all. Typical Neanderthal!

[mattrix]

I found a reference that states that 99.7% of neanderthal DNA is the same as sapiens DNA.

I don't see why we can't say, when relatively small numbers of sapiens from Africa migrated to Eurasia, they were subsumed into the larger neanderthal population and the sapiens contributed a small amount of new DNA into the population that went on to populate the world. (this is only half tongue in cheek)

With such a small difference in DNA and the ability to interbreed, how many generations would it take for the 2 populations to converge? I know Chimps also have 98.8%, but I believe there are chromosome differences, one ancestral chromosome split in Pan, Or two chromosomes fused in homo?. Still why don't we get hybrids, as do other genera , walleroo, mule, ass etc

Clearly I don't understand evolutionary genetics. Can anyone suggest a good book?

[CharonY]

1 hour ago, mattrix said:

Clearly I don't understand evolutionary genetics. Can anyone suggest a good book?

I think the seminal undergrad text book on evolution is still Futuyma. 

The 1-2% with chimpanzees is a different type of count, and was really base on looking at genes (i.e. excluding large non-coding areas) and even then it was based on a subset of genes. In addition, I believe they were based on substitutions. For example, let's say humans have a stretch of DNA being GCTTA and chimpanzees at the same locus it would be GGTTA then there would be one substitution (C->G). But there are also regions with deletions and insertions. E.g. GCTTA becomes GCAAGCGCTTA, the question is how you quantify the additional AAGCGC (or the missing part, depending on perspective). The original 1-2% differences simply ignored them. I believe lining up the genomes and matching the bases would still yield something like 80% match, but not entirely, memory gets a bit hazy.