What does it mean to have 2% Neanderthal DNA when all humans presumably share basically 100% of our DNA with them?

Submitted by The_Imperial_Moose t3_yl3gz7 in askscience

I never understood it when I hear things like 2% Europeans DNA comes from Neanderthals, and other similar statements. Given that anatomically modern humans bred with Neanderthals wouldn't that mean our genetics were basically already identical, so how could you have 2% Neanderthal DNA when were already at the basically 100% shared genetics required for breeding? Could someone explain this please.

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newappeal t1_iuwownz wrote

The "basically 100%" figure is a nucleotide-for-nucleotide comparison of the genomes. You line up a human and Neanderthal genome, count how many nucleotides have the same identity (A/T/C/G) and divide that by the total length of the genome. (Because the genomes are not exactly the same length, the metric would have to be more nuanced than that, but this imperfect definition is fine for illustrative purposes.) This measure is agnostic to the actual genetic history of each species or individual being compared, but it is broadly reflective of time since the last common ancestor.

The "2%" figure is based on heritage. Here, we're comparing loci (regions of the genome; genes are loci, but "locus" is a more general term than "gene") instead of individual nucleotides. We probe the human genome for long sequences that as a whole resemble a sequence at the same location in the Neanderthal genome, count all those up and then either divide that count by the number of loci examined, or divide the base-pair length of all the like loci by the base-pair length of each genome. Loci determined to be Neanderthal in origin (and determining whether a shared locus was transferred from H. sapiens to H. neanderthalensis or the other way around is its own problem) do not necessarily have 100% sequence identity with the ancestral Neanderthal strain - indeed, we would not expect them to - but they are more similar to Neanderthals than other regions of the genome. A higher similarity indicates more recent divergence from Neanderthals, through horizontal gene transfer (mating and recombination) rather than through common descent from humans' and Neanderthals' last common ancestor.

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iayork t1_iuwvvw8 wrote

To give OP an example: Imagine two books, 10 chapters long, almost exactly the same, but each page has a typo or two. In Chapter 7, say, one book may say "teh" instead of "the" on page 2, and the other may say "Neandertal" instead of "Neanderthal" on page 3; and so on. Overall, the books are 99.9% identical, but each chapter has a set of diagnostic typos.

Now we create a third book, by replacing chapter 7 of book 1 with chapter 7 of book 2. By comparing the pattern of typos with the parent books, we can clearly tell that chapter 7 comes from a different source.

Are the books 99.9% identical? Yes. Did book 3 get 10% of its content from a different source? Also yes.

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Rabwull t1_iuzpdhb wrote

I have never seen haplotypes described so simply and clearly. May I steal your analogy every time I explain this, forever? I can cite you as iayork (2022) if you like.

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newappeal t1_iv0ovwe wrote

I too will be using this analogy in the future. Thank you for adding this, u/iayork!

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Dan13l_N t1_iv0y384 wrote

But how do you know that the whole chapter 7 comes from a different source? What if only one paragraph comes from another source?

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Rabwull t1_iv2gbcz wrote

This is an excellent question. In reality, you only know the source between consistent diagnostic typos. If we run out of these typos 10 pages before the end of Chapter 7, we can't be sure from which source those last 10 pages come.

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doc_nano t1_iuwuoze wrote

I don't blame you for being confused -- there is no single standard for comparing how similar two genomes are, since it depends a lot on what kind of comparison you're making. Nucleotide-for-nucleotide, you are right that there are almost no differences between the protein-coding sections of Homo sapiens and Neanderthal genomes. I don't know the exact number off hand, but it's surely much closer to 100% identity than 99%.

However, when people talk about what % Neanderthal DNA a person has, it's usually talking about larger "chunks" of the DNA. This is a measure of heredity that is more akin to saying a person has 50% European ancestry and 50% Asian (or whatever). The European and Asian human genomes are almost 100% identical, but you could analyze that person's DNA to figure out what fraction of the DNA was likely to have come from European populations and what fraction was likely to come from Asian populations. A common way to do this is to look for single-nucleotide variants (called SNPs or "snips") that are common in one population but rare in others. If you find several such SNPs in a region of the genome, the probability is high that the person has heredity from that population.

Edit: Also, it gets even more complicated when you start taking into account non-protein-coding parts of the genome, which can be more variable in sequence and size, as well as situations where whole parts of the genome might have been duplicated.

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Ok-Championship-2036 t1_iv0qer5 wrote

Gene testing to prove ethnicity/individuality is bad science. This is how I was taught in my anthro degree, that we should move away from trying to isolate social constructs like ethnicity/"subspecies" (doesnt exist in bio). The way we use it really is not how science works. Basically, they take a "perfect sample" (the only one available) and then compare everything else to it. They make a 1:1 comparison between one unique sample and another, equally unique sample. Then they say something like, "You are 56% asian pacific islander."

The reason this doesnt work is because EVERY place has more variety than similarity. You could take two samples from New York and record drastically different genomes, but someone decided that the one on the left was a Nigerian sample while the one on the right is a caucasian sample. I hope I've explained a little bit how the system is flawed due to humans choosing which sample means what and NOT based on any actual genetics/science. Its just comparing "perfect" ideals to one another. But nature has no such thing. This is why you see twins with different results or re-testing with lots of changes.

https://humgenomics.biomedcentral.com/articles/10.1186/s40246-022-00391-2 The link between ancestry testing and ethnic superiority

https://www.vox.com/science-and-health/2019/1/28/18194560/ancestry-dna-23-me-myheritage-science-explainer Limits of Genetic testing

scientificamerican.com/article/white-nationalists-are-flocking-to-genetic-ancestry-tests-with-surprising-results/ Nazis facing severe cognitive dissonance after realizing "pure white" isnt a racial group used by genetic testers.

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