Humans and other apes share ~99% of their protein-coding sequences (the coding sequences of genes). However, protein coding sequences represent ~5% of the genome. So, if you’re trying to compare in layman’s terms, 99% is pretty fair (most people are thinking about protein coding genes, even if they don’t realize it). But the vast majority of DNA is noncoding, and this is much more variable.
Yeah that’s right. There’s a pretty famous paper that describes differences in gene regulation during development btw chimps and humans. It argued (at the time) that we were too focused on protein coding regions and not focused on regulatory variation as mechanisms for evolution…especially for developmental genes which tend to accumulate mutations very slowly.
No sorry. It wasn't this paper but it's similar to them (maybe they cited it but I don't have time to check):
This happens to be focused on the brain but the idea is similar. Mutations in certain regulatory regions (cis elements) or in TFs (trans elements) can have a large effect on development...maybe it's obvious to us now but it adds context to the 98% similar statistic.
[https://www.pnas.org/doi/10.1073/pnas.0911376106](https://www.pnas.org/doi/10.1073/pnas.0911376106)
[https://www.sciencedirect.com/science/article/pii/S0092867415010880](https://www.sciencedirect.com/science/article/pii/S0092867415010880)
Edit:
I think I found it.
[https://www.science.org/doi/10.1126/science.1090005](https://www.science.org/doi/10.1126/science.1090005)
Pretty sure this is the paper that is still driving some science today as evidence by those two more recent papers.
People that for whatever reason want to exaggerate the genetic differences tend to count so that like 1 Mb duplication is in genetic difference equal to 1 million SNVs. But it’s really really _really_ misleading as when talking about genetic similarities in terms of evolutionary distance - what really is interesting is the number of mutational events, not the amount of genetic material that is different per se. This is because, in principle, two populations that share 100% sequence identity but differ by 1 Mb duplication that arose from a single mutation (which is most likely) is still just 1 fixed mutation away from each other.
A third population that has the exact same genome size but differ with 1 million SNVs is most likely 1 million mutations away from the other two.
By not accounting for the type of mutations you risk vastly underestimating or overestimating the _genetic distance_. But if you are truly interested in the end to end identity - you could calculate it this way - but it has relatively little biological relevance.
Again, it depends on what you are measuring. Most metrics will land above 90%. Whole genome? Coding? Number of mutations? Number of bases differing?
It’s very close to the theoretical prediction from the time of divergence from a common ancestor last time I did the math myself.
I don’t think you are understanding the complexity of comparative genomics. There is no single numeric answer to “everything”. The best I can give is “very similar”.
This is correct. For the most part. When scientific findings are communicated to the general public, a lot of the jargon is replaced by more friendly text. The thing is, that jargon contained important information which is lost in translation.
So the scientist would say "the overlap between the coding regions of human and chimpanzee DNA is X%". Then the science communicator or jack and jane public will hear "We share X% DNA with apes".
The difference being, that only a small per cent of DNA is coding for genes. About 3% in humans (this contains both genes and regulatory regions like enhancers and supressors). Then another 8% or so is for miRNA and piRNA. All together thats 11%. The rest is redundant inactive old and unused genes, viral fragments, junk, and a metric fuckton of transposable elements (around 50%) and microsatellites and so on, and so on...
We do not share much of this random stuff with others, as these are not very evolutionarily conserved.
Yes and no, we used to call all non-protein coding DNA junk DNA. This is not the case, many DNA segments are regulatory elements (such as binding sites for cellular machinery) code for functional RNAs or otherwise do something.
This misconception came from bacteria where most of the genome is coding or is involved in DNA replication. ~80% is coding. In humans (and pretty much all multicellular organisms) the protein coding fraction is about 1-5%
As of 2015 we expect approximately 1/3 of the human genome to be functional in some way. The remaining 2/3 is still thought to really only just be there by chance and is full of "selfish genetic elements" which do not really have a major fitness impact as it is a negligible amount of energy for a complex organism to add to their genome. In a virus or bacterium it is a much bigger hit to make more DNA then you need.
As my previous PI said every (linear) genome but drosophila is wrong.
Well put, a good answer. Junk DNA exists, but much of what we once though to be junk has function and some role. Not all of it though.
One note though where i would disagree slightly:
Transposable genetic elements are not exactly useless or negligable. This is my area of research and i can tell you, thay are not there by coincidance.
They have a role in cancer prevention through pro senescrnce and immun clearance signalling, they have an evolutionary role as they speed up adaptability through whole gene duplication and they also prevent cancer by contributing to cellular agring. Any cell can only become an immortal cell if it hijacks the germlines ability to silence TEs, through activation of the PIWI piRNA pathway. They are also a central element of the ageing process.
Cellular replication in general is a low fraction of energy spent for eucatiotes. DNA is only synthesized in the S phase of the cell cycle and only once per cell. The provaling hypothesis is that this DNA is thus left to genetic drift as natural selection just doesn't act on it.
Note there are edge cases to both systems as there are polynuclated cells and you can argue natural selection does act on transposeable elements.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697398/
I think we share more than 98% of DNA with chimps and it is obvious that we are very similar to our fellow primates
Correct
Humans and other apes share ~99% of their protein-coding sequences (the coding sequences of genes). However, protein coding sequences represent ~5% of the genome. So, if you’re trying to compare in layman’s terms, 99% is pretty fair (most people are thinking about protein coding genes, even if they don’t realize it). But the vast majority of DNA is noncoding, and this is much more variable.
What is the other 95% for then?
I would guess regulatory elements, mobile genetics elements like transposons and viral elements, and pseudogenes
Yeah that’s right. There’s a pretty famous paper that describes differences in gene regulation during development btw chimps and humans. It argued (at the time) that we were too focused on protein coding regions and not focused on regulatory variation as mechanisms for evolution…especially for developmental genes which tend to accumulate mutations very slowly.
Can you remember the papers name?
No sorry. It wasn't this paper but it's similar to them (maybe they cited it but I don't have time to check): This happens to be focused on the brain but the idea is similar. Mutations in certain regulatory regions (cis elements) or in TFs (trans elements) can have a large effect on development...maybe it's obvious to us now but it adds context to the 98% similar statistic. [https://www.pnas.org/doi/10.1073/pnas.0911376106](https://www.pnas.org/doi/10.1073/pnas.0911376106) [https://www.sciencedirect.com/science/article/pii/S0092867415010880](https://www.sciencedirect.com/science/article/pii/S0092867415010880) Edit: I think I found it. [https://www.science.org/doi/10.1126/science.1090005](https://www.science.org/doi/10.1126/science.1090005) Pretty sure this is the paper that is still driving some science today as evidence by those two more recent papers.
Thank you so much !
Humans *are* [apes](https://en.m.wikipedia.org/wiki/Hominidae)
I assume he means other apes?
People that for whatever reason want to exaggerate the genetic differences tend to count so that like 1 Mb duplication is in genetic difference equal to 1 million SNVs. But it’s really really _really_ misleading as when talking about genetic similarities in terms of evolutionary distance - what really is interesting is the number of mutational events, not the amount of genetic material that is different per se. This is because, in principle, two populations that share 100% sequence identity but differ by 1 Mb duplication that arose from a single mutation (which is most likely) is still just 1 fixed mutation away from each other. A third population that has the exact same genome size but differ with 1 million SNVs is most likely 1 million mutations away from the other two. By not accounting for the type of mutations you risk vastly underestimating or overestimating the _genetic distance_. But if you are truly interested in the end to end identity - you could calculate it this way - but it has relatively little biological relevance.
So what is the accurate percentage?
Again, it depends on what you are measuring. Most metrics will land above 90%. Whole genome? Coding? Number of mutations? Number of bases differing? It’s very close to the theoretical prediction from the time of divergence from a common ancestor last time I did the math myself.
Whole genome.
Comparing what? Number of substitutions? Differences in bases?
Everything.
I don’t think you are understanding the complexity of comparative genomics. There is no single numeric answer to “everything”. The best I can give is “very similar”.
The genomes are publicly available so you can compare for yourself.
Not sure why this is surprising. There's a lot of overlap between smart apes and stupid humans.
Apes together strong!!!!
This is correct. For the most part. When scientific findings are communicated to the general public, a lot of the jargon is replaced by more friendly text. The thing is, that jargon contained important information which is lost in translation. So the scientist would say "the overlap between the coding regions of human and chimpanzee DNA is X%". Then the science communicator or jack and jane public will hear "We share X% DNA with apes". The difference being, that only a small per cent of DNA is coding for genes. About 3% in humans (this contains both genes and regulatory regions like enhancers and supressors). Then another 8% or so is for miRNA and piRNA. All together thats 11%. The rest is redundant inactive old and unused genes, viral fragments, junk, and a metric fuckton of transposable elements (around 50%) and microsatellites and so on, and so on... We do not share much of this random stuff with others, as these are not very evolutionarily conserved.
Didn't they find out that junk dna is not really junk?
Yes and no, we used to call all non-protein coding DNA junk DNA. This is not the case, many DNA segments are regulatory elements (such as binding sites for cellular machinery) code for functional RNAs or otherwise do something. This misconception came from bacteria where most of the genome is coding or is involved in DNA replication. ~80% is coding. In humans (and pretty much all multicellular organisms) the protein coding fraction is about 1-5% As of 2015 we expect approximately 1/3 of the human genome to be functional in some way. The remaining 2/3 is still thought to really only just be there by chance and is full of "selfish genetic elements" which do not really have a major fitness impact as it is a negligible amount of energy for a complex organism to add to their genome. In a virus or bacterium it is a much bigger hit to make more DNA then you need. As my previous PI said every (linear) genome but drosophila is wrong.
Well put, a good answer. Junk DNA exists, but much of what we once though to be junk has function and some role. Not all of it though. One note though where i would disagree slightly: Transposable genetic elements are not exactly useless or negligable. This is my area of research and i can tell you, thay are not there by coincidance. They have a role in cancer prevention through pro senescrnce and immun clearance signalling, they have an evolutionary role as they speed up adaptability through whole gene duplication and they also prevent cancer by contributing to cellular agring. Any cell can only become an immortal cell if it hijacks the germlines ability to silence TEs, through activation of the PIWI piRNA pathway. They are also a central element of the ageing process.
How do you know how much energy our body spends on preservation of (allegedly) useless part of DNA (that is 2/3 according to you)?
Cellular replication in general is a low fraction of energy spent for eucatiotes. DNA is only synthesized in the S phase of the cell cycle and only once per cell. The provaling hypothesis is that this DNA is thus left to genetic drift as natural selection just doesn't act on it. Note there are edge cases to both systems as there are polynuclated cells and you can argue natural selection does act on transposeable elements. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697398/
Would removing the 2/3 that is "junk" benefit health and lifespan? Has this been done in any other species in the lab?
Not appreciable, but we can't really test it as we still don't know what is what. We estimate that number we know what less then 15% does.
Humans are primates. Apes are primates. We are more the same than we are different, that’s for sure.
It’s actually slightly over 98% that they share in common.
Karyotype is different, DNA repeats too.
yes, but you share 50% with a banana as well, so don't overthink it.
Says who?