One point that has always boggled my n00b understanding of this field is what unit of measure geneticists are using when they speak of humans and chimps being 99% the same genetically, but then also say that modern humans have 2-4% DNA in common with Neandersovans?
Clearly those two statements are each using a radically different metric, which never seems to be explained! (/old man yells at the clouds)
"The confusion comes from how percentages are used in different places. What the 2-4% refers to is how much DNA from a Caucasian or Asian is 100% identical to Neanderthal DNA.
In other words, a typical European and a Neanderthal are 99.7% similar over 96-98% of their DNA and 100% similar to a Neanderthal over 2-4% of their DNA. A sub-Saharan African will be 99.7% the same as a Neanderthal over 100% of their DNA.
There are many brilliant numerate people reading Razib that can correct this if wrong. I scrub toilets for a living, but was curious of the numerically concrete answer to your question, so I asked the internet and the above is the answer I received. So take that for what it is worth. There is more at the link about "DNA Similarity Between Species". ie. Humans and chimpanzees.
Thank you very much, Carleton. That article you cited clears it up nicely. I come away with two conclusions:
1. Geneticists have been using sloppy language when they throw these unqualified percentages into their writings targeted at lay persons.
2. More fundamentally, I have to assume that when geneticists talk amongst themselves they have way more precise and nuanced ways of expressing degrees of (dis)similarity. So the use of simple percentages must have been arrived at for the express purpose of popular science writing aimed at laypersons, and in that regard the choice of using percentages was, in my humble opinion, a Fail. The percentages do not intuitively convey anything meaningful to a lay person even if one was to somehow recognize which one of those different ways of measuring was actually being reported. I am wondering if some other unit of measure would resonate more: # of generations since last common ancestor? The fraction of 1 represented by the last common ancestor (i.e., 1 over some power of 2)? Metrics like this would start to embed an intuitive feel for the scales of time we are talking about.
I'm not sure more percentages from that link really cleared it up and elucidated the differences for me. The genome is over 3 billion base pairs. Even a 0.006% difference is a massive number of base pairs. Also, I don't think lay people, myself included, grasp the complexity present within the genome. We had the computational power and knowledge to send a man to the moon 40 years before we were able to sequence the human genome.
Little Kenny, that's a good question and I am surprised it hasn't been simply answered. My understanding is that when someone says we are 99% the same genetically as chimps (or bananas) they are referring to the structure of the genome itself. I.E. humans and chimps have mostly the same genes in the same spots and the same number of genes (as opposed to duplicated [extra] genes etc). But they also differ in their genomes by 1%, i.e. maybe they have an extra copy of this or that gene and maybe they have genes that we don't and vice versa.
When someone is referring to the differences in DNA between two modern humans they generally aren't talking about the structure of the genome or whether we have the same genes in the same places or if one person carries a gene that another doesn't carry. All modern humans have the same genes in the same place. The differences between them is alleles not genes. In other words all humans have the same genes but they have different flavors or versions of those genes.
Put another way comparing humans to chimps is an apples to oranges comparison (genomic structure etc.) while comparing humans to humans is an apples to apples comparison (differences in alleles). The percentages of each comparison are referring to different things. Generally speaking humans acquire different alleles (flavors) of genes from Neanderthals and Denisovans. Although this may not be entirely true since much of what is acquired during hybridization is quickly deleted in ensuing generations (purifying selection) which could be because new genes are inserted into the genomes and causes a negative effect, but that is beyond my knowledge.
Thanks for the response, Andrew Ramos. Actually my inquiry did get a thorough response, as Razib made a whole post on this topic on July 31 ("I wanna be like you"). Your explanation that cross-species comparisons measure gene differences while intra-human comparisons measure allele differences is a nice simple way of summing it up -- if you read the July 31 post, is it saying the same thing just in more words?
A further noob question I can't figure in my mind is exactly how humans have decent amounts of neanderthal and denisovan DNA intermixed but zero mtDNA introgression? What are the scenarios in which that happens? Is it only males of these other human groups intermixing? Is it mothers staying with their children in their own groups and thus the mtDNA from neanderthal/denisovan mothers disappeared with their groups/cultures?
Great summary article this one Razib. I have some keen multi-regionalist friends and a couple of things that always come up in conversations that I think I have answers to but curious on your take.
1. Some research suggests that some mtDNA can sometimes come from the male line. To me that would add some variation and if anything make the date to a common female ancestor look deeper in time than it really is? The small amount of potential added variation would not greatly alter the story though even if possible.
2. What about the possibility that extra variation was inherited from European migration back into Africa? To my mind that would then require all those Europeans to have left no genetic trace back in Europe if is to look like unique variation in African populations. They then posit the plague as something that would have then depleted European variation. To me this would require much more than the plague to have European mtDNA variation so reduced relative to African variation.
I guess another way of approaching this is to consider just how much of the West Eurasia population would have had to mix back into Africa and then subsequently genetically disappear to get to the unique relative variation we now see. Seems to me it would need to be quite an extreme scenario. Even with the plague much of the genetic material of Europeans would have still been largely intact?
plague wouldn't do it. yeah, it would be extreme. there are some models of eurasian backflow from europe/mid east. they're complicated...i haven't tested the different simulations myself
IANaG (I am not a geneticist, or even a biologist), so take this FWIW. What I got out of reading David Reich's book is that our current technology cannot see differences in the mtDNA going back more than 160,000 years (to the origin of H sapiens sapiens as a distinct species). I.e., at that distance they all look the same. I do not know whether the issue is our limited techniques or that there is not enough codons from which to extract the information.
One point that has always boggled my n00b understanding of this field is what unit of measure geneticists are using when they speak of humans and chimps being 99% the same genetically, but then also say that modern humans have 2-4% DNA in common with Neandersovans?
Clearly those two statements are each using a radically different metric, which never seems to be explained! (/old man yells at the clouds)
Can anybody enlighten me please?
"The confusion comes from how percentages are used in different places. What the 2-4% refers to is how much DNA from a Caucasian or Asian is 100% identical to Neanderthal DNA.
In other words, a typical European and a Neanderthal are 99.7% similar over 96-98% of their DNA and 100% similar to a Neanderthal over 2-4% of their DNA. A sub-Saharan African will be 99.7% the same as a Neanderthal over 100% of their DNA.
So the 2-4% of a non-African person’s genome that is of Neanderthal origin will still be 99.7% similar to the matching stretch of DNA in an African person’s genome. In terms of the whole genome, that is only 0.006% of actual difference!" - https://genetics.thetech.org/ask-a-geneticist/human-neanderthal-similarity-africans-europeans
There are many brilliant numerate people reading Razib that can correct this if wrong. I scrub toilets for a living, but was curious of the numerically concrete answer to your question, so I asked the internet and the above is the answer I received. So take that for what it is worth. There is more at the link about "DNA Similarity Between Species". ie. Humans and chimpanzees.
Thank you very much, Carleton. That article you cited clears it up nicely. I come away with two conclusions:
1. Geneticists have been using sloppy language when they throw these unqualified percentages into their writings targeted at lay persons.
2. More fundamentally, I have to assume that when geneticists talk amongst themselves they have way more precise and nuanced ways of expressing degrees of (dis)similarity. So the use of simple percentages must have been arrived at for the express purpose of popular science writing aimed at laypersons, and in that regard the choice of using percentages was, in my humble opinion, a Fail. The percentages do not intuitively convey anything meaningful to a lay person even if one was to somehow recognize which one of those different ways of measuring was actually being reported. I am wondering if some other unit of measure would resonate more: # of generations since last common ancestor? The fraction of 1 represented by the last common ancestor (i.e., 1 over some power of 2)? Metrics like this would start to embed an intuitive feel for the scales of time we are talking about.
LK, the 99% number is confusing to a lot of geneticists and relies i think on old amino acid metrics. i will look up genomewide data to confirm
I'm not sure more percentages from that link really cleared it up and elucidated the differences for me. The genome is over 3 billion base pairs. Even a 0.006% difference is a massive number of base pairs. Also, I don't think lay people, myself included, grasp the complexity present within the genome. We had the computational power and knowledge to send a man to the moon 40 years before we were able to sequence the human genome.
Little Kenny, that's a good question and I am surprised it hasn't been simply answered. My understanding is that when someone says we are 99% the same genetically as chimps (or bananas) they are referring to the structure of the genome itself. I.E. humans and chimps have mostly the same genes in the same spots and the same number of genes (as opposed to duplicated [extra] genes etc). But they also differ in their genomes by 1%, i.e. maybe they have an extra copy of this or that gene and maybe they have genes that we don't and vice versa.
When someone is referring to the differences in DNA between two modern humans they generally aren't talking about the structure of the genome or whether we have the same genes in the same places or if one person carries a gene that another doesn't carry. All modern humans have the same genes in the same place. The differences between them is alleles not genes. In other words all humans have the same genes but they have different flavors or versions of those genes.
Put another way comparing humans to chimps is an apples to oranges comparison (genomic structure etc.) while comparing humans to humans is an apples to apples comparison (differences in alleles). The percentages of each comparison are referring to different things. Generally speaking humans acquire different alleles (flavors) of genes from Neanderthals and Denisovans. Although this may not be entirely true since much of what is acquired during hybridization is quickly deleted in ensuing generations (purifying selection) which could be because new genes are inserted into the genomes and causes a negative effect, but that is beyond my knowledge.
Thanks for the response, Andrew Ramos. Actually my inquiry did get a thorough response, as Razib made a whole post on this topic on July 31 ("I wanna be like you"). Your explanation that cross-species comparisons measure gene differences while intra-human comparisons measure allele differences is a nice simple way of summing it up -- if you read the July 31 post, is it saying the same thing just in more words?
Thanks for asking, I wondered how I could be 95% close to a banana (or whatever the number) but only 50% to my mom...
What is a 2000-year-old mtDNA molecule like? Is it still a circle? Is it still inside of a mitochondrion?
my understanding is that it's pretty fragmented
A further noob question I can't figure in my mind is exactly how humans have decent amounts of neanderthal and denisovan DNA intermixed but zero mtDNA introgression? What are the scenarios in which that happens? Is it only males of these other human groups intermixing? Is it mothers staying with their children in their own groups and thus the mtDNA from neanderthal/denisovan mothers disappeared with their groups/cultures?
Great summary article this one Razib. I have some keen multi-regionalist friends and a couple of things that always come up in conversations that I think I have answers to but curious on your take.
1. Some research suggests that some mtDNA can sometimes come from the male line. To me that would add some variation and if anything make the date to a common female ancestor look deeper in time than it really is? The small amount of potential added variation would not greatly alter the story though even if possible.
2. What about the possibility that extra variation was inherited from European migration back into Africa? To my mind that would then require all those Europeans to have left no genetic trace back in Europe if is to look like unique variation in African populations. They then posit the plague as something that would have then depleted European variation. To me this would require much more than the plague to have European mtDNA variation so reduced relative to African variation.
1 - i'm skeptical. if it happens, it is VERY rare https://en.wikipedia.org/wiki/Paternal_mtDNA_transmission#In_humans
2 - there is evidence for west eurasian back migration. but the old european lineages that died out don't seem to have had an impact in africa
Thanks muchly Razib. Is the finding of the European lineages that died out not being much present genetically in Africa covered in some articles?
i haven't written on it, but you can google oase romania ancient dna. that's one old lineage in europe that died out
I guess another way of approaching this is to consider just how much of the West Eurasia population would have had to mix back into Africa and then subsequently genetically disappear to get to the unique relative variation we now see. Seems to me it would need to be quite an extreme scenario. Even with the plague much of the genetic material of Europeans would have still been largely intact?
plague wouldn't do it. yeah, it would be extreme. there are some models of eurasian backflow from europe/mid east. they're complicated...i haven't tested the different simulations myself
IANaG (I am not a geneticist, or even a biologist), so take this FWIW. What I got out of reading David Reich's book is that our current technology cannot see differences in the mtDNA going back more than 160,000 years (to the origin of H sapiens sapiens as a distinct species). I.e., at that distance they all look the same. I do not know whether the issue is our limited techniques or that there is not enough codons from which to extract the information.
yep. the issue is that mtDNA evolves fast and has a small effec pop size. so there is a limitation in perception beyond the TMRCA
TMRCA = The Most Recent Common Ancestor?