What fraction of genes do we share with relatives and with other species?

[fluidistic]

Hello, I am reading the Selfish gene by Richard Dawkins. I am confused on genes. In some part of the book he gives us clues on how to compute the percentage of genes we have in common with relatives, such as parents and brothers and sisters, in those particular cases it is stated that we share 50% of our genes with them, i.e. about half our genes are to be found in any brother/sister/parent. Great, it kind of makes sense.

Mentally, if I zoom into almost any cell (i.e. excluding gametes and cells lacking nucleus) in an organism and I focus on the nucleus (if there is any), then I should see the different chromosomes that contain the DNA (as well as the "junk DNA"), i.e. the "code" to build that organism. The DNA is just an assembly of four proteins, i.e. large molecules. What differs, at that level, between an onion and a human is the sequence of those 4 proteins. Most of the DNA is not useful information, roughly 2% of it really contains the information necessary to build the body. This information is separated by chunks of apparent useless protein molecules (ACDG). Ok great. Now, a gene would be a sequence of ACDG proteins that is not cut during meiosis and so can be passed on future generations. So natural selection can act on those genes. A "bad" gene would be a gene that is less successful in making an individual able to pass on its genes. But it is not so easy to tag a gene as bad or good, not only because most of the genes are affected by other genes (so a seemingly bad gene can turn out to be a good gene if there is another gene present in a particular individual but not in other), but because it is also dependent on the environment of the individual. Etc.

It is also stated that if we take two non relative individuals in a population, it is safe to assume that they share no gene, their relatedness is 0%. I can imagine this to be true in a species that has had enough time to have hundred of thousands if not millions of generations, and a non negligible rate of mutations, but ok, let's assume this to be true for humans. Then why is it stated on the Internet, that we share about 40% of our genes with a banana for example? If this were true, then we should care more about the future of a banana than the future of our cousins, or grandparents / grandsons/granddaughters. Because, by ensuring the banana is successful in passing its genes, we also ensure a good part of our own genes are passed into the next generation. And thus more of our genes are passed to the next generations than if we had saved, for example, our grandson. This doesn't seem intuitively correct to me. What am I missing?

 

[epenguin]

My first reaction reading your post was to worry I am seriously out of date. I thought what is this ACGT protein I have never heard of? etc.

Then I realized these are the initials of the DNA bases not a protein, the junk DNA does not code for any proteins – that's why it's called junk. There are huge misunderstandings like that in your post and you need to inform yourself of some elements of molecular biology I would say. I have not read this book, but possibly it is not the best place for the basic information. If there are no pictures in it it will certainly not be good enough for this purpose. Then there may be some problem arising but you need to be at least into a position to formulate it first.

 

[fluidistic]

My first reaction reading your post was to worry I am seriously out of date. I thought what is this ACGT protein I have never heard of? etc.

Then I realized these are the initials of the DNA bases not a protein, the junk DNA does not code for any proteins – that's why it's called junk. There are huge misunderstandings like that in your post and you need to inform yourself of some elements of molecular biology I would say. I have not read this book, but possibly it is not the best place for the basic information. If there are no pictures in it it will certainly not be good enough for this purpose. Then there may be some problem arising but you need to be at least into a position to formulate it first.

Ok about the nucleotides not being protein, dully noted. Would the following recast of my question be meaningful?

If we share 40% of our genes with any banana and "only" 25% of our genes with a grandson/niece and even less with a cousin, and if the selfish gene theory is correct, shouldn't imply that we would tend to save bananas from being eaten rather than giving them to these relatives, in an extreme situation where our relatives are starving and bananas would save them? If the goal, after all, is that most of our genes get passed on, we should focus on helping the banana, not these relatives.

My intuition tells me that the assumption that we share more genes with a banana compared to a grandson is not correct.

Google returns ""You share 50 percent of your DNA with each of your parents. But with bananas, we share about 50 percent of our genes, which turns out to be only about 1 percent of our DNA," emails Mike Francis, a Ph.D. student in bioinformatics at the University of Georgia". So there might lie the answer. How many percent of our genes do we share with our parents, if not 1/2? It seems like the number is much higher than 1/2, and this would go against the Dawkins book (which, as you point out, should probably not used to learn modern biology/evolution theory from). I just want to have a clearer picture in my mind.

I am, I hope, not asking for a string theory-level like explanation. Something a pop science physics book cannot really do successfully (I think).

 

[DrClaude]

The DNA is just an assembly of four proteins, i.e. large molecules.

You are confusing proteins with nucleotides.

Most of the DNA is not useful information, roughly 2% of it really contains the information necessary to build the body. This information is separated by chunks of apparent useless protein molecules (ACDG).

This is grossly incorrect. Just because a segment of DNA does not code for a protein doesn't mean that it is useless, see https://en.wikipedia.org/wiki/Non-coding_DNA

As a rule of thumb, you should always assume that Nature is efficient. The cost in storing and transmitting DNA is high, so it would be absurd to think that most of it is "junk" (shame on the biologists how coined the term). Like we are only using 10% of our brain...

It is also stated that if we take two non relative individuals in a population, it is safe to assume that they share no gene, their relatedness is 0%.

Does this make any sense? It would mean that there are billion of different genes to code for a given protein that is shared by all humans.

You should read https://en.wikipedia.org/wiki/Human_genetic_variation

 

[Ygggdrasil]

When we talk about the amount of genetic similarity between species, there are varying ways of calculating how similar they are. For the figure that human DNA is 40% similar to banana DNA, this is not exactly true:

About 60 percent of our genes have a recognizable counterpart in the banana genome! "Of those 60 percent, the proteins encoded by them are roughly 40 percent identical when we compare the amino acid sequence of the human protein to its equivalent in the banana," Brody adds.

https://science.howstuffworks.com/life/genetic/people-bananas-share-dna.htm (note, this would be a good article to read to get further clarity on the point)

Now, as you said, about 2% of the human genome codes for proteins. So, the comparison is really between 1.2% of the human genome (the 60% of human genes that have a banana counterpart) and the corresponding part of the banana genome. In contrast, if one were to do comparison between two "unrelated" humans, 100% of genes in individual A would have a counterpart in individual B and the sequence of these genes would be >99% identical.

Indeed, all humans have the same set of genes, and according to the Wikipedia link cited above, the typical difference between the genomes of two individuals was estimated at 20 million base pairs (or 0.6% of the total of 3.2 billion base pairs).

What do we mean when 50% of our DNA comes from each parent? That, in the a one-celled fertilized zygote, 50% of its DNA literarly came from the father's sperm and 50% of the DNA literally came from the mother's egg. The DNA from the father's sperm is >99% identical to the DNA from the mother's egg, so in many cases, the DNA will be exactly identical, but at those rare positions where there is a disagreement between the mother's DNA and the father's DNA, we can see that there is one chromosome that came from the father and one chromosome that came from the mother.

 

[Ygggdrasil]

This is grossly incorrect. Just because a segment of DNA does not code for a protein doesn't mean that it is useless, see https://en.wikipedia.org/wiki/Non-coding_DNA

As a rule of thumb, you should always assume that Nature is efficient. The cost in storing and transmitting DNA is high, so it would be absurd to think that most of it is "junk" (shame on the biologists how coined the term). Like we are only using 10% of our brain...

While the percent of our DNA that is functional is certainly not 2%, it is also not 100% either. About 10% of the human genome is evolutionarily conserved, which probably sets the lower limit (and also makes the point in our genomes, about 5x as much DNA is devoted to regulation when genes are turned on and off versus the actual proteins that the genes encode). Quite a large fraction (~50%) of the genome is repetitive DNA, much of which are derived from various transposable elements like endogenous retroviruses.

For a good discussion, see this previous PF thread: https://www.physicsforums.com/threads/researchers-claim-only-8-of-human-dna-is-functional.779450/

or this nice article from the journal PLOS Genetics: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004351

 

[fluidistic]

When we talk about the amount of genetic similarity between species, there are varying ways of calculating how similar they are. For the figure that human DNA is 40% similar to banana DNA, this is not exactly true:https://science.howstuffworks.com/life/genetic/people-bananas-share-dna.htm (note, this would be a good article to read to get further clarity on the point)

Now, as you said, about 2% of the human genome codes for proteins. So, the comparison is really between 1.2% of the human genome (the 60% of human genes that have a banana counterpart) and the corresponding part of the banana genome. In contrast, if one were to do comparison between two "unrelated" humans, 100% of genes in individual A would have a counterpart in individual B and the sequence of these genes would be >99% identical.

Indeed, all humans have the same set of genes, and according to the Wikipedia link cited above, the typical difference between the genomes of two individuals was estimated at 20 million base pairs (or 0.6% of the total of 3.2 billion base pairs).

What do we mean when 50% of our DNA comes from each parent? That, in the a one-celled fertilized zygote, 50% of its DNA literarly came from the father's sperm and 50% of the DNA literally came from the mother's egg. The DNA from the father's sperm is >99% identical to the DNA from the mother's egg, so in many cases, the DNA will be exactly identical, but at those rare positions where there is a disagreement between the mother's DNA and the father's DNA, we can see that there is one chromosome that came from the father and one chromosome that came from the mother.

Thank you very much for the reply.
I was careful enough not to mix DNA with genes. I really meant that we shared 40% of our genes (not DNA!) with bananas. The focus on genes is because I have in mind the selfish gene theory, as is explained in Dawkins' book. The book really claims that we share 1/2 of our genes with our parents, and that this number goes to 0 pretty quickly the further we move to unrelatives. He really insists on genes, not DNA, hence, I guess, the choice of the name of the title of the book and on the theory of the selfish gene. The theory claims that evolution is driven as if it was the genes that acted "selfishly", as in "wanting to be passed onto the next generation(s)." This is mentioned at the beginning of the book, most of the rest of the book deals with showing how this theory explains the behavior of animals.

But if I am now told that we share nearly 100% of our genes (I'm not talking about DNA) with any other human (which goes completely opposite to what the book claims), then I really do not understand the selfish gene theory at all. If the gene of a given rat is to be found in most rats, then... the individual should treat any rat as itself, and should favor the young and healthy above any other rat. That is, as far as I know, not observed in nature, for such an altruism would disappear over time by natural selection. Maybe Dawkins meant "gene" as in "allele", I suppose. Say there was a single gene determining the eye's color in a human. For Dawkins, a gene would be the allele, so two humans having a different eye colors would have two different genes related to the eye's color. I think that's the point he makes. In that case, would it be true that most of our alleles differ between 2 non relative humans? And that we would share only 50% with brother/sister/parents, as he claims? I guess so. (I have checked https://en.wikipedia.org/wiki/Human_genetic_variation, it looks like this may not hold in some human populations where consanguinity might be "high", but generally it would be true.)
In that particular view, do we really share 40% of "alleles" with a banana? The website https://science.howstuffworks.com/life/genetic/people-bananas-share-dna.htm is extremely confusing to me, in particular one reads

This gave us the result of about 40 percent," he says. "This is the average similarity between proteins (gene products), not genes.

and the feeling I get is that many of our "genes" have a counterpart in a banana (which is indeed not surprising because of the origin of life on Earth).

To summarize, the confusion seems to be about the definition of a gene. The one used in Dawkins' book does not match the one in some websites, apparently. For some websites, there would be, say, a "gene" for breathing that we could find in most animals. However, molecularly even if it is very similar to the one we could find in a particular person, it is not exactly the same. Even from person to person it would differ (different alleles). For Dawkins, a gene seems to be what most people/website consider a particular allele. In that aspect a banana and a human probably (I guess?) have nothing in common. And so natural selection at a Dawkins' gene level acts in such a way that we do not really care if a banana gets smashed, eaten by a relative or a random person on the street. It is not our genes that are getting destroyed. Very different from the case than if it was our child that was being eaten.

 

[pinball1970]

And so natural selection at a Dawkins' gene level acts in such a way that we do not really care if a banana gets smashed, eaten by a relative or a random person on the street. It is not our genes that are getting destroyed. Very different from the case than if it was our child that was being eaten.

Try not to forget that our DNA has evolved over millions of years to build brains in a replicating machine that happens to be a social animal.

Social animals have on the whole have evolved to not eat their young (examples where this can happen under severe duress) via learned behaviour as well as genes that can be passed on.

We have also evolved to recognize not only members of our own species but members of our own family (within reason )

We have not evolved to recognize genes, we did not know what they were and how they worked till Mendel in the 19thC.

We evolved to recognize a banana as lunch and this happened way before Homo sapiens.

 

[fluidistic]

Try not to forget that our DNA has evolved over millions of years to build brains in a replicating machine that happens to be a social animal.

According to the book I am reading, this is not correct. The replicators are the genes, not the individuals. Your children are far from copies of yourselves. Individuals are mortals and do not last long while genes can go a long way.

Social animals have on the whole have evolved to not eat their young (examples where this can happen under severe duress) via learned behaviour as well as genes that can be passed on.

We have also evolved to recognize not only members of our own species but members of our own family (within reason )

We have not evolved to recognize genes, we did not know what they were and how they worked till Mendel in the 19thC.

We evolved to recognize a banana as lunch and this happened way before Homo sapiens.

Not sure why the emphasis in on "we" (as in human?), this could be said for most of living species, I believe. I mostly agree with what you wrote.

 

[Buzz Bloom]

about half our genes are to be found in any brother/sister/parent.

Just checking this.

On the average, siblings share about 1/2 of their genes with each other, but it is possible for them to not share any. I have never seen what the standard deviation is for this distribution, but it of course depends on the number of genes that might be shared.

The Human Genome Project has revealed that there are probably about 20,000-25,000 'haploid' protein coding genes.​

https://www.edinformatics.com/math_science/human-genome.html​

The number of matching genes is a binomial distribution. If we assume N = 22,500, and that the likelihood of a particular gene being shared is independedan of another gene being shared, then the mean is 11,250, and the standard deviation (σ) is 0.5×√N = 75 . This means that two siblings will share between (11,100 and 11,400 genes) 49.3% and 50.7% about 95% of the time (mean +/- 2σ).

However, this is an unrealistic assumption. Also, unrealistic, but much closer to realism, is that the chromosomes are the units that are inherited (although there are crossovers which switch a fraction of one chromosome with its paired chromosome. If we ignore the crossovers, and for convenient simplicity assume all 23 pairs have the same number of genes, then the mean is 11.5 and the standard deviation is 2.4.
Therefore, the 2σ range is between 4.3 and 13.9, meaning 95% of the time the sharing will be between 18.7% and 81.3%. This does not seem to be matching "about half our genes are to be found in any" sibling.

 

[pinball1970]

According to the book I am reading, this is not correct. The replicators are the genes, not the individuals. Your children are far from copies of yourselves. Individuals are mortals and do not last long while genes can go a long way.Not sure why the emphasis in on "we" (as in human?), this could be said for most of living species, I believe. I mostly agree with what you wrote.

Apologies it's a while since I read it.
We are the vessel, the genes are the replicators.
I tried to use his terminology.

You referred to 'we' wrt the banana so I followed on with that.

 

[jim mcnamara]

FWIW - something to think about on this topic.

A. siblings from birth may not have expected DNA.

https://www.psychologytoday.com/us/...-age/201911/dna-testing-expect-the-unexpected

This is a pop sci blog about people who found out that Dad was not really Dad, genetically. And everyone in the family had thought otherwise for years. Since none were adopted.

This problem is common enough, such that companies like 23andMe include warnings about unwanted or possibly distressing results for the people involved.

B. Chimeras -

Two separate and complete sets of DNA in one human do occur. Chimeras are common in plants and some animals. But they also may rarely occur in humans.

Woman who had her children taken by the state after a DNA test indicted she was not the mother.
Turns out she was a chimera, apparently.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1808039/

C. Hopping genes

Then there are transposons, 'jumping genes'. People thought Barbara McClintock was mistaken. But no.
https://en.wikipedia.org/wiki/Transposable_element
https://en.wikipedia.org/wiki/Barbara_McClintock

This is why Biology can be unsettling scientifically for a non-biologist. And scrambles things up a bit for thinking about comparing DNA, with folks who are biologists.

 

[BillTre]

According to the book I am reading, this is not correct. The replicators are the genes, not the individuals. Your children are far from copies of yourselves. Individuals are mortals and do not last long while genes can go a long way.

Replicators can be found at different hierarchical levels in the biological world.
Different things can be considered replicators in different situations.

Genes expanding in a organism's genome can certainly be considered selfish within the genomic environment.

On the other hand, within the environment of a eukaryotic cell, mitochondria can compete for success within the internal eukaryotic cellular environment. Those that replicate the most rapidly will be selected in the cellular environment. In that way these replicators (the mitochondria) can be considered selfish.

Individual metazoan organisms can similarly considered replicators whose overall success in their environment is determined by different internal factors (like genes) affecting their effectiveness in dealing with their environment. There replicators can also be considered selfish.

No replicator at these different levels are always going to make perfect copies from their previous generation. Replicated genes can have errors. Each mitochondria is not an identical copy of its predecessors, just like an organisms which creates imperfect copies of it's parent's adult forms through its generative developmental programs are not perfect copies.