than how we explain that a mouse genome is so similar to the human genome? mouse generation time is about less than a year. so after about 30 my the entire genome of the mouse should be different (3 bbp/100 (mutations rate)=30 million generations). how does it fit with a junk DNA?
by the way john; if we will make a phylogeny out of junk DNA, do we will get a similar nested hierarchy pattern like the coding genes phylogeny?
The experts will correct me if I am wrong, but I think what you are referring to there is the neutral mutation rate. Obviously, regions of the genome that are conserved by selection will change more slowly, if at all.
Even I know the answer to that one, which is āYes.ā
You really think no one in the field had thought of that already?
Sorry, but your mutation rate was gibberish. It looks like the germline mutation rate in Mus musculus is around 5 * 10^-9 /bp/generation. In 30 million generations thatās a bit over 10% expected difference.
In general, yes. Junk DNA evolution is actually easier to model than coding sequence evolution, so the phylogeny can be expected to be estimated more correctly, if itās alignable.
ok. so what if we will look at a mosquito or a fly?
can you give me an example of a phylogenetic tree (suppose a general tree like of verterbrate or mammals) that was made out of junk DNA and show a nested hierarchy? thanks.
yep. but they are the minority of course.
Donāt know. At some point junk DNA becomes difficult to align.
Sure. Here. Introns are quite popular for phylogenetic analysis.
if a fly generation time is about 1 month, and one generation=1 new mutation, its whole genome (or actually 75% of it) sould be different after about 15 my. so how a fly genome is very similar to other genomes?
thanks. although I meant to something that is realy junk (introns can be functional) but never mind. lets leave it at that for now.
Because some parts of the fly genome are subject to more strong negative selection than others. So those parts will accumulate mutations at a slower rate.
Those parts which are truly nonfunctional junk will accumulate mutations more quickly, because thereās only a very low degree of negative selection operating on it. Those parts that are functional will have higher degrees of negative selection operating on it, making it evolve slower and thus remain recognizable after longer periods of time. Such parts of the genome that evolve more slowly are considered to be more āconservedā over time.
This conservation, due to negative selection, comes in degrees from almost total conservation (all mutational changes are removed) to no conservation (all changes are allowed).
Some things are very strongly conserved, they almost never change. On the other end of the spectrum some things are not at all conserved, they change very quickly. And there are things in between.
What other genomes? And what point are you ever so clumsily trying to make here?
Although introns can sometimes contain functional sequences, theyāre mostly junk. I gave you exactly what you asked for.
ok but we are talking about junk DNA and not about coding genes.
i guess that any animal genome that we will check. im sure that they are not different by 75% compare to a fly genome.
see here for instance:
āTaken together, introns are clearly not junk, and they provide selective advantages to cells to be evolutionarily maintained, nevertheless, it has expensive energetic costs.ā
The explanation is still the same for why some regions are more conserved while others are less conserved. Itās due to differences in the strength of negative selection.
Let me know when you can do more than guess. The fact is that thereās no way even to align the junk DNA in a flyās genome with the junk DNA in a humanās genome. Thereās no way even to come up with a difference measure.
You have discovered an ambiguity in the definition of ājunkā. Should DNA whose function is unrelated to its sequence, i.e. ābulk DNAā whose only function is to be present, be considered junk? For the purpose of sequence conservation or lack thereof, which is what youāre talking about, definitely yes.
As I understand correctly, the most reliable way to determine whether a sequence is junk is to determine its degree of conservation. And, in turn, conservation is best measured by comparing sequences between lineages that have descended from a common ancestor.
If Iām correct about that, it is difficult to see how one can have a productive discussion of the subject of junk DNA with someone who does not even accept common ancestry in the first place. Even above and beyond the obstacles that already exist when trying to get creationists to understand and accept science.
That depends on whether you count bulk DNA as junk. If, for example, an intron has to be there for some reason, but the only thing that matters is that it contain two spice signals and be of a certain minimum length, it can evolve entirely neutrally. So is it junk?
I donāt know if thatās the most reliable way; itās certainly the most convenient.
The reasoning employed in that paper is honestly embarrassingly, catastrophically bad.
Look at this assertion from the conclusion:
Besides, introns may give some advantages as a mutational buffer in eukaryotic genomes protecting coding sequences from being affected by randomly occurring deleterious mutations. Introns occupy about 40% on average of the total length of genes, which means that most randomly occurring mutations will fall into intron regions, and do not affect protein sequences and functions.
To borrow a term from Dan Graur, this is imbecilic!
Guess I should have looked at the paper rather than relying on @scdās quotes. Itās a credulous review, very sloppy and poorly written. In one sentence it claims that only eukaryotes have introns, and in another it claims that introns originated in type II self-splicing introns of bacteria. It uncritically accepts that all detected protein isoforms are functional. And so on.
No. Orphan genes are not junk but by definition donāt display high degree of conservation.
How does one measure the degree of conservation that āorphan genesā are subject to?
This isnāt true. Many supposed orphan genes are artifacts, that is, open reading frames that donāt actually produce proteins, and are not conserved because they actually are junk. Some orphan genes are real genes that arose recently, and thereās no way to use interspecific comparisons to tell whether they are or are not being conserved.
Conservation is convenient, but itās not perfectly reliable. Recently evolved genes may show only evidence of past non-conservation, and may even evolve by positive selection at greater than the neutral rate. Genes that have recently become pseudogenes may show only the evidence of past conservation. Some duplicated genes may be under selection promoting divergence or specialization. But such cases are likely to be a small minority, and conservation is still a pretty good guide to functionality.
Geneticist John Mattick:
āI want to say to you that conservation is totally misunderstood. High conservation imputes function. No question. Low conservation imputes nothing. Think about your phone number.ā
From here (the YouTube clip should start at 31:58; if it doesnāt, thatās where he makes this comment):
How do you know that an orphan gene is an artifact?
I really donāt understand what you mean here. Isnāt the case that interspecific conservation can only be measured by interspecific comparaison?
Agree. But absence of conservation doesnāt mean absence of functionality.