Introduction to Genetics

Negative selection is probably the easiest to detect, but my population genetics is not the greatest so feel free to correct me on that one.

I still don't follow that. Yes, if you make the gene longer, than there's more likely to be two indels in it, but there's also more likely to be one, or three which are not all of the same kind, or four, or ... etc. The ideal number is zero.Also, how would it help if you got a compensating indel in an intron? This intron is taken out before the translation. If it was translated and then the amino acid sequence corresponding to the intron was taken out after the translation, then an indel in the intron would compensate for an opposite indel in an exon, but it isn't ...... I don't really see what you're getting at, or if I do, it isn't right. One or the other.Edited by Dr Adequate, : No reason given.

I don't follow; introns are excised by the gene machinery - indels in them make no odds corrected or not - it's only indels in exons that are relevant and the chance for them to occur remains constant regardless of how many introns you insert or how widely spaced genes are on the genome.

Not quite, purifying selection is the removal of harmful alleles from the population, not simply the removal of mutations. Neutral and positive mutations will persist.

I'm pretty sure that Crashfrog is wrong, because if it worked that way an indel IN the intron would affect the gene, so overall the risk of frameshift mutations would go up. The statistics don't work out in a way that favours his view, either.If, on the other hand introns reset the reading frame, then the effect of indels would be limited to the start of the next intron - assuming that the frameshift doesn't mess that up. I'm speculating here, but it sounds like something that might be true....

Introns don't reset the frame; you can get codons split between two exons.

Look, you guys can be as skeptical as you like, but this is straight out of Leninger Principles of Biochemistry, Inferring Phylogenies, and for that matter Wikipedia:

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Noncoding DNA separate genes from each other with long gaps, so mutation in one gene or part of a chromosome, for example deletion or insertion, does not have the "frameshift mutation" on the whole chromosome. When genome complexity is relatively high, like in the case of human genome, not only different genes, but also inside one gene there are gaps of introns to protect the entire coding segment to minimise the changes caused by mutation.

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Probably not the clearest way to put it - this doesn't seem like it was written by a native English speaker, actually - but I'm hardly running off the edge of the science, here.Edited by crashfrog, : No reason given.

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Look, you guys can be as skeptical as you like, but this is straight out of Leninger Principles of Biochemistry, Inferring Phylogenies, and for that matter Wikipedia:

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Crash, that quote doesn't say anything about the non-coding regions being an advantage because they might get extra mutations putting things right. That idea is still very implausible just from statistical principles.The question I'm really interested in is how this protection works, and your quote doesn't address that at all.

It seems to be referring to something like this (unfortunately the paper's in Russian which I can't read). I can see that against chemical mutagens non-coding DNA could be protective (although I doubt it would be against radiation) but I don't see how it's particularly relevant to indels (thought to occur primarily through slippage during replication).

Hrm, then maybe I misunderstood. I'll see if I can dig up a better reference. I know I've gone back and forth on this over the years, so in the meantime I'm happy to have people consider the claim withdrawn. I'll see if I can find some support for it. This is a good thread, I think the potential for informing Faith is pretty high, and I like to not drag it off-topic towards confusion.Edited by crashfrog, : No reason given.

I just skimmed this thread starting with my original questions. A lot of them did get answered although the thread took a much too technical turn for me.The question that brought me back to this thread is really a wish to know what differentiates the genome of one species from another. Like they say there is only about 5% difference between the human genome and the chimp genome. That 5% of the human genome then must contain the coding for what is specifically human and not ape, and same with the ape genome. But is that particular 5% even recognizable, is it clear in the genome where it is located and what it codes for? In other words I'd really like to know the specifics about that part of every genome for every creature that differentiates it from all the others. What makes a cat genome a cat genome, a dog genome a dog genome etc?Edited by Faith, : No reason given.

This might help explain a bit. It's not technical and will not answer all your questions but it does give you an idea of the problems in trying to give these answers.In short, we may know enough to look at two specific genomes and say in general this is probably a bonobo and this a human, but we do not yet know how some of these differences work. For instance, humans and bonobos have some genes that are identical but, for reasons we do not yet understand, work in different ways. The proteins created are identical but under the influence of the full score of proteins in the system these identical proteins do different things in different places within the different species. This, of course, will lead to differences in phenotype just as well as a gene difference. Differences in DNA structure are but a beginning point in determining what creature is being made.The study of proteomics is the study of the interrelationships of the proteins produced by the genome. As you can imagine this is highly complex and we have just barely begun. To fully determine what makes such a different animal, a bonobo, from a nearly identical genome as a human will be decades in the future. here

There IS a case in China where a man has 44 chromosomes, because he got a fusion event.Ask a Geneticist | The Tech InteractiveThis seems very rare, but possible.

The answer is the order of nucleotides on the DNA strands. That means that when you compare 2 homologous strands of DNA there will be the same base 19 out of 20 times when comparing the two genomes. The 5% difference between chimps and humans also contains the chimp specific mutations that differentiate them from the other apes. It is also worth mentioning that we are the chimps closest relative. Chimps share more DNA with us than they do with the other apes, such as gorillas and orangutans. If chimp DNA is ape DNA, then we are apes, too. It is easily recognizable once the sequencing and assembly is done. It is as simple as doing a BLAST search using nucleotide sequence from one species to query the genome of another species.BLAST: Basic Local Alignment Search Tool The differences are going to be found throuhgout the billions of bases in the genome.Perhaps it would help if I show a specific example. What I did was copy a smaller chunk of DNA sequence from human chromosome 1. You can find the entire sequence of chromosome 1 here:Homo sapiens chromosome 1, GRCh38.p14 Primary Assembly - Nucleotide - NCBINext, I went to the BLAST page for the chimp genome, which can be found here:Nucleotide BLAST: Search nucleotide databases using a nucleotide queryI pasted the copied portion of the human genome into the query sequence box at the top of the page, then clicked on the BLAST button towards the bottom of the page. I got one hit back, and here is a screen cap of the alignment between human (query) and chimp (subject) genomic DNA: Edited by Taq, : No reason given.Edited by Taq, : No reason given.

I think it is also important to point out that there are differences between one human genome and another. The HapMap project is trying to catalogue human genetic variation, and other projects are looking at the variation in different species.https://www.genome.gov/10001688You can even zoom in to the actual sequence and find where humans differ at a given base, and the percentages of people with those variants among the pools they have tested.