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> * A gene called ARHGAP11B, which was created by one such duplication, causes the cortex to develop the myriad folds that support complex thought; SRGAP2C, als

> * A gene called ARHGAP11B, which was created by one such duplication, causes the cortex to develop the myriad folds that support complex thought; SRGAP2C, also a duplication, triggers brain development.* A question I've never seen addressed: is one justification for junk DNA to create space for beneficial mutations? Obviously some mutations are actively harmful, but the reason most mutations are destructive is that they break something already-useful into something inert. That's not a risk with non-coding (or irrelevantly-coding) DNA, which means that in return for spending energy on copying junk DNA, we get space where even barely-useful changes will be net positive. Is this obvious to experts? Completely stupid for reasons I don't know? Even a possibility worth discussing?

deleted 9y ago
[deleted]
pjschlic 9y ago
If I recall correctly from my bioinformatcs classes (years ago) - the non-coding DNA still serve many functions - a protective role by containing sequences which stabilize the structure of the DNA, or providing binding sites used in promoting or suppress gene expression. The non-coding are recognizable by different characteristics from the coding sections. Not to mention the fact that by definition, at least half the sequences are just the complement of a coding sequence - so putting in stop codons before and after on the complement would be useful to make sure it's not expressed. Add in structural sequences to create preferences of where it's safe to swap genes with the sister chromosome DNA during meiosis, and all sorts of other things, and you end up with quite a but of non-coding DNA still serving a purpose.
nkrumm 9y ago
Perhaps not exactly "junk dna" but you are right in your thinking about gene duplications... duplications are thought to promote "neofunctionalization" (a new function) or "subfunctionalization" (specialization). See wikipedia [1] for an overview. [1] https://en.wikipedia.org/wiki/Gene_duplication#As_an_evolutionary_event https://en.wikipedia.org/wiki/Gene_duplication#As_an_evoluti...
searine 9y ago
>A question I've never seen addressed: is one justification for junk DNA to create space for beneficial mutations? Yes, gene/genome duplications can help create raw material for adaptation, or be adaptive by their own right. >That's not a risk with non-coding (or irrelevantly-coding) DNA It's not risk free. It's just less risky. There are all sorts of elements within the "intergenic" region of genomes which can impact fitness. Duplications in these regions can change the "dosage" of genes or the availability of DNA to be transcribed. Duplicating these regions is mostly dependent on how tolerate the species is of dosage changes. Humans for example are very intolerant, while plants are very tolerant. Also, please stop using "junk DNA". It is outdated term ;).
- Bartweiss 9y ago
  Thanks! And yes, I'll be dropping "junk DNA" from my vocabulary immediately. I knew some non-coding regions had been found to have uses, but this thread taught me just how extensively relevant it is!
Obi_Juan_Kenobi 9y ago
Not stupid at all. If you're interested in that, I'd look up "Whole Genome Duplications". For instance, corn underwent a WGD about 7 million years ago (IIRC, the number might be off), and we can identify an 'a' and 'b' genome. After these events, most of the duplicated genes will be lost, either through purging selection or drift. However, some will stick around and take on new subset functions (see nkrumm reply). If you really want to get into the weeds on this, there are many metrics that could, in theory, affect the 'evolvability' of a genome. Higher transposon (or any sort of repetitive element) content can lead to large-scale shuffling of genome structure, such as inversions, duplications, etc. The ecological success of the grass family, for instance, may have it's roots in genome structure. Now, there's not a whole lot we can say about this because it's not something we have a really good grasp of. It's mostly some hypotheses that are quite difficult to test, but this is some of the most interesting genomic research going on, in my opinion. All of this is quite difficult to understand, however, as it really depends on epigenetic mechanisms like chromatin state, dicers, RISC, and all that. Figure that out, and you'll realize there's no 'junk' DNA, just various non-coding sequence that's part of this larger-scale genome evolution.
- quotemstr 9y ago
  Why is it that plants are so much better than animals at tolerating chromosomal shenanigans? Plants can be highly polyploid, get chromes swapped out, randomly get duplicates, etc., and not seem to suffer massive problems. In a human, you duplicate one chromosome, and you get a very buggy phenotype.
  - a_bonobo 9y ago
    This has, as usual, several reasons :) One reason is the absence of sex chromosomes in plants. If humans get a duplicated sex chromosomes things go completely haywire. Another reason is that due to so many WGDs, plants have ample gene copies, so the copies can freely mutate around or even break, there's always a backup. Not all of these shenanigans work out, in plants this has the wonderful name 'genomic shock'. In wheat there's a candidate gene (Ph-1) which seems to somehow stabilise these instabilities between chromosome copies. In other species people have been trying for a few years to make polyploids but have been failing because there is no stability mechanism - for example, there are only few papers where people managed to make a Brassica hexaploid, these hexaploids are usually very unstable and have problems generating offspring (see for example http://www.cropj.com/malek_7_9_2013_1375_1382.pdf http://www.cropj.com/malek_7_9_2013_1375_1382.pdf )

deleted 9y ago

[deleted]

pjschlic 9y ago

If I recall correctly from my bioinformatcs classes (years ago) - the non-coding DNA still serve many functions - a protective role by containing sequences which stabilize the structure of the DNA, or providing binding sites used in promoting or suppress gene expression. The non-coding are recognizable by different characteristics from the coding sections. Not to mention the fact that by definition, at least half the sequences are just the complement of a coding sequence - so putting in stop codons before and after on the complement would be useful to make sure it's not expressed. Add in structural sequences to create preferences of where it's safe to swap genes with the sister chromosome DNA during meiosis, and all sorts of other things, and you end up with quite a but of non-coding DNA still serving a purpose.

nkrumm 9y ago

Perhaps not exactly "junk dna" but you are right in your thinking about gene duplications... duplications are thought to promote "neofunctionalization" (a new function) or "subfunctionalization" (specialization). See wikipedia [1] for an overview. [1] https://en.wikipedia.org/wiki/Gene_duplication#As_an_evolutionary_event https://en.wikipedia.org/wiki/Gene_duplication#As_an_evoluti...

searine 9y ago

>A question I've never seen addressed: is one justification for junk DNA to create space for beneficial mutations? Yes, gene/genome duplications can help create raw material for adaptation, or be adaptive by their own right. >That's not a risk with non-coding (or irrelevantly-coding) DNA It's not risk free. It's just less risky. There are all sorts of elements within the "intergenic" region of genomes which can impact fitness. Duplications in these regions can change the "dosage" of genes or the availability of DNA to be transcribed. Duplicating these regions is mostly dependent on how tolerate the species is of dosage changes. Humans for example are very intolerant, while plants are very tolerant. Also, please stop using "junk DNA". It is outdated term ;).

Bartweiss 9y ago
Thanks! And yes, I'll be dropping "junk DNA" from my vocabulary immediately. I knew some non-coding regions had been found to have uses, but this thread taught me just how extensively relevant it is!

Obi_Juan_Kenobi 9y ago

Not stupid at all. If you're interested in that, I'd look up "Whole Genome Duplications". For instance, corn underwent a WGD about 7 million years ago (IIRC, the number might be off), and we can identify an 'a' and 'b' genome. After these events, most of the duplicated genes will be lost, either through purging selection or drift. However, some will stick around and take on new subset functions (see nkrumm reply). If you really want to get into the weeds on this, there are many metrics that could, in theory, affect the 'evolvability' of a genome. Higher transposon (or any sort of repetitive element) content can lead to large-scale shuffling of genome structure, such as inversions, duplications, etc. The ecological success of the grass family, for instance, may have it's roots in genome structure. Now, there's not a whole lot we can say about this because it's not something we have a really good grasp of. It's mostly some hypotheses that are quite difficult to test, but this is some of the most interesting genomic research going on, in my opinion. All of this is quite difficult to understand, however, as it really depends on epigenetic mechanisms like chromatin state, dicers, RISC, and all that. Figure that out, and you'll realize there's no 'junk' DNA, just various non-coding sequence that's part of this larger-scale genome evolution.

quotemstr 9y ago
Why is it that plants are so much better than animals at tolerating chromosomal shenanigans? Plants can be highly polyploid, get chromes swapped out, randomly get duplicates, etc., and not seem to suffer massive problems. In a human, you duplicate one chromosome, and you get a very buggy phenotype.
- a_bonobo 9y ago
  This has, as usual, several reasons :) One reason is the absence of sex chromosomes in plants. If humans get a duplicated sex chromosomes things go completely haywire. Another reason is that due to so many WGDs, plants have ample gene copies, so the copies can freely mutate around or even break, there's always a backup. Not all of these shenanigans work out, in plants this has the wonderful name 'genomic shock'. In wheat there's a candidate gene (Ph-1) which seems to somehow stabilise these instabilities between chromosome copies. In other species people have been trying for a few years to make polyploids but have been failing because there is no stability mechanism - for example, there are only few papers where people managed to make a Brassica hexaploid, these hexaploids are usually very unstable and have problems generating offspring (see for example http://www.cropj.com/malek_7_9_2013_1375_1382.pdf http://www.cropj.com/malek_7_9_2013_1375_1382.pdf )