Genetics questions you were afraid to ask...

[TCReptile]

I think i'll just stick to bearded dragons... they're much less confusing

[GlasgowGecko]

When constructing a pseudogene phylogeny of the cpDNA intron region trnL-trnF, why is it more parsimonious to assume chimeric copy formation than simple copy loss?

never fail to make myself laugh...

Andy

[intravenous]

Originally Posted by GlasgowGecko

When constructing a pseudogene phylogeny of the cpDNA intron region trnL-trnF, why is it more parsimonious to assume chimeric copy formation than simple copy loss?

never fail to make myself laugh...

Andy

I don't believe there is a plant section on here . As far as I'm aware reptiles don't have chloroplasts .

[GlasgowGecko]

Originally Posted by intravenous

I don't believe there is a plant section on here . As far as I'm aware reptiles don't have chloroplasts .

Well aside from the fact it is posted in the genetics section, in the "questions you were afraid to ask" thread where reptiles are only implied and not specifically delimited...
And the fact that the actual problem transends species AND organelles, It was infact a joke (shock horror!), the joke being, its a pretty tough question to answer.

Feel free to have a go at answering though....

Andy

[Ssthisto]

Well, Andy, I did have to go and look up some of those words... can you tell me if I've got the gist of it basically right AND a roughly correct answer given that I'm a web designer and not a geneticist? If I've misunderstood, please PM me an explanation - I'm not at all "up" with some of these terms and anything that will teach me more would be very much appreciated.

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Originally Posted by GlasgowGecko

When constructing a pseudogene phylogeny of the cpDNA intron region trnL-trnF, why is it more parsimonious to assume chimeric copy formation than simple copy loss?

It makes more logical sense (and is the simplest explanation) when you are trying to explain how closely related a group of orchids are - by looking at "junk DNA" strands that no longer appear to code proteins within a specific location - to state that it is more likely that the "repeats" at this location are due to abnormal creation of repeated code, rather than the loss of code in between the repeats. This is the more logical explanation because mispairing during the DNA replication stage (AKA "mutation") happens more often than outright DNA loss during the DNA replication stage.

[GlasgowGecko]

Hey SSthisto,

I actually wrote this question, because I hadn't seen this sticky before (good job by the way) and needed a little light refreshment from my daily grind... of pseudogenes.... Yes, my daft idea of a joke. But seeing as you are pretty hot on many genetic topics I was prepared to be surprised by your answer.

Intron regions, which you are right in saying do not code for proteins, are not under selection, which makes them ideal for phylogeny studies. A pseudogene is a copy or partial copy of a gene that has be copied into an intron (through various processes). Its a bit of a contentious issue as to whether these can be used for phylogeny construction, and whether or not there a single point mutation is more or less likely to occur than the generation of a whole pseudogene copy, which then brings into question how informative they are.

My question then referred to copy loss through intra-molecular recombination, and whether the formation of chimeric copy (a copy formed by two halves of different pseudogene copies) is more likely explanation of "new" copy generation, or whether full copy loss (thus the same copy in a new position) is more parsimonious. The answer is that I don't know. The paper I'm currently working on will suggest copy loss, although through sequence alignment it is possible to suggest chimeric copies.

Andy

[Ssthisto]

Thank you, Andy, for further explanation

I still don't FULLY understand it (shows I'm not a geneticist, just that I look at things from a mathematical perspective when it comes down to simple genetic traits and see the inheritance as a series of four relatively simple rules) but I appreciate your trying to explain it

[GlasgowGecko]

It is a pretty complicated, and I do feel a little bit childish for putting it up now, it wasn't meant to attempt to outsmart anyone.

Andy

[eeji]

Originally Posted by GlasgowGecko

When constructing a pseudogene phylogeny of the cpDNA intron region trnL-trnF, why is it more parsimonious to assume chimeric copy formation than simple copy loss?

never fail to make myself laugh...

Andy

Because coco-pops and milk make a bowl full of fun?

(I'm not a genetecist either, can you tell?! )

[intravenous]

Originally Posted by GlasgowGecko

Well aside from the fact it is posted in the genetics section, in the "questions you were afraid to ask" thread where reptiles are only implied and not specifically delimited...
And the fact that the actual problem transends species AND organelles, It was infact a joke (shock horror!), the joke being, its a pretty tough question to answer.

Feel free to have a go at answering though....

Andy

Yes, I guessed you were having a laugh . That was my attempt at humour...I obviously fail . On a more serious note though...I know what all those terms mean but who in their right mind would actually know that unless they were a)writing a paper on it or b) researching a paper on it ?

Edit: oh and...evolutionary genetics make me cry .