Mutations and Evolution - (Sep/04/2012 )
bob1 on Wed Sep 5 09:22:39 2012 said:
I presume you are talking about the evolutionary changes predicted by such things as parsimony analysis - this is just a liklihood, analysis, meaning that it is looking for the minimum number of changes to get the tree - it makes NO statement about the order of these events, or that it is the true evolutionary path, just that this is the minimum number of changes needed to get the end result.
Then If one takes a samples(mutated) which one is not supposed to take will they have effect on how parsimony analysis gives tree ( not Evolutionary path). I know that by phylogeny we can not determine age of which organism evolved when it shows based on homology which organism is more closely related with whom?
Absolutely, adding samples to your analysis will often change the trees that are drawn, especially if the sample is not easily related to the ones already in the analysis.
prabhubct on Wed Sep 5 10:54:51 2012 said:
Is it possible that you have making it confusing by how you are explaining this? Are you talking about efg as mutant forms of A, B and D? If so, they would be better described as A*, B* and D* or something similar
You can't state whether or not the order of the changes is possible from the analysis; a completely non-related sample where you only have efg,and no ABCD, should form its own clade, joined only at the base (if you are drawing a based tree). If the efg mutant also contains the ABCD traits, and the ABCD non-mutants, contain basal forms of the efg traits, then it is entirely possible that there will be a change in the tree drawn.
You must, must, must, understand that this is only minimum number of changes analysis - it may have no bearing on what actually happened. It makes the assumption that the changes proceed by a minimum number of steps, when in fact the traits could have formed several times completely independently. For instance if you look at the kingdom Animalia - you have three major groups of flying organisms - insects, birds and mammals (bats). If you did an analysis where you looked at the form of locomotion, trait A could be walking/ running, trait B could be swimming, and trait C could be flying. Under this analysis, flying insects, flying birds and bats would all group together - yet if you go and look at the actual animals, it is very very obvious that they have evolved the trait independently, whales, dolphins, frogs and fishes would also group together - yet so far as we know, fish have never left the water, whales and dolhins used to inhabit the land, and frogs are somewhere inbetween...
Do you see where this is going?
Thanks Bob and all,
I agree that I may be confusing it more, or I have to give it more thought. Right now First option seems right. Good Day.
I've been out of this discussion for a while, but wow!!!
Just a small comment, besides: I totally agree with bob about: know your limitations of your analysis. Half of the things I do are computational blah-blah and I literally pray everytime my predictions are put under experimental challenge by smb (lately I do predictions for other people's project). I pray because I know that anything we have now, in many fields of computational biology/bioinformatics takes into account many assumptions to ease the computational load/substitute for lack of knowledge. However, people rely on these bioinformatic predictions like they are always 100% true. They are not a coin toss (50% true) but let's say 70%.
Now to my small comment/observation: when I was taking the class in which they (physicists with no biology clue) were telling us about the blast algorithm and how you build phylogenetic trees (algorithm), the prof made an observation: no matter what protein/gene you take, the phylogenetic tree over all species for that protein will look the same (more or less) as the phylogenetic tree of any other protein/gene i.e. the yeasts will group together, so will bacteria and so on; more, the yeasts that were closer together in terms of gene A, will be also closer together in terms of gene B. So it is not so random. And more: evolution is really happening over a whole organism in the same manner for all the genes. End observation from professor.
Andreea
Hi guys,
Could you please let me know the reason for using some expression cassettes in the forward orientation and some in the reverse, in most of the Plant expression constructs?
Thanking you.
It's usually so that promoters don't read through and transripts don't produce overlapping sequences.