User talk:Aoshaver/sandbox

Hey All, I did some major consolidating of the article in the sandbox. Please feel free to view the history to copy and paste your favorite lines back in if I have cut them out, but I did try to only simplify, not leave any concepts out. I will add in my information from Degnan and Salter over the weekend. These two areas need attention so far: 1. Citations: I am not positive they should be of where they are, exactly, I just tried to not take any out. We should probably add some more in, even just based on what we have now. 2. Equations: I don't really understand the part about the equation, especially the last line. Can anyone clarify?

Kelly.n.petersen (talk) 16:56, 11 February 2016 (UTC)

I also don't understand the equation, it would be great if someone could add detail to the description of the equation. Could someone add a citation for the second sentence? and the last two sentences in the assumptions paragraph. KarenKarenbobier (talk) 21:26, 15 February 2016 (UTC)

Notes from Ma 2008 PNAS paper:

One way to think of the ISM is in how it applies to genome evolution. To understand the ISM as it applies to genome evolution we first need to think of chromosomes. Chromosomes are made up of sites, which are nucleotides represented by either A, C, G, or T. While individual chromosomes are not infinite, we must think of chromosomes as continuous intervals or continuous circles.

Multiple assumptions are applied to understanding the ISM in terms of genome evolution:
 * Assume that k breaks are made in these chromosomes, which leaves 2k free ends available. The 2k free ends will rejoin in a new manner rearranging the set of chromosomes (i.e. reciprocal translocation, fusion, fission, inversion, circularized incision, circularized excision).
 * Assume that no breakpoint is ever used twice.
 * A set of chromosomes can be duplicated or lost.
 * DNA that never existed before can be observed in the chromosomes, such as horizontal gene transfer of DNA or viral integration
 * If the chromosomes become different enough evolution can form a new species.
 * Assume that substitutions that alter a single base pair are individually invisible in this genome evolution model and that substitutions occur at a finite rate per site.
 * The substitution rate is the same for all sites in a species, but is allowed to vary between species (i.e. no molecular clock is assumed).
 * In thinking of the ISM in terms of genome evolution, instead of thinking about substitutions themselves, think about the effect of the substitution at each point along the chromosome as a continuous increase in evolutionary distance between the previous version of the genome at that site and the next version of the genome at the corresponding site in the descendant. Aoshaver (talk) 01:20, 16 February 2016 (UTC)

Heres what I have from the 1968 Kimura paper. Sorry this took so long, and let me know if this is easy to understand.

In his original formulation of the model, Motoo Kimura uses a hypothetical population governed by Mendelian genetics and having diploid individuals with a chromosome set consisting of a large number of sites. A "bi-allelic" system is assumed in this model due to the nature of the DNA base pairs involved. Two purine bases and two pyrimidine bases allow for four possible bases but, substitution mutations from purine to purine and pyrimidine to pyrimidine are much more likely than purine to pyrimidine or vice versa so, only two possibilities are considered per site. Although the assumptions of the model state that there are an infinite number of sites, this can be reconciled by Kimuras assertion that the model adequately represents the reality of a finite number of sites if the number of available sites is much larger that the number of currently segregating sites.

The average number of heterozygous sites per individual in a population of N individuals can be expressed as

(2vmNe)/N

where Ne is the effective breeding population and vm is the number of sites with new mutations per generation.

Im still working on a few equations dealing with selection and neutrality of the mutations and will add more as soon as I think I actually understand what hes talking about. BGochnour (talk) 02:29, 24 February 2016 (UTC)

Degnan & Salter 2005

Ma 2008

Hobolth et al 2008

Kimura 1969

Tsitrone et al 2001

Watterson 1979 Aoshaver (talk) 19:55, 25 February 2016 (UTC)