A followup from the last post.  I have used Mathematica to create an animation of the effect of changing genotype fitness values.  There is a lot of background information I am skipping over at the moment--I plan to put together a separate page to go through this in more detail.  However, for now, In short, if you have two alleles (alleles are types of a gene) in a population, you can have homozygotes (individuals that have two copies of the same allele) or heterozygotes (individuals that have a copy of each type of allele).  So two alleles (A and a) result in three genotypes (AA, Aa, and aa).  In this example AA and aa are the two homozygotes and Aa is the heterozygote.  These genotypes can have different fitnesses which affect how many descendants organisms have in future generations.

In the illustration above, on the right is a plot of genotype fitnesses.  Underdominance is the case where heterozygotes (Aa, green bar) have a lower fitness than either homozygote (AA, purple, aa, red).  On the left is a plot of the predicted change in allele frequencies over 10 generations (x-axis) from a range of starting frequencies (y-axis).  If the "a" allele starts at a low frequency it declines and is lost in the population.  However, if it starts at a high enough frequency it can actually increase to 100% over the next few generations.  (The population ends up as all "aa" homozygotes, despite the fact that they have a substatially lower fitness than "AA" homozygotes!)  The boundary between these two regions (where the "a" allele increases or decreases) is indicated by the dashed line.

I've made an animation (that runs too fast, but I don't know how to slow down the frame rate yet) that shows the change in trajectories over a range of fitness values.  I will put a link to it here

Underdominance Animation (click to see)

and, at least for the time being, it is uploaded to the index page of this site.

This is still not interactive.  I am thinking of exploring using the Processing programing language next to see if this might be a way to fully implement this.

One thing I've wanted to make available for years now is a user interactive way to illustrate evolutionary dynamics--specifically underdominance.  I have been using Mathematica for about six years now and tried exporting a video of a table of plots that sequentially increment a value.  This example is just of a sine wave, and it is not interactive, but it is a first step.

Sine Wave Animation (Click link to see animation.)

...and below is a screen capture of the Mathematica notebook to create the animation.

Obviously, I have installed a blog already or you couldn't be reading this...so this is a retroactive announcement.

We now have a Word Press blog (that has yet to have a lot of detail configured) and a Media Wiki wiki (ditto) installed on the site and linked from the front page, http://hawaiireedlab.com/ .

Hello World,

I am an assistant professor starting a new research group in the Department of Biology at the University of Hawai'i and wanted to start on online website for and about the group.  I want to do this for several reasons; to help us communicate with each other, to start an alternative and accessible record of projects, but most of all to let anyone out there that is interested see what we do and are up to.

Part of this is motivated by a perception I have run into "out there" that professors only teach classes--but this is only part of what we do.  First and foremost I am a scientist and I went into the profession to do research.

I am new to Hawai'i and this is an exciting place to be for anyone working in the biological sciences, especially in fields related to evolution.  Hawai'i is unique in several respects and is unparallelled in the potential research opportunities here.  One of my first jobs/projects (and one that will never be finished) is to learn more about the natural history of Hawai'i.

Testing, testing, 1, 2, 3...

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