Hardy Weinberg

Here is a link to the Geisel's Songbirds activity.
Please read the intro section which goes over stuff done in class today. Note that this was originally written up a in 2011. The date is given as "Apocalypse Friday" because it was the day that the world was supposed to end based on the predictions of this weird apocalyptic prophet named Harold Camping. I never rewrote it. Also, it makes reference to a screencast of the lecture, which is not any longer maintained on the web.
But, the background is there in the writeup. What I think we will do is work on the main part of the assignment in class while we are waiting for various steps in the procedure we will be doing.
So, read the background, and read over the main part to get the gist of it. Look up some of the terms in the vocabulary list, especially the bold ones. The types of selection and types of "speciation" events are presented on the last pages.
We can then talk about the assignment and work on it in class.

Chi Squared problem

Here are the data for the problem. Sorry Kira that I didn't get this posted early enough for you. Tomorrow is fine.
This is a Dihybrid cross, meaning AaBb x AaBa. That means the expected results are 9:3:3:1. That won’t be what you get.
Cage 17 is the F1 dihybrid. Cages 12 and 16 are their because the were the source of the P1 generation.The remaining three cages, 18, 21 and 25 are just increasing numbers of offspring. Try performing a chi-square for 18, 21 and 25. It’s pretty striking how the size of the data set makes such a difference. There is a chi-square table below to assess the probabilities. For the homework, submit the chi-square value for each cage. What are the “Parental” types you expect to see more frequently if the genes are linked. Do you think the genes are linked? Explain your reasoning.
FlyCrosses

probab2

More genetics

Chi Square


Here is a link to a short discussion of
chi square.
There is a problem for you to do in another entry.

Single Locus



As we've learned, if there are two alleles at one locus not on sex chromosome, the hybrid cross (Aa x Aa) must produce the 1:2:1 assortment. However, the 3:1 dominance is only predicted if there is a simple dominance relationship. aa x aa is boring. The other three types of crosses are shown below, AA x aa; Aa x aa and Aa x Aa
monohybridcross

Sex linked


Here's how that maps out for a simple dominance on the X chromosome:
Sex Linked
For incomplete dominance, the case is interesting because the heterozygous phenotype ONLY shows up in females.


Multiple Loci


The first think is how do we deal with multiple loci? There is a way that is done purely with math…that's what we do when there are more than two loci. However, I'm going to show you how to do it with a punnet square.
You can download a plot of the possible gametes and that
4x4 matrix here. It is also shown below.
Dihybrid&test cross-dihybrid
The expected 9:3:3:1 ratio assumes independent assortment (not on the same chromosome). We can use that prediction to ask whether there is linkage (are they really on the same chromosome) and test the model out using a statistical test we will cover next.

Some variants in inheritance.


Multi-gene trait.
There's really not much to this. Some traits…really most interesting traits…may be inherited, but be based on more than one gene. So, there is no single gene for being tall. There is no allele for being 6' tall. But, that doesn't mean that height is not inherited. Many different loci may contribute to it. Here is a hypothetical plot of what you might expect if there are three loci that contribute to height, each with two alleles where the dominant of each allele contributes positively to height (note, there is no reason any of those assumptions should be true). You might see a distribution that looks something like this:
Multigenedist

So, you can get a distribution of heights based on some combination of alleles at different loci. In this case, we are assuming simple additive interactions among the genes. It an be more complex (See below(.

Pleiotropy
This is sort of the opposite of multi-gene trait. Here, one gene can affect many traits. We've discussed this in the context of cytoskeletal proteins before. For example, mutations to a microtubule-associated motor protein could affect male fertility (sperm flagellum), airway function (cilia on airway epithelium) and vesicle transport and secretion of proteins. Everywhere that protein is needed, you would see some effect.

Epistasis
Finally, there is epistasis. Proteins interact with other proteins, so variations in one gene can affect how you see the phenotype caused by another. Here is a classic example I stole from another website at the university of Georgia. It covers coat color in.
Labrador retrievers. One locus, the B locus, controls the color of the pigment eumelanin. Eumelanin can be either brown in color (bb) or black BB or Bb.
Another gene, known as the "E" locus (for extensor…never mind) is needed to deposit eumelanin in the fur of the dog. It encodes a protein called MC1R and where it is expressed determines whether the eumelanin gets into the fur. The ee homozygote does not deposit eumelanin at all in the fur while Ee or EE do.
Thus, if the dog is ee, it will be yellow no matter whether it makes black or brown melanin. All the possibilities on the 4x4 matrix are shown below.

Epistasis



Intro Genetics

Some of this is redundant. But, it's worth thinking about in this new context.
Read More…

Punnet squares

Examples of the types of punnet squares Read More…