Biology classes often include a lesson on human characters to illustrate basic Mendelian genetics. Most of you at some point have been asked whether you can roll your tongue, whether your earlobes are attached, or whether you have a hitchhiker's thumb. Unfortunately, the textbooks are wrong; most of the human traits used to illustrate genetics are either not genetic at all, or the genetics are more complicated than the simple one-locus, two-allele model. Plus, if these easily visible characters really did fit a simple genetic model, some students would find out from a classroom exercise that the person they call "Dad" isn't their biological father, and that would be awkward. So it would be nice to have easily observable characters in some other familiar organism that could be used to illustrate genetic principles.
In this lab, you will look at four characters in domestic cats, Felis catus (also sometimes called Felis domesticus, Felis sylvestris catus, or Felis sylvestris domesticus). You will collect data by looking at pictures of cats up for adoption in animal shelters. For the orange locus, it is well-established that there is one sex-linked locus with two alleles. You will be able to calculate allele frequencies and compare the genotype frequencies in females to those expected under Hardy-Weinberg equilibrium. For two loci, spotting and longhair, it is not entirely clear how well they fit a simple genetic model. You will collect some data on these two loci, analyze it as if they do fit the simple genetic model, then think about how you could investigate them in more detail. Later in the semester, one or two teams may investigate this in more depth. The white locus fits a simple genetic model well, with white dominant over non-white. Finally, you will think about possible problems with your sample and better ways of obtaining a more random sample of cats.
The goals of this lab are to reinforce basic concepts in Mendelian genetics (dominant/recessive, codominance, locus, allele), population genetics (Hardy-Weinberg), population sampling, and statistics. Specific questions to be addressed are whether genotype frequencies at the orange locus fit Hardy-Weinberg proportions; whether allele frequencies are correlated with climate; and whether allele frequencies in North America are similar to the allele frequencies in Europe where the first European human settlers came from.
For those of you who will become teachers, variations on this lab are a good introduction to genetics for students ranging from third grade ("Are there more long-haired cats in colder areas?") to grad school ("What is the molecular basis of variable expression of piebald spotting?").
Domestic cats have several characters that seem to be inherited in a simple Mendelian fashion; each is largely determined by one locus with two alleles. Cat breeders have worked out the inheritance of each character, deterimining which loci were autosomal and which were sex-linked, which alleles were dominant and recessive. This makes it easy to estimate allele frequencies by merely looking at a sample of cats; no breeding studies or molecular tests are necessary. For this reason, underfunded population geneticists in many parts of the world have surveyed allele frequencies in local populations of cats and have used the data to infer the processes of selection, migration and drift that have influenced them.
In this lab, you and a partner will look at pictures of cats up for adoption in a city in either North America or Europe. You will determine the phenotype of each cat, then estimate the allele frequencies in the area. For the orange locus, you will be able to count the allele frequencies directly; you can therefore test the fit of the genotype frequencies to Hardy-Weinberg proportions, using the chi-square test of goodness-of-fit. For the spotting, longhair, and white loci, you will assume that they fit the Hardy-Weinberg proportions and estimate the allele frequencies.
On Thursday, you will analyze the data by testing the fit to Hardy-Weinberg proportions, looking for correlations between climate temperature and allele frequency, and computing the genetic distance between each pair of populations.
You and your lab partner will be assigned one of the following locations, either in North America or in Europe. Each European location is near the source of the first European human settlers to found the North American city. For locations in North America, go to http://www.petfinder.com, choose "Cat," enter the city, and click "Search." You should get a list of cats for adoption in and near the city you entered. Click on each thumbnail picture to get more details on each cat. There may be more than one picture of each cat, and clicking on the pictures may enlarge them.
New York, NY (if there are shelters in different boroughs, use Manhattan or Brooklyn)
Amsterdam, Netherlands: Shelter 1; Shelter 2
southern England: Portsmouth, UK; Poole, UK; Southampton, UK; Ipplepen, UK; Devon, UK
Le Havre, France: Shelter
Santa Fe, NM
southern Spain: Shelter 1; Shelter 2; Shelter 3; Shelter 4
Gotheburg, Sweden: Shelter 1; Shelter 2; Shelter 3; Shelter 4; Shelter 5
Look at the pictures and descriptions of as many cats as you can from each location. I'd like you to get information for at least 100 cats from each location, if possible.
I suggest that one of you score the cats while the other writes down the information; switch roles when you get tired. You can record the information in a spreadsheet instead of writing it down, if you'd like.
Ignore young kittens, as it may be difficult to tell whether their hair has reached its full length. You may also want to ignore cats with really bad photos, but be sure to write down the explicit rules you and your partner use to decide when a photo is so bad you won't use it.
For each cat, record the following information:
Name: So you don't score the same cat twice, and because some people give their cats goofy names.
Hair length: long or short. Hair length is said to be controlled by the longhair locus, with the alleles L and l. ll cats have long hair, while Ll and LL cats have short hair. Are there really just two hair lengths, or are there cats with medium-length hair? This may be a topic for one of the teams to investigate later in the semester.
Presence and amount of white spotting: Record whether each cat has some white patches on it, or is completely colored. If it has some white on it, record whether it is more than 50% white or less than 50% white. Cats with the ss genotype at the spotting locus have no white fur, while the Ss and SS genotypes have white patches. The extent of white fur in Ss and SS cats is variable, being determined by other genes and by environmental factors. Some sources say that cats with the SS genotype have white fur on more than half their body, while cats with the Ss genotype have white on less than half their body; this may be a topic for one of the teams to investigate later in the semester.
Orange/cream color present or not: The orange locus is on the X chromosome, so males are either OY or oY. An OY male is orange or cream colored, while an oY male is black, brown or gray. The darkness of the color (orange vs. cream or black vs. brown vs. gray) is determined by other genes that we won't try to score. An OO female is orange or cream colored, while an oo female is black, brown or gray. In an Oo female, one allele is inactivated in each cell early in development. Cells descended from a cell in which the O allele was inactivated will make black fur, while cells with the o allele inactivated will make orange fur. The result is a cat with patches of orange and black (or cream and gray) fur. This is generally called a "tortoiseshell" if there are no white patches and a "calico" if there are white patches.