| Primate relationships | ||
| Squirrel taxonomy | ||
| Color vision in primates and other animals (research project) |
Squirrel taxonomy contributed by Steven Rice, Wake Forest University, Winston-Salem, NC
Primate relationships
Compare hemoglobin genes from human, chimpanzee, and gorilla to determine how closely related these species are. Two types of analyses can be performed using restriction enzyme digestion and gel electrophoresis:
a. Digest each DNA sample with restriction enzyme(s) (choose one or a combination) and compare the fragment patterns generated. Are the patterns for one pair of species more similar than another pair (e.g. is gorilla more similar to chimp or to human)? How many different enzymes do you need to use in order to yield reliable data?
b. After digestion, perform a Southern blot with one of the hemoglobin probes from chimp. With the probe stringency (match) set at 100%, does the probe hybridize to DNA from either of the other species? If not, how much do you have to reduce the stringency before the probe hybridizes to the other samples?
Bioinformatics approach: Compare these sequences, plus additional primate hemoglobin sequences, using the sequence alignment and phylogenetic tree building feature. How do these results compare to your original analysis?
Squirrel taxonomy
In this example you will compare mitochondrial cytochrome b sequences from various squirrel populations. Cytochrome b is an integral part of the mitochondrial electron transport system. One DNA sample is from Sciurus aberti aberti, the tassel-eared squirrel that resides in Arizona, extending to the southern rim of the Grand Canyon. DNA samples also are available for individuals from a different subspecies, Sciurus aberti ferreus, and also from another species in the genus, Sciurus niger. The former is an individual of the Kaibab squirrel that has been isolated on the north rim of the Grand Canyon. The latter is a fox squirrel that is common in the midwest.
Open each DNA sample, digest the DNA fragments with the AluI enzyme, load each into a different well and run the gel. Use a short run time (10 minutes).
- Which of the types had similar restriction fragments?
- How do these differences compare with what you would expect based on the taxonomic differences among the individuals?
Bioinformatics approach: Compare the squirrel sequences using the sequence alignment and phylogenetic tree building feature. How do these results compare with your original analysis? Re-construct the tree including the cytochrome c sequences from other organisms. Does this change the relative relationships between the squirrels?
Color vision in primates and other animals (research project)
Background: Color vision in humans and other primates, and in many other animals, is dependent upon amino acids present at three critical positions in the opsin gene (position 180 in exon 3 and positions 277 and 285 in exon 5). Differences of a single amino acid at these positions determines wavelengths of maximum light absorption. Combinations of amino acids at these three locations is a predictor of whether vision is dichromatic (two-color) or trichromatic (three-color). For example, trichromatic vision is most common in Old World primates including humans, whereas color vision is highly variable in New World primates, with a mixture of dichromatic and trichromatic vision even within individuals of the same species. Because of the ecological and evolutionary significance of these variations among primates and other animals, the study of genetic sequences related to color vision has considerable potential for undergraduate research projects.
A good basic overview of this topic is the Monkey Opsin section of the Evo-Ed web site. A more in-depth overview of color vision in humans is Genetics of variation in human color vision and the retinal cone mosaic.
Other articles of interest include:
Highly polymorphic colour vision in a New World monkey with red facial skin, the bald uakari
Color Vision Polymorphism in Wild Capuchins and Spider Monkeys in Costa Rica
Elephants and Human Color-Blind Deuteranopes Have Identical Sets of Visual Pigments
Many other research articles are available on this topic that provide background information and generate ideas for hypothesis testing.
Research project
Start by reviewing the tutorial on searching sequences format for an overview of how sequence searching works in Case It using color vision as an example. After reviewing the tutorial and background publications linked above, examine the following folders and see if you can propose a hypothesis and devise a research project to test this hypothesis. This is just a starting point for investigation, as you are encouraged to use the NCBI web site to acquire and analyze sequences related to your proposed hypothesis.
Folders available:
- DNA for 180 277 285 locations
- Primers for exons 3 and 5
- New World monkeys
- Old World monkeys
- Vertebrate comparisons
- Sample sequences