Genetics and Markers Measure aspects of an organisms structure and function How do genes and environment influence individual differences and fitness? What aspects should we measure? Morphological (measurements of the body of the organism) Behavioral Molecular
Genetic markers Phenotype is the result of genotype How much of a trait depends only on the genes? How much do differences in genes drive differences in appearance? How different are organisms in the same species from each other? How different are organisms in difference genus’ from each other?
Relatedness Whales to Hippos Even-toed, hoofed mammals are called artiodactyls. This is further broken down to Camels + llamas Cattle + deer Pigs + peccaries Hippopotamuses Cetaceans don’t have toes – ancestors had an even number of appendages.
What is a molecular marker? A piece of DNA on a chromosome May be part of or closely linked to a gene that makes a protein that affects cell survival May be part of controlling elements May be in the larger area of ‘non-coding’ DNA Markers have a known location What is being marked?
DNA can have very simple sequences, like CACACACACA, or sequences that are unique across a long distance. The simple ones are present at much higher concentration than the unique ones, so the recombine (‘reanneal’) quickly after separation.
SSRs and Length Polymorphisms Simple sequence repeats The number of units have a certain number of can vary if the units of the repeat: polymerase stutters (CA)13 has 13 of the CA (loses its place). units in a row. Two individuals differ by the number of repeats: CA 3 repeats vs 5 repeats produces length differences.
Turning SSRs into markers You can use a restriction enzyme that recognizes a sequence just outside the boundaries. But it takes a lot of DNA and you will have a lot of other fragments cluttering up the gel CCATGG GGTACC AATT TTAA Fragment 1 Fragment 2 CCATGG GGTACC AATT TTAA
Turning SSRs into markers You can use PCR with primer sequences that lie just outside the boundaries. Primer 1 Primer 2 Primers match conserved sequence, lie just outside the repeated region and amplify across is, so most of the PCR product is the repeated region Fragment 1 Fragment 2