Up to this point in our project, students were involved in finding turtles, weighing them, naming them, photographing them, and determining the spots where they preferred to roam. No sequencing or data analysis… up until yesterday, when they actually started analyzing genetic data, which was a major step in the right direction.
Many hands eager to get involved!
I decided that, for this project to really capture my students’ imaginations and ensure that they are able to maintain a strong foothold in this material, I should use tools (whenever possible, at least) that are accessible to children in the elementary grades. For computer programming, that meant Scratch, a drag and drop programming environment that allows children to do just about anything one might do on a computer, including (it appears), data analysis. So while I have been teaching myself about processing genetic data with computer languages such as Python, I decided that I really wanted my students to see the process of crafting a program that would allow them to determine which of our turtles’ genetic markers would be the most useful in investigating the maternity and paternity of the hatchlings in our courtyard. What I developed was this:
Now in order to use this program, I had to cover a few terms with my “beta tester” students (beta testers give new software a run-through and try to identify any problems). Microsatellites are a concept that is becoming more familiar to everyone, as I’ve presented on this topic before, and they are usually able to identify these markers as repeats in regions of DNA that aren’t contained within genes. Unfortunately, I selected the repeated sequence “CACACACACACACACACACACACACA…” on Monday (it is, in fact, one of the repeats that we are using), and many students quickly picked up that my board now said “caca” over and over. Lesson learned; next time I will use “TATCTATCTATC…” and see what happens.
The other major term for students to understand was “locus,” which are positions on chromosomes where a particular microsatellite (or other feature) is found. For those who aren’t familiar, DNA strands are packaged into structures called chromosomes, and the DNA sequence is usually represented by the letters A, T, C, and G, representing the four building blocks (nucleotides) of the genetic code. Humans have 23 pairs of chromosomes, for a total of 46, while box turtles have 25 pairs, and a total of 50. Now since turtles have two copies of each chromosome (one from Mom, and one from Dad), they will also have two copies of each microsatellite, which I identified as “A” and “B,” to distinguish from the numbers that I used for each locus. Students therefore received a sheet that gave number values (which were actually microsatellite lengths) for a group of turtles, with the loci (plural of locus) identified as Locus 1 (A and B), Locus 2 (A and B)…and so on.
Without further ado, I will give an example of one of our baby turtles and see if anybody wants to try finding out who the mother and father might be. The program is set to match loci from my example baby (named Tiny) with microsatellite lengths of possible parents, which I’ve determined could be any one of the five adult females or ten adult males in the courtyard. Of course, there might still be a few “bugs” in the program, so please feel free to let me know if any problems arise. I will soon have all of these data uploaded for every turtle, and possibly integrate these microsatellite lengths directly into the game; that is my side project for the next few weeks. Until then, we can all try to determine the parentage of Tiny (pictured below), whose microsatellite loci have the following values. Just select a mother or father and start plugging these numbers in!
A big question that I want students to answer is whether these microsatellites can actually be used to narrow our possibilities to one father and one mother. This population does appear to have many of the same microsatellites (possibly due to inbreeding), which means that parentage might be hard to resolve. Of course, we’ll never know if we don’t try! I’m looking forward to more investigations tomorrow.
Did you find Tiny’s mom and dad? I will add an opportunity to answer that question on each turtle’s page, and see what we can learn!