Slow and steady progress
I haven’t posted much about the progress of the Tomato frog project, but there is lots of good news to report.
I’ve been busy the past two weeks or so with the samples: first isolating DNA from tissue samples (muscle, liver, toes, other unidentifiable body parts), then running PCR on the extracted DNA for a gene in cytochrome b of the mitochondria, and finally sequencing the subsequent PCR product. I received my sequences back from the Sequencing Lab (located conveniently just down the hall in BioSci) at the beginning of the week. I edited the sequences using this pretty awesome program called Sequencher; then I used another fancy program to compare the sequences to each other and also to Tomato frog samples from a previous study.
For various reasons along the way, some samples didn’t work as well as I had hoped. Maybe they were bad samples, maybe the primers didn’t work so well, or maybe I contaminated the samples along the way. (I’m hoping the last reason is not the case, but when a handful sequenced samples register as “Homo sapiens” with the online genome database, I get worried).
So anyways, I started with 36 frog samples and only 12 of them made it all the way through to sequencing. For the 24 other miscreants, the process starts over again: re-sequencing, re-PCRing, and even re-extracting.
I don’t mind all the re-do’s, though, because we got pretty good data from the 12 successful samples. I’ll try to briefly explain what we think we’ve found…
A previous paper looked at two species of Tomato frogs from eastern Madagascar and suggested that the genomes were so similar, maybe these two distinct species shouldn’t be separate at all. Our project looked at ONE species of Tomato frog from various populations in western Madagascar. When we compared the frogs to each other, we found an enormous amount of genetic variation– and after comparing the eastern frogs to the western frogs, we found that there was more variation WITHIN our single western species than there was between the previous paper’s TWO separate eastern species.
So what does this mean? Hopefully, that what we thought was one species located along the western coast is actually two — or even more — distinct species. But of course, we’ll need to sequence the rest of the samples to confirm this.
Anyways, I was pretty excited when I saw what had come out of four weeks of non-stop pipetting. Looks like hard work might actually pay off…