I went in today with my mind set on doing work, specifically pop gen stuff. With deadlines closing in, I've really needed to get on this bit. It shouldn't take long thankfully, but it has to start to actually end. In order to do this properly, the genome basically needs to be cleansed. Mitochondrial DNA is usually fairly clean, but there are still some chunks that aren't coding and some alignments will have voids in them due to the mapping to reference process. Once everything is cleaned up and properly arranged, each set of genes for each specimen goes through a partitioning procedure that takes a few hours identifying the best evolutionary model for each gene. The whole thing is fairly tedious as a lot of this has to be done manually, and in my case it's being done twice for two different analyses (whole mito genome and partial genome with more samples).
| Human mtDNA. Unlike nuclear DNA, mtDNA is circular - a remnant of its origin as an endosymbiotic bacteria |
That will be the last new thing I actually need to do apparently.
While cleaning out the genome, my adviser comes, and in his lackadaisical manner just points at it and says, "That's the last you'll need for your thesis!"
Shocked, I turn to ask him about the eDNA. I was expecting my third chapter to be eDNA. Lo and behold though, my last chapter was changed... without my knowledge...
My adviser has a habit of doing this, and everyone in the lab has experienced it multiple times. I was just under the impression that my thesis was set. Turns out, my third chapter will now be a broader discussion of the novel survey methods I pioneered and developed for newts. This includes three main components: eDNA, borescope, and artificial burrows.
Previously, I had already been able to show that our eDNA primers are effective, working even in low concentration samples. I was expecting to do a few more trials to get a good set of data for some stats. I guess that's going to my lab partner now. All the same, this is some fairly exciting work because we were able to use standard procedures and nested primers to identify newt DNA in some rather murky water from our local resacas (similar to oxbow lakes, but some key differences). Over the next few months I'm sure I'll still get around to doing those trials, but now they just won't be a part of my thesis. No big.
The other two novelties are my own making. Prior work with black-spotted newts had found them buried underground. With the implementation of a borescope, I was able to do the same thing, but without ripping up the ground and still get data on how deep they were. In addition, the borescope technology can take photos or video of the entire process so that we can document other cohabitants of these microhabitats. In the past I've been able to document tarantulas, centipedes, snakes, and even a full grown neotoma rat! I'm really excited about this development because there are actually a lot of practical uses for borescopes in the field. Consider the standard flip board. Snakes love 'em. Try flipping one without a stick though, and there's a good risk of getting bit. In addition, just the act of lifting the board exposes the ground underneath, breaking the humidity barrier that made it so enticing. By using a borescope to look underneath, there's a reduced risk of snake bite, the humidity barrier wouldn't be broken, and everything there would remained relatively undisturbed.
But the other addition I made to surveys was the use of artificial burrows. I feel like they were probably considered before, but they were impractical because they would have to be destroyed to find whatever was in them. With the inclusion of the borescope, that is no longer a problem. Artificial burrows have a dual practicality to them. 1. It's a very passive form of trap - anything can crawl in or out at it's own leisure. 2. When a creature is found, we can quickly see just how deep it is underground. Subterranean lifestyles are hard to study, but are incredibly important, especially for something that lives in, effectively, a desert. Soil characteristics, humidity, water table level, temperature - all are potentially important variables when considering an ecological niche, and by knowing how deep something goes we actually have an idea of where to measure! Of course this won't replace the utility of coverboards, but it adds another handy tool that can provide guidance on how to collect a wealth of other data, broadening our scope of research potential.
While upset that I didn't get much of a say in this change, I am actually really glad that I'll have the chance to provide a deep discussion on the utility of each. It's not a typical research paper in that we don't have much data to analyze. But we have enough to confirm that things work. I'm hopful that my adviser will expand on these in the future, I know I plan on it.
This was a lot more off-the-cuff than I had original intended.
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