Anoles and DNA degradation

As field biologists, one of our most important considerations is maximizing the utility of the animals we collect for our research. Often, there are tradeoffs to consider in making decisions about how best to do this. Specimens of the individuals we collect (along with associated tissue samples for DNA extraction) are ultimately placed into natural history collections for long term storage and use by future researchers. Ideally, we would be able to euthanize and preserve animals (and DNA samples) immediately upon collecting them in the field. For the most part, however, that is not a feasible option from an efficiency standpoint. For example, at the very least, we have to wait until we have finished collecting for the day (or night), as lizards are only active (or sleeping) for a limited amount of time, and we need to maximize the time we spend observing and searching for them during that period. Often, other aspects of our fieldwork also factor into when we are able to preserve animals (such as moving between field sites, scouting new localities, sleeping, eating, etc.).

So, each day in the field we block out some time for specimen preparation, and this decision impacts how useful certain aspects of the animal will be to future researchers. For example, the longer we wait to euthanize an animal, the more it digests the meal it obtained foraging that morning. This makes a specimen less valuable to biologists who examine the stomach contents of museum specimens in order to understand basic natural history and ecology, since this information is being lost as the animal digests. Alternatively, if we euthanize an animal immediately to make it more useful for future diet studies, the longer we wait before preserving it’s DNA, the more the DNA degrades. This could potentially have a significant impact when we start trying to perform genomic sequencing of the tissue samples we collect. From that perspective, we would like to preserve a DNA sample as soon as the animal is sacrificed. Additionally, the longer we wait to fix the animal in formaldehyde, the more difficult it becomes to position the specimen properly such that phenotypic data can easily be collected from specimens by researchers interested in external morphology. Other times when we are out collecting, we come across animals that have been hit by vehicles when they are crossing the road and have to make a decision about whether or not we should salvage a tissue sample that is potentially degraded. As you can see, there are a lot of things to consider!

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UH undergraduate Ann Marsolais capturing her first lizard!

All these issues led to some interesting discussions between Bob, Amber, Greg Pauly (our collaborator from the Los Angeles County Museum of Natural History), and I during fieldwork in the Mojave Desert this past spring. This semester, Ann Marsolais (a UH undergrad I’ve been working with in the lab) started a research project to try and quantify how quickly DNA degrades after an animal is euthanized in order improve our understanding of the impact of these decisions in the field. To do this, we are using invasive brown anoles that are commonly found around Oahu. After capturing several individuals around campus, Ann has been taking tissue samples at various time points and extracting DNA to assess degradation. She is also comparing a different tissue types including tail, liver, and liver + gallbladder (some researchers have suggested including the gallbladder in a tissue sample reduces DNA quality), as well as extraction protocols, to see if we find any differences. It’s too early to tell what the results will be, but Ann has already noosed her first lizard, and developed some serious molecular lab skills!

 

Ann'sFirstGel
Ann’s first gel electrophoresis run. Not bad!
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Preserving tissues samples for DNA extraction.

 

 


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