Conclusion

The goal for this summer was to have sampling, DNA extraction, Polymerase Chain Reaction (PCR), and fragment analysis sent off (to be later analyzed) completed on all 400 of the subsamples. Sampling and DNA extraction were finished. PCR unfortunately was not, delaying fragment analysis as well. Though the PCR protocol was developed during spring semester of 2017, new primers and a host of other problems made this step tricky. The first batch sent off for analysis came back blank, requiring adjusting of the protocol and the second had nebulous results. A delay in shipment meant that only 3 of the 7 primers were available for much of the summer. However, all extractions were completed successfully, and in the last remaining weeks of July, PCR was done on all 400 of the plants for 3 of the primers. All PCR products were shipped off for fragment analysis. Training began on using a fragment analysis software, so once results do come back, analysis will be smoother.

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Labwork (PCR)

Following DNA extractions, it was time for amplification of DNA through Polymerase Chain Reaction (PCR). PCR amplifies the DNA by denaturing, copying, and synthesizing over and over again. Denaturing occurs via temperature, first during the DNA extraction process, and then again using the Thermocline machine (or PCR machine). The thermocline helps to regulate temperature allowing for PCR to go through its different steps, such as synthesis or denaturing. Synthesis occurs using a special polymerase Taq.

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Labwork

Following the collection of data and samples, it was time for lab work to begin. The first step of my procedure was DNA extractions. With around 800 plant samples, I quickly realized financially and time wise doing all 800 would not be practical. This led to many discussions on how to subsample. Was it better to do more transects, with fewer plants from each transect? More plants, with fewer coverage of overall transects? How do you account for the difference in densities between transects? Overtime, with more and more discussions, it became clear that sampling more transects would be a better option, even if that meant fewer plants per transect. Additionally, for any transect with ~30 or fewer plants, the entire transect would be sampled. For any plant over that, a subsample would be done using a random number generator to randomly select which plants should be extracted.

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Fieldwork

The month of June was predominantly spent on fieldwork and preparation for fieldwork. Preparation included obtaining materials, packing and planning ahead for the visits. There are 5 sites for field work: Presquile National Wildlife Reserve (PWR), Blandy Meadows (BLD-M), Blandy Thistle Thicket (BLD-T), Sky Meadows (SKY), and Greenspring (GRN). For PWR, BLD-M, BLD-T, and SKY, overnight visits were required. We were fortunate enough to have access to research housing for all of these. PWR is an island so that required intensive planning as nothing could be forgotten. Once we arrived at each site, we jumped right into fieldwork. [Read more…]

Final Summary: Modeling Milkweed Population Dynamics

Since the summer research session is coming to an end and the first major phase to my project is almost “finished”, this seems like a good time to write my final post, wrapping up what I’ve been doing all summer, what has come from my work, and how this will transition into the next phases of the project. Just as a friendly reminder, this project is focussed on community ecology and population dynamics of the Common Milkweed, with the specific goal of modeling the size and demographic behavior of the population as a function of factors like herbivory and leaf chemistry. We use field-collected data and computational/statistical models in the R programming language to determine these relationships, that could inform management policies and conservation strategies.

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