Peter Breslin

Peter Breslin

Apr 17, 2018

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Weird Science

So far, the population viability analysis, habitat suitability modeling and molecular phylogeny of the Mammillaria of Baja have all moved forward with very few hitches or glitches. This landscape genetics project, on the other hand, has posed some unexpected challenges.

In particular, a subset of my tissue samples from the field ended up not yielding the minimum required mass of clean DNA for the RADseq process. I am not sure if the tissue, sampled from lower down on the stem from the epidermis, which looked green, just didn't have much DNA, or if the silica gel I used incompletely preserved the tissue and most of the DNA denatured. Usually, putting freshly collected tissue into silica keeps the DNA from unraveling, but in this case perhaps there was a problem there. Collecting tissue in the field is a challenge anyway.

However, I developed a redesign of the sampling space and I still have plenty of viable DNA extractions for a statistically significant sample distributed in interesting ways over the landscape.

Old school mortar and pestle is the best way to grind cactus tissue

The full plate of samples. I'll be finding the DNA quantities of a bunch of samples today, so wish me luck!

Anyway, the project continues to move forward, albeit at a slower pace than I had originally envisioned. The research process can be that way sometimes, for sure. If the permitting process through the Mexican government were easier, I would be able to recollect tissue on this upcoming trip to Baja in May. But my Mexican botanist colleagues don't even have collection permits at the moment, and haven't for the past year or so. The process was shifted to a new federal agency in Mexico and there's a huge backlog.

Here's an excellent overview of the sequencing method and approaches to data analysis that we'll be using once we finally get the data back.

https://academic.oup.com/bfg/article/9/5-6/416/182576

Thanks again for the support and onward we go!

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About This Project

I am developing and applying innovative population genetics data analysis with habitat suitability modeling to solve longstanding challenges in the effort to save endangered plant species. Combining high throughput RADseq data analysis with species distribution models, I am exploring relatively inexpensive, feasible methods to generate powerful population viability assessments, estimates of threshold population size and the constraints on the habitats of rare plants.

Blast off!

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