Lots of time in the lab this last week making 70 QuantSeq mRNA libraries from Olympia oyster RNA samples during the rangewide low pH experiment. Submitted to the sequencing core today! You can see the lab notebook for these libraries, along with extraction and library prep protocol here.
This summer I’ve embarked on my first official “field season”, collecting oyster tissue from two species on the West Coast of North America for an exploratory project to help me determine which species will be favorable for my thesis research. If you’re feeling up to a potential snoozefest, here is a proposal I wrote for the Hinds fund, an award for evolutionary biology students at UChicago primarily in their 1st or 2nd years to help support preliminary data collection and develop grant writing skills. It outlines some of the where/what/why/how of this project. Hinds Proposal 2014
Meet The Players
Starting out, I had three (overly ambitious) aims for this project:
- Analyze the fine scale phylogeographic structure of Olympia oysters from San Diego, California to Ladysmith Harbor, British Columbia; incorporate records of local extinctions/introductions into the analysis, estimate parameters of gene flow and dispersal, and correlate with environmental parameters.
- Use larvae and adults from both naturalized (producing successful offspring without human aid) and commercially reared populations of Pacific oysters to help elucidate how commercial practices either homogenize or diversify the species (or if there even are any detectable patterns)
- Sample newly settled oyster recruits, juveniles, and breeding adults from both species in Washington that experience different means and variances in pH and upwelling. These will be sequenced to identify the areas of the genome that experience allele frequency shifts between life stages.
As of writing, I’m about halfway through my field season and already there have been some reality checks about what is and isn’t feasible, though I’ve picked up some new ideas, too! Stay tuned, as I’ll try to retroactively write up some of my coastal adventures so that I can update the second half of my season in real time.