TL;DR - Plans and new developments for additional Olympia oyster genetics work. Opportunity to work with lcWGS data from WDFW using machine learning to address the question of local adaptation. Moving forward with NW CASC Fellowship work despite uncertainty over funding.

Wrapping Up Oly Hatchery Vs. Wild Manuscript

We’re nearing completion of the manuscript for this study, pretty much just the discussion left. Quick summation of this work:

Wild samples were collected from North Sound (Fidalgo Bay) in 2018, Central Sound (Mud Bay) in 2017 and South Sound (North Bay) in 2018. Hatchery samples were collected from North Sound (Fidalgo Bay) progeny in 2017, Central Sound (Mud Bay) progeny in 2018 and South Sound (North Bay) progeny in 2018. RAD-seq data was generated for the 561 sampled individuals. Comparisons reveal high similarity between wild and coupled hatchery populations with little inbreeding observed. Results generally support the claim that hatchery individuals are both similar enough to their wild counterparts and genetically diverse enough to limit domestication selection resulting from outplanting.

NW CASC Fellowship Plans

My full proposal is viewable here.

This proposal was accepted! However, I’m still in limbo as to whether or not the program will be cut due to budgetary changes at USGS. Regardless, I intend to continue with the work described in my proposal. The natural first step will be getting my hand’s on Natalie Lowell’s population genetic diversity model to make adaptations discussed with Julieta Martinelli at WDFW.

The rest of the proposed actions will take shape as we discuss how to approach the environmental genetics machine learning analysis…

Low Coverage WGS Samples from WDFW

I’m working with Julieta to scope out working with lcWGS data for 110 individuals that will be available this fall. The idea would be to use this data with the machine learning platform RDAforest to examine relationships between population specific genetic traits and environmental variables. My original plan was to do a more rudimentary version of this with the RAD-seq data we have been using. But the lcWGS data provides the opportunity to do a much more in-depth analysis. My plan is to adapt the RDAforest pipelines created by Evelyn Abbott for a WGS kelp project. I’m meeting with Evelyn, Julieta, and Ryan Crim on July 21st to discuss this further. Overall a very exciting opportunity!