There seem to be some major genetic groups popping up in Pacific cod. Ingrid, Laura Timm and I are examining whole-genome sequencing datasets from multiple studies. In one of their datasets two distinct genetic groups pop out, with no apparent ecological explanation. I’ll leave the cause for another post, but here I want to show that I do believe we have both genetic groups in our experimental fish.

To recap- I have lcWGS data from experimental juvenile fish all caught off Kodiak and subjected to four temperatures (0C, 5C, 9C, 16C). I ran a PCA using ~20k sites sufficiently sequenced in both an adult data that Laura/Ingrid is working with (“BIOGEO”) and my experimental fish and ran a PCA. I’m seeing a slight clustering into 2 groups along PC2 (y-axis in first figure below ), particularly in my experimental fish (in gray).

I cross-checked the fish that cluster together from the BIOGEO samples (blue, red) when I analyze them alongside my experimental fish (figure above) vs. when I analyze them alone (figure below) and the same BIOGEO fish segregate, so that suggests that I do indeed have both “genotypes” represented in my experimental fish.

Now I’m curious whether the two “genotypes” could respond differently to our experimental temperatures. Below I’ve plotted various metrics by temperature and “genotype A” (bottom gray cluster in figure 1) or “genotype B” (top gray cluster in figure 1). I see no convincing patterns (although I still need to do stats)! This suggests that whatever is different genetically did not influence how these juveniles (all collected off Kodiak, mind you) responded to major temperature differences. This is all very fresh!