Crab Plasticity

In our previous post, we created PCAs for each transcriptome, with each point as one library. This raised some interesting questions, notably that we didn’t necessarily see libraries from the same crab clustered together (though for some crab, they did clearly cluster). This could be an indication of crab plasticity, as they adjust to both tank effects and the temperature treatment. We initially considered looking at plasticity qualitatively, but figured it’d be better to go the extra mile and take a quantitative approach. Therefore, we modified our DESeq2 analysis scripts for our three transcriptomes – cbai_v2.0, cbai_v4.0, and hemat_v1.6. Yet another reminder – cbai_v2.0 is unfiltered, cbai_v4.0 is presumably Chionoecetes genes only, and hemat_v1.6 is presumably Hematodinium genes only. These modifications created a PCA for each, extracted the coordinates for PC1 and PC2 for each library, used that to get the centroid for each crab, and then calculated the mean…

from Aidan F. Coyle