Creating a phylogeny and understanding invertebrate colour

I had the realisation today that it has been a long time in between posts. Mostly because I’ve been banging my head against the wall working out how exactly to build my phylogeny for 151 species and then do phylogenetic independent contrasts (PICs). In the end gone with MrBayes tree using an HKY model, but it would be interesting to see what other readers thought. For the PIC’s I’m using Mesquite’s PDAP which hopefully shouldn’t be too difficult. I can nearly see the light at the end of the tunnel and I’m currently waiting for genetic data to come back from Macrogen and then I can do the final trees.

Otherwise I’ve been measuring colour variables of each species, which has been interesting if not fiddly. Positioning the dorsal surface of specimens that are less than 1 mm in length in front of a reflectance probe that is 600 or so microns across was a challenge! The community wide colour shifts are really interesting and will be a topic of a future post (once I get my head around them). Out of the bewildering numbers of variables we could have recorded from the USB 4000 spectrometer, we chose dominant wavelength and the  CIE ( International Commission on Illumination) LAB variables (L: lightness, A: ratio of red/green and B: ratio of blue/yellow) based on the very limited literature. We did the measurements just using the daylight illuminant (D65), but it would be interesting to see the effect of different illuminant on the results – particularly something mimicking shade. It would also be interesting to see the effect of measurement angle – we chose just to do 90 degrees due to time constraints, but I’m sure you could get some interesting results if you changed the angle of measurement. We looked at the infrared spectra but didn’t see any signal there which was interesting. We didn’t get a chance to look at UV though…… I have come to the realisation that I could have done my phD just on colour alone!