Link dump

In the tradition of BioDiverse Perspectives (a site well worth watching – I’m doing a mini link dump.

The first one is a fantastic series of webinars about scientific writing. Kristin Sainani is an engaging speaker, and even though she’s aiming these talks at chemists I think these talks are really useful.

I’m also a fan of Prof Andy Field who always provides amusing on-line lectures going over statistical basics (it’s always good to refresh)


Finally, for something different, FDiversity is a free software developed by Fernando Casanoves, Julio Di Rienzo y Laura Pla, that provides an easy way to quickly calculate functional diversity indices. I just found this program yesterday and already I think it’s going to useful and efficient way to generate the various indices.

My molecular phylogeny work this week

At the moment I’m currently working on  building a molecular phylogeny*  for the beetles I have collected during my phD. The intention is to overlay this phylogeny to help better understand the really interesting beetle trait patterns we’ve found so far. Basically, is the beetle bigger in old-growth because it’s relatives are bigger, or is it due to environmental conditions? Going into this I thought molecular work would be straightforward ….how wrong I was! (N.B. previous to my phD, I had never really done genetics before – hence the naivety)

At this stage I’ve extracted DNA from 155 specimens and it  looked like we got reasonable yields of DNA. However, there also looked to be other stuff in the mix (carbohydrates etc.) that was getting in the way – the nano-drop (a spectrophotometer)  showed some pretty strange readings. The reason behind this probably stemmed from my extraction technique. Instead of doing the traditional  ‘pulverising the specimen’ technique, I simply put the whole beetle in an enzyme bath and left it there for 24 hours. It turns out that this technique left the irritating residue. So now I have to purify all of this DNA so I can do the PCR and then finally get some sequences back! I’m going to try either the Ethanol precipitation method or Propyethylene Glycol (PEG) method, and hopefully I have some success! I will let you know.

*a family tree using DNA to work out who is related to whom

Revisiting Honours

What seems like a long time ago now, I was doing my Honours project focussing on the ‘hidden’ biodiversity that lives on tree ferns. I was reminded of this recently as I am only now starting to generate a few citations from my paper  (hooray!) They are such an important part of Tasmanian wet forest, it’s strange that they are basically an unstudied niche in Tasmania and across the world. I found an unusual assemblage, including many Anthribids (primitive weevils – see below). This community significantly differed from a typical ground and canopy assemblage and included a few species that haven’t been seen before (and heaps of un-described morpho-species of course).