When you choose to publish with PLOS, your research makes an impact. Make your work accessible to all, without restrictions, and accelerate scientific discovery with options like preprints and published peer review that make your work more Open.

Journals
More Content
PLOS BLOGS The Official PLOS Blog
Browse all PLOS Blogs
Browse all PLOS Blogs

SVP Conference Workshop: Calculating Disparity and Rates from Discrete Phenotypic Data

Andrew Farke Open Research

Plot showing changes in morphospace through time, from Sakamoto and Ruta, 2013. CC-BY.
Plot showing changes in morphospace through time, from Sakamoto and Ruta, 2012. CC-BY.

The 2016 Society of Vertebrate Paleontology conference officially starts on Wednesday, but was already well underway with a series of field trips and workshops. I had a little time to do a workshop this year, but the selection was so good that it was hard to choose! In the end, I settled on “Morphological Evolution in Deep Time: Calculating Disparity and Rates from Discrete Phenotypic Data”, co-led by Graeme Lloyd and Dani Fraser.

Looking at disparity (morphological diversity) and evolutionary rates is a pretty hot topic in ecology and evolutionary biology these days. Graeme gave some nice summary lectures on concepts and basic mathematics; I can’t really do that justice in a single blog post, so instead will highlight a few basic tools, documents, and tutorials that were presented at the workshop.

  1. Claddis. Graeme and colleagues are working on an R package that estimates disparity and rate functions, etc., and works with data visualization tools in R to display the results. The main emphasis is on discrete data, rather than continuous characters. The whole package is available via github. [it was also exciting to see that Claddis will serve the same functions as TAXEQ3, an old DOS program used for Safe Taxonomic Reduction; the software is useful, but hard to run on new computers]
  2. Three nice tutorials were presented (downloadable as .r files, viewable in any text editor), which provide extensively commented examples. These include:
    1. Importing Data
    2. Calculating and Plotting Disparity Metrics
    3. Character Rate Evolution
  3. If you want more on disparity, check out Thomas Guillerme’s dispRity package. It is still in development, but available via github.

Overall, this was a great workshop. I found the heavily documented examples to be particularly useful, alongside the peek into some useful software tools. As someone who has disparity and evolutionary rates on my radar, but also as someone with a fairly shallow understanding of the topics, this workshop was incredibly worthwhile!

A big thanks to Graeme, for permission to post the various links and information given here.

Back to top