Trait-based phylogenetics and the evolution of EVERYTHING(!!!)

Organised by - Joe Hilton

Abstract -

Phylogenetics is the study of the evolutionary relationship between groups of organisms. By comparing the phenomes and/or genomes of different species we can infer an evolutionary tree which visualises their evolutionary history. Phylogenetic methods are also used outside of biology to construct family trees for other kinds of entities which have some sort of evolutionary relationship, most notably languages. This project is an introduction to trait-based (in biological terms phenome-level) phylogentics using the Matlab package Traitlab. Traitlab was primarily developed to construct language family trees, but can be used to infer relationships between any set of entities for which we can provide a list of traits and their presence/absence. My plan is to get some suitable datasets together (possibly before the retreat) and then let Traitlab loose on them, hopefully figuring out how it works along the way. Since these datasets can come from just about anywhere, we can use Traitlab to generate "family trees" for lots of weird non-biological stuff, possibly throwing any sort of scientific rigour out the window. Some examples I've thought of are:

  1. Metal subgenres (traits could include speed, growliness, and spookiness)
  2. Pokemon species (traits could include type, number of evolutionary stages, standard phenomic stuff from biology)
  3. Types of sandwich (fillings, type of bread, country of origin etc)

If you're interested in the project, try to come up with some ideas for datasets so this isn't just "let's classify stuff Joe likes". If all goes well we will be experts in phylogenetics by the end of the retreat. If not, we will at least have some nice pictures of trees that we can show to people.

Aims and Objectives -

  • Get to grips with some of the basic concepts of phylogenetics
  • Get some experience using statistical inference and MCMC in a practical setting
  • Misuse scientific concepts and experience a thrill of naughtiness
  • Obtain biological proof that the sprites for Butterfree and Venomoth are the wrong way round

Of Interest to -

Mathematical biologists, people who like MCMC/inference, linguistics geeks, geeks in general

Resources Necessary -

  • Traitlab package for Matlab, available here: https://sites.google.com/site/traitlab/
  • Between now and the retreat it's possible that I'll find other/better packages, in which case I'll add them to the thread.
  • Fun datasets/ideas for datasets. Since we possibly/probably/definitely won't have wi-fi, it'll be useful to either have data or a useful way to construct data before the project starts.

References -

  • G. K. Nicholls, R. J. Ryder and D. Welch, TraitLab: a MatLab Package for Fitting and Simulating Binary Trait-Like Data, Technical report

Recommended background reading for those interested in the project -