Tuesday 5 February 2013

Evolutionary inference for functions

How might we reason about the forms of our unseen ancestors? I discuss a possible application to speech sounds in an earlier blog article (necrophonetics). A paper with John Moriarty which provides relevant theory came out lately in Royal Society Interface as "Evolutionary inference for function-valued traits: Gaussian process regression on phylogenies" (free version from this page). The gist of the idea is that some things in nature, like sounds or patterns, evolve in time and are best described as mathematical functions. Gaussian processes are a class of process which are very suited to the evolution of functions. An example of an evolving function would be a drawing of a line which is copied repeatedly (see here for a movie of us making school students do this). Having done the theory, Pantelis Hadjipantelis from Warwick (a student of John Aston) and  Chris Knight and David Springate helped take this further. They investigated whether our theory could be made to work in practice and considered careful simulated examples. In these we could see how our best estimate about characteristics of the evolutionary process and the form of the ancestors compared against (simulated) reality. We did reasonably well. On the way we used Independent Components Analysis - a very handy method. This work will be appearing shortly in Royal Society Interface as "Function-Valued Traits in Evolution" free version here. Having convinced ourselves of the relevance of the method for simulated data the next step was to consider real data that Chris Knight has - that paper is under-way. If this interests you then Mhairi Kerr produced a masters thesis on the topic working with Vincent Macaulay. This has some further introductory content. Nick

Functions can evolve along evolutionary trees - just like genetic sequences. On the left-hand we provide a simulation of function evolution. On the right we use the data from the leaves of the evolutionary tree to reconstruct the common ancestral function. Red line is the value of the function we expect/predict and black line is an actual value (in grey is a measure of our uncertainty)

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