Functional Phylogenies

We're composed of:

And we're a mix of biologically inclined statisticians, mathematicians and physicists interested in new directions in the study of shape evolution. We've been funded by the EPSRC to pursue questions of this nature.

A brief explanation of our project:
We now regularly use the genetic sequences of different creatures to make guesses about their common ancestors. A creature's genetic sequence is a long string of symbols. But how can we discuss common ancestors if, instead of knowing strings of symbols about each creature, we only have information about their shapes? Though this is a particularly difficult situation, it is very common. Many objects in the world around us evolve and change their shape but do not have a genetic sequence. For example, the shapes of consumer items, from toothbrushes to cars, are under continual shape evolution but no-one supposes they have genomes. The challenge of making inferences about the past evolution of shapes, and of making guesses about which shapes have recent ancestors in common, is well established. The standard approach to this challenge is to extract sets of numbers that describe the shapes of interest and to use these summary sets to make guesses about the past. This work takes a different approach. We are developing mathematical techniques that use the shapes themselves, rather than summaries of them, to make inferences about the past. This approach has some advantages: it uses more of the information that we have; it allows us to characterize the process that yields shape evolution; and it allows us to make guesses about the shapes of unseen ancestors (rather than guesses about a restricted set of their features). We aim to advance the study of shape evolution by considering the evolution of mathematical functions. A functional phylogeny is akin to a genetic evolutionary tree where it is a mathematical function, rather than a genetic sequence, that changes through time. We are testing our theory by: using computer generated data; performing `Spatial Chinese Whispers' experiments; and investigating how the pronunciation of words has evolved in Romance languages. Just as information about current genetic sequences allow us to make guesses about the sequences of past organisms, this approach might allow us to test hypotheses about the sounds of languages we can no longer hear. This work has relevance to those interested in designing shapes for the future, as well as those interested in past shapes. By understanding past shape evolution one can use this to generate reasonable shape transformations which might help in product design. This work aims to take sets of shapes and to make guesses about which is most related to which: this can be very useful in areas which have nothing to do with shape evolution. The ability to detect unusual or familiar shapes has relevance to numerous public and commercial challenges from spotting unusual vehicles to guessing the shapes of letters.

Our papers:

Evolutionary Inference for Functional Data: Using Gaussian Processes on Phylogenies to Study Shape Evolution arXiv:1004.4668 BLOG Public Experiment

Nick S. Jones, John Moriarty

Characterizing fundamental frequency in Mandarin: A functional principal component approach utilizing mixed effect models
Journal of the Acoustical Society of America, in press
PZ Hadjipantelis, JAD Aston and JP Evans,

Phylogenetic inference for function-valued traits: speech sound evolution

Trends in Evolution and Ecology (free version and non-free weblink) 27, 160-166 BLOG article

John Aston, Dorothy Buck, John Coleman, Colin Cotter, Nick S. Jones, Vincent Macaulay, Norman Macleod, John Moriarty, Andrew Nevins.

On the left is Schleicher's original tree of Indo-European languages, from 1860. On the right is a numerical experiment where, given knowledge of the three black curves at the bottom and the evolutionary tree (thick black object) we can put a probability distribution over possible ancestral curves and sample from that distribution (red curve is the mean, blue a measure of standard deviation and dotted black is a sample from that distribution).

Events and Activities:

- We organised a two day workshop on the 27/28th of September 2010 on the topic of new approaches to shape evolution. This washeld in the Physics department in Oxford. This Workshop will bring together researchers from several theoretical and application areas to discuss new approaches to the evolution of shapes such as: continuous biological data; bone morphology; and speech evolution along linguistic phylogenies. The aim of the Workshop is to discuss possible directions for the development of new methods to investigate shape evolution, informed by related existing approaches and with a focus on applications. We also organised a further two day follow on workshop in the Summer of 2011.

- Details and video of our public experiment at the Swinton High School

- Selected talks at: the SAMSI meeting on the Analysis of Object Oriented Data (Phylogenetic Trees with Dialects as Leaves) in Oxford Phonetics (Investigating Chinese dialects using Functional Data Analysis) in Oxford Statistics and the CICADA workshop (Functional Phylogenies)

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