Animal evolution discovery made possible with supercomputing

Animal evolution discovery made possible with supercomputing
December 17, 2014 Sarah Nisbet

Professor Michael Lee

Associate Professor Michael Lee

Professor Mike Lee has always been interested in animals – growing up he kept a mini-zoo in the family’s rambling Queenslander in suburban Brisbane – so it was only natural he became an evolutionary biologist.

In his joint role with the University of Adelaide and the South Australian Museum, Mike relies on eResearch SA’s high performance computing facilities to process the complex data sets required to unravel millions of years of evolutionary patterns.

“One of the biggest aims of evolutionary biology is to try and understand the family (or phylogenetic) tree which links all of life and shows how all organisms are related and have evolved over millions of years,” Mike explains.

“There are nearly two million different species of animals and plants known to science, and several million more to be described, so inferring the timing and patterns of the branching structure of the tree of life is a tremendously complex endeavour.”

In the past, evolutionary biologists such as Mike would infer relationships between organisms based on their anatomical features, but the development of genetic tools such as DNA sequencing has opened up an avalanche of new data, which is overturning many old ideas about animal relationships.

“Getting enough data is no longer a challenge for evolutionary biologists, as a vast amount of DNA information is publicly available online via sources such as GenBank. The challenge is now interpreting and analysing this flood of information to answer important evolutionary issues.

A standard desktop computer can no longer process the vast amount of data available, so Mike relies on eResearch SA’s two supercomputers – Corvus and Tizard – which draw on the combined power of hundreds of processors to conduct complicated modelling.

The newer Tizard machine is South Australia’s most powerful high-performance computing system. Unlike previous supercomputers, Tizard is a powerful mix of different computing systems, optimised to complete specific tasks faster than ever before.

Mike says some of his research would be impossible without these supercomputers.

“One of the projects I am leading is working out rates of evolution during the Cambrian explosion – or the ‘Big Bang’ of animal evolution – around 550 million years ago, when the many groups of modern organisms all evolved.

“Kangaroo Island has the best Cambrian fossil deposit in the southern hemisphere, so we spent four years collecting fossils, as well as DNA data from living organisms. We have used eResearch SA’s computers for the past year to undertake the highly complex and computationally demanding analysis required to determine relationships between species, when they first appeared, and how rapidly they evolved.

“The supercomputing facilities at eResearch SA permit analysis of a host of interesting problems in evolutionary biology. It is the only computer system in SA that can perform certain complex calculations required to infer large evolutionary trees and associated patterns of evolution.

“In this rapidly evolving field, the computational techniques keep changing, but eResearch SA have been extremely helpful and efficient in always rapidly installing and updating all the required cutting-edge software.”

Tizard machine: South Australia’s fastest supercomputer from eResearch SA on Vimeo.

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