A mathematical perspective for evolutionary biologists

A new mathematical method is being used to manage and interpret genetic data more efficiently.

Developed by scientists at The University of Queensland’s Institute for Molecular Bioscience, the method offers a faster way to create evolutionary trees from the massive amounts of genetic data being produced by DNA sequencing.

Evolutionary or phylogenetic trees - also called ‘trees of life’ - first appeared in Charles Darwin’s 1859 book The Origin of the Species. The trees enable relationships between groups of organisms to be visualised and better understood.

Lead researcher Professor Mark Ragan has spent 15 years exploring ways to enhance the production of these ‘trees of life’.

Ragan said creating the trees required complex comparisons between large numbers of genetic sequences from selected organisms, which was a laborious, time-consuming task requiring immense computing power.

“For more than 50 years, researchers have thought that to compare the genetic sequences of organisms, it was necessary to begin by making a multiple alignment of the genes,” he said.

“Multiple-sequence alignment is tough to get right, so we have developed an alignment-free method that can create a robust phylogenetic tree that can be equally or more accurate, but is much quicker to produce.

“With our method, you can skip the alignment step, which means you don’t have to painstakingly assemble the genetic data first, so we can create these trees thousands of times more quickly than ever before.”

Ragan said he hoped the new method would have useful applications beyond evolutionary biology.

“Researchers can also use this method to study how genetic material moves between bacterial genomes to cause disease, and to better understand and manage complex natural environments such as agricultural soils or coral reefs,” he said.

The study has been published in Scientific Reports.