Communications of the ACM
Evolution Software Looks Beyond the Branches
Software by scientists at Rice University aims to reveal far more about species evolutionary histories than traditional tree models can.
Credit: Luay Nakhleh/Rice University
Rice University researchers have developed PhyloNet, an open source Java-based program that accounts for both the horizontal and vertical inheritance of genetic material among genomes.
The researchers also have developed a "maximum likelihood" method that enables PhyloNet to infer network models that better describe the evolution of certain groups of species than do tree models.
Inferring means analyzing genes to determine their evolutionary history with the highest probability of connections between species. The software infers the probability of variations that phylogenetic trees cannot illustrate, such as horizontal gene transfers, which circumvent simple parent-to-offspring evolution and enable genetic variations to move from one species to another by means other than reproduction.
"We are the first group to develop a general model that will allow biologists to estimate hybridization while accounting for all these complexities in evolution," says Rice researcher Luay Nakhleh.
The researchers used two data sets to test the program. One was a computer-generated set of data that mimics a realistic model of evolution and enabled the researchers to evaluate the accuracy of the program, while the other involved multiple genomes of mice found across Europe and Asia.
From Rice University
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