Solving the mystery of life with sixfold speedup

To understand the evolutionary process from the beginning of life itself to present-day species, we must first determine the “tree of life.” In this tree, called a phylogeny, known species reside at the tree’s leaves, while conjectured ancestor (extinct) species reside where the tree’s branches split. We follow this process down to the tree’s base, normally represented by the three major limbs for plants, animals, and single-celled organisms.

In recent years, geneticists have made wondrous progress in determining genetic sequences from generation to generation; they have now mapped complete genomes for several species. Evolutionary models are approximations at best, but nevertheless provide the best guidance for determining the interrelation between species. Biologists are often concerned with a small portion of the phylogeny (a subtree) containing a family of related species. They believe that Nature follows a path of minimizing evolutionary processes, but even computing the minimum evolutionary tree (called phylogeny reconstruction) for a handful of species is intractable on several levels.

At the University of New Mexico’s Albuquerque High Performance Computing Center (www.ahpcc.unm. edu), David Bader, Bernard Moret, and Tandy Warnow have achieved a nearly one-million-fold speedup on the UNM/Alliance LosLobos supercluster in solving the phylogeny reconstruction problem for the family of twelve Bluebell species. The problem size includes a thirteenth plant, tobacco, used as a distantly related outgroup. The LosLobos supercluster has 512 733-MHz Pentium III processors, interconnected with four 64-way Myrinet 2000 switches and running the Linux 2.2 operating system. The parallelization uses MPI and includes techniques for concurrently evaluating candidate trees and sharing improved upper and lower bounds by the processors.

The LosLobos supercluster executed the problem in about one hour and 40 minutes using the new phylogeny reconstruction code, Grappa (freely available as open source from Run on a single processor, Grappa performs 2,500 times faster than previous methods but takes full advantage of parallel processing for additional speedups. Hence, the total speedup for the new solution is one million— equivalent to going from an estimated 200 years down to 100 minutes. Phylogenies derived from gene-order data might prove crucial in answering fundamental open questions in biomolecular evolution

David A. Bader
David A. Bader
Distinguished Professor and Director of the Institute for Data Science

David A. Bader is a Distinguished Professor in the Department of Computer Science at New Jersey Institute of Technology.