The role of diverse populations in phylogenetic analysis

The most popular approaches for reconstructing phylogenetic trees attempt to solve NP-hard optimization criteria such as maximum parsimony (MP). Currently, the bestperforming heuristic for reconstructing MP trees is RecursiveIterative DCM3 (Rec-I-DCM3), which uses a single tree (or solution) to guide its way through an exponentially-sized tree space. To improve performance further, we designed Cooperative Rec-I-DCM3, a population-based approach for utilizing a population of Rec-I-DCM3 trees. We compare the performance of Cooperative Rec-I-DCM3 to Rec-I-DCM3 on four large biological datasets. Of particular interest is Cooperative Rec-I-DCM3's selection criteria for maintaining a population of solutions. Our experiments reveal that diverse populations outperform Rec-I-DCM3 in terms of average rates of convergence to best-known MP scores. To achieve greater performance, we designed an elitist population strategy, in which each solution's tree score matches that of the best scor...

• Type: Conference
• Year: 2006
• Where: GECCO
• Authors: Tiffani L. Williams, Marc L. Smith
• Keywords: Cooperative Rec-I-DCM3, Elitist Population Strategy, GECCO 2006, Maximum Parsimony, Optimization