Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction

Abstract

We introduce a distance-based phylogeny reconstruction method called "weighted neighbor joining," or "Weighbor" for short. As in neighbor joining, two taxa are joined in each iteration; however, the Weighbor criterion for choosing a pair of taxa to join takes into account that errors in distance estimates are exponentially larger for longer distances. The criterion embodies a likelihood function on the distances, which are modeled as correlated Gaussian random variables with different means and variances, computed under a probabilistic model for sequence evolution. The Weighbor criterion consists of two terms, an additivity term and a positivity term, that quantify the implications of joining the pair. The first term evaluates deviations from additivity of the implied external branches, while the second term evaluates confidence that the implied internal branch has a positive branch length. Compared with maximum-likelihood phylogeny reconstruction, Weighbor is much faster, while building trees that are qualitatively and quantitatively similar. Weighbor appears to be relatively immune to the "long branches attract" and "long branch distracts" drawbacks observed with neighbor joining, BIONJ, and parsimony.

Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities

“…The phylogenetic tree is based on best matching RDP (Ribosomal Database Project) (41200 bp) sequences, and was constructed using the Weighbor algorithm (Bruno et al, 2000) in RDP. Only OTUs with an RDP best match of at least 97% identity over at least 50 bp were included.…”

Diversification of the cold-adapted butterfly genus Oeneis related to Holarctic biogeography and climatic niche shifts

“…First, we performed the model tests of substitution rates. The best fit of the model of evolution was determined by using the FindModel tool of the Los Alamos HIV databases and compendia (www.hiv.lanl.gov), which implements Modeltest script (Posada and Crandall, 2001) calculating AIC scores, and the program Weighbor (Bruno et al, 2000) generating the tree based on Jukes-Cantor distances.…”

Phylogenetic trees and Euclidean embeddings

“…The BIONJ algorithm of Gascuel [1997] introduced an important modification to NJ that improves performance on certain types of trees, without significantly degrading it on others. (This modification is also adopted by WEIGHBOR [Bruno et al, 2000], which further changes the cherry picking criterion.) Here we present the BIONJ modification in a new light, as arising naturally from the point configuration and Theorem 3.2.…”