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Systematic Biology 2005 54(2):218-229; doi:10.1080/10635150590923308
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© 2005 Society of Systematic Biologists

Weighted Least-Squares Likelihood Ratio Test for Branch Testing in Phylogenies Reconstructed from Distance Measures

Rafael Sanjuán1 and Borys Wróbel1,2

1 Institut Cavanilles de Biodiversitat i Biología Evolutiva, Universitat de València, Edifici d' Instituts de Paterna Apartat 2085 46071 València, Spain E-mail: rafael.sanjuan{at}uv.es borys.wrobel{at}uv.es (R.S.)
2 Department of Marine Genetics and Biotechnology, Institute of Oceanology, Polish Academy of Sciences Gdynia, Poland

Edited by Junhyong Kim: Associate Editor Chris Simon Editor


  Abstract

A variety of analytical methods is available for branch testing in distance-based phylogenies. However, these methods are rarely used, possibly because the estimation of some of their statistics, especially the covariances, is not always feasible. We show that these difficulties can be overcome if some simplifying assumptions are made, namely distance independence. The weighted least-squares likelihood ratio test (WLS-LRT) we propose is easy to perform, using only the distances and some of their associated variances. If no variances are known, the use of the Felsenstein F-test, also based on weighted least squares, is discussed. Using simulated data and a data set of 43 mammalian mitochondrial sequences we demonstrate that the WLS-LRT performs as well as the generalized least-squares test, and indeed better for a large number of taxa data set. We thus show that the assumption of independence does not negatively affect the reliability or the accuracy of the least-squares approach. The results of the WLS-LRT are no worse than the results of the bootstrap methods, such as the Felsenstein bootstrap selection probability test and the Dopazo test. We also show that WLS-LRT can be applied in instances where other analytical methods are inappropriate. This point is illustrated by analyzing the relationships between human immunodeficiency virus type 1 (HIV-1) sequences isolated from various organs of different individuals.

Keywords: Analytical branch test; bootstrap; distance; generalized least-squares; maximum likelihood; phylogeny; weighted least-squares

Received August 12, 2003; Revised December 14, 2003; Accepted November 10, 2004
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