Journal of Molecular Evolution
, Volume 35, Issue 4, pp 367375
First online:
Statistical properties of the ordinary leastsquares, generalized leastsquares, and minimumevolution methods of phylogenetic inference
 Andrey RzhetskyAffiliated withInstitute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University
 , Masatoshi NeiAffiliated withInstitute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University
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Statistical properties of the ordinary leastsquares (OLS), generalized leastsquares (GLS), and minimumevolution (ME) methods of phylogenetic inference were studied by considering the case of four DNA sequences. Analytical study has shown that all three methods are statistically consistent in the sense that as the number of nucleotides examined (m) increases they tend to choose the true tree as long as the evolutionary distances used are unbiased. When evolutionary distances (d_{ij}'s) are large and sequences under study are not very long, however, the OLS criterion is often biased and may choose an incorrect tree more often than expected under random choice. It is also shown that the variancecovariance matrix of d_{ij}'s becomes singular as d_{ij}'s approach zero and thus the GLS may not be applicable when d_{ij}'s are small. The ME method suffers from neither of these problems, and the ME criterion is statistically unbiased. Computer simulation has shown that the ME method is more efficient in obtaining the true tree than the OLS and GLS methods and that the OLS is more efficient than the GLS when d_{ij}'s are small, but otherwise the GLS is more efficient.
Key words
Phylogenetic inference Leastsquares method Minimumevolution method Statistical biases Efficiency of obtaining the true tree Title
 Statistical properties of the ordinary leastsquares, generalized leastsquares, and minimumevolution methods of phylogenetic inference
 Journal

Journal of Molecular Evolution
Volume 35, Issue 4 , pp 367375
 Cover Date
 199210
 DOI
 10.1007/BF00161174
 Print ISSN
 00222844
 Online ISSN
 14321432
 Publisher
 SpringerVerlag
 Additional Links
 Topics
 Keywords

 Phylogenetic inference
 Leastsquares method
 Minimumevolution method
 Statistical biases
 Efficiency of obtaining the true tree
 Industry Sectors
 Authors

 Andrey Rzhetsky ^{(1)}
 Masatoshi Nei ^{(1)}
 Author Affiliations

 1. Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, 16802, University Park, PA, USA