PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR‐JOINING

Abstract— Because they are designed to produced just one tree, neighbor‐joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor‐joining programs may give misleading bootstrap frequencies because they do not suppress zero‐length branches and/or are sensitive to the order of terminals in the data. A new procedure, parsimony jackknifing, overcomes these problems while running hundreds of times faster than existing programs for neighbor‐joining bootstrapping. For analysis of large matrices, parsimony jackknifing is hundreds of thousands of times faster than extensive branch‐swapping, yet is better able to screen out poorly‐supported groups.

[1]  J. Harshman.  The effect of irrelevant characters on bootstrap values , 1994 .

[2]  K. Bremer,et al.  Morphology and phylogenetic interrelationships of the Asteraceae, Calyceraceae, Campanulaceae, Goodeniaceae, and related families (Asterales) , 1995 .

[3]  B. Efron,et al.  A Leisurely Look at the Bootstrap, the Jackknife, and , 1983 .

[4]  M. Chase,et al.  Carnivorous plants: phylogeny and structural evolution. , 1992, Science.

[5]  J. Farris.  Estimating Phylogenetic Trees from Distance Matrices , 1972, The American Naturalist.

[6]  J. Carpenter.  UNINFORMATIVE BOOTSTRAPPING , 1996 .

[7]  A. Rodrigo,et al.  Inadequate Support for an Evolutionary Link between the Metazoa and the Fungi , 1994 .

[8]  S. Sherry,et al.  Geographic origin of human mitochondrial DNA revisited , 1992 .

[9]  N. Platnick,et al.  ON MISSING ENTRIES IN CLADISTIC ANALYSIS , 1991 .

[10]  J. A. Studier,et al.  A note on the neighbor-joining algorithm of Saitou and Nei. , 1988, Molecular biology and evolution.

[11]  Kurt Jordaens,et al.  Multiple UPGMA and Neighbor-joining Trees and the Performance of Some Computer Packages , 1996 .

[12]  J. Palmer,et al.  A parsimony analysis of the Asteridae sensu lato based on rbcL sequences. , 1993 .

[13]  J. Farris,et al.  The implications of congruence in Menidia , 1981 .

[14]  M. Nei,et al.  A Simple Method for Estimating and Testing Minimum-Evolution Trees , 1992 .

[15]  M. Nei,et al.  Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. , 1988, Molecular biology and evolution.

[16]  J. Farris.  Methods for Computing Wagner Trees , 1970 .

[17]  Andrey Rzhetsky,et al.  METREE: a program package for inferring and testing minimum-evolution trees , 1994, Comput. Appl. Biosci..

[18]  N. Saitou,et al.  Relative Efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining Methods of Phylogenetic Tree Construction in Obtaining the Correct Tree , 1989 .

[19]  A. von Haeseler,et al.  Independent origins of New Zealand moas and kiwis. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[20]  K. Bremer.  THE LIMITS OF AMINO ACID SEQUENCE DATA IN ANGIOSPERM PHYLOGENETIC RECONSTRUCTION , 1988, Evolution; international journal of organic evolution.

[21]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[22]  S. Stickel,et al.  Monophyletic origins of the metazoa: an evolutionary link with fungi , 1993, Science.

[23]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[24]  J. Farris.  The Hypothesis of Nonspecificity and Taxonomic Congruence , 1971 .

[25]  James F. Smith.  Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL , 1993 .

[26]  J. Farris.  On the Phenetic Approach to Vertebrate Classification , 1977 .

[27]  C. Bult,et al.  SKEWNESS AND PERMUTATION , 1992, Cladistics : the international journal of the Willi Hennig Society.