Brooks Parsimony Analysis: a valiant failure

A recent comparison of two methods for examining correlated host and parasite phylogenies, namely TreeMap 1.0 and Brooks Parsimony Analysis concluded that the latter method performed better and is to be preferred. Reevaluation of the examples contrived for that study demonstrates that the two methods were only compared on one kind of problem (widespread parasite) for which there is an easy fix for TreeMap 1.0. Other kinds of problems like host‐switching among sister taxa or host‐switching over great distances across a host tree befuddle BPA even as they are readily resolved parsimoniously by TreeMap 1.0. These difficulties, compounded with inaccurate counting of ad hoc hypotheses required by its solutions render BPA unsuitable for comparison of host and parasite phylogenies.

[1]  Nick Goldman,et al.  MAXIMUM LIKELIHOOD INFERENCE OF PHYLOGENETIC TREES, WITH SPECIAL REFERENCE TO A POISSON PROCESS MODEL OF DNA SUBSTITUTION AND TO PARSIMONY ANALYSES , 1990 .

[2]  M. Siddall.  Phylogeny of the leech family Erpobdellidae (Hirudinida : Oligochaeta) , 2002 .

[3]  Roderic D. M. Page,et al.  QUANTITATIVE CLADISTIC BIOGEOGRAPHY: CONSTRUCTING AND COMPARING AREA CLADOGRAMS , 1988 .

[4]  F. Hoffmann,et al.  Tangled Trees: Phylogeny, Cospeciation, and Coevolution , 2004 .

[5]  M. Siddall,et al.  PHYLOGENETIC COVARIANCE PROBABILITY: CONFIDENCE AND HISTORICAL ASSOCIATIONS , 1996 .

[6]  D. Brooks,et al.  Parascript: Parasites and the Language of Evolution , 1994 .

[7]  Wayne P. Maddison,et al.  Macclade: Analysis of Phylogeny and Character Evolution/Version 3 , 1992 .

[8]  Fredrik Ronquist,et al.  RECONSTRUCTING THE HISTORY OF HOST‐PARASITE ASSOCIATIONS USING GENERALISED PARSIMONY , 1995, Cladistics : the international journal of the Willi Hennig Society.

[9]  C. Humphries,et al.  Cladistic biogeography and the art of discovery , 2002 .

[10]  A. Dowling.  Testing the accuracy of TreeMap and Brooks parsimony analyses of coevolutionary patterns using artificial associations , 2002 .

[11]  S. Perkins,et al.  A MOLECULAR PHYLOGENY OF MALARIAL PARASITES RECOVERED FROM CYTOCHROME b GENE SEQUENCES , 2002, The Journal of parasitology.

[12]  J. Felsenstein.  Numerical Methods for Inferring Evolutionary Trees , 1982, The Quarterly Review of Biology.

[13]  Mark Ridley,et al.  Phylogeny, ecology, and behavior: A research program in comparative biology , 1991 .

[14]  Hidetoshi Shimodaira,et al.  Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference , 1999, Molecular Biology and Evolution.

[15]  Fredrik Ronquist,et al.  Three‐Dimensional Cost‐Matrix Optimization and Maximum Cospeciation , 1998, Cladistics : the international journal of the Willi Hennig Society.

[16]  Daniel R. Brooks,et al.  HISTORICAL ECOLOGY: A NEW APPROACH TO STUDYING THE EVOLUTION OF ECOLOGICAL ASSOCIATIONS , 1985 .

[17]  M. Nei,et al.  The neighbor-joining method , 1987 .

[18]  Daniel R. Brooks,et al.  How to do BPA, really , 2001 .

[19]  H. Kishino,et al.  Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea , 1989, Journal of Molecular Evolution.

[20]  E. Hoberg,et al.  Congruent and synchronic patterns in biogeography and speciation among seabirds, pinnipeds, and cestodes. , 1992, The Journal of parasitology.

[21]  L. Avilan,et al.  Interaction of different Leishmania mexicana morphotypes with plasminogen , 2002, Parasitology Research.

[22]  Roderic D. M. Page,et al.  Genes, organisms, and areas: the problem of multiple lineages , 1993 .

[23]  R. O'Grady,et al.  Coding Multistate Characters, with Special Reference to the Use of Parasites as Characters of their Hosts , 1987 .

[24]  R. Page.  Maps between trees and cladistic analysis of historical associations among genes , 1994 .

[25]  Fredrik Ronquist,et al.  Process and Pattern in the Evolution of Species Associations , 1990 .

[26]  J. Felsenstein.  Cases in which Parsimony or Compatibility Methods will be Positively Misleading , 1978 .

[27]  Daniel R. Brooks,et al.  Hennig's Parasitological Method: A Proposed Solution , 1981 .

[28]  A. Kluge.  Parsimony in vicariance biogeography : a quantitative method and a greater antillean example , 1988 .

[29]  D. Kornet,et al.  Regular ArticleMethods in Vicariance Biogeography: Assessment of the Implementations of Assumptions 0, 1, and 2☆ , 2000 .

[30]  Roderic D. M. Page,et al.  COMPONENT ANALYSIS: A VALIANT FAILURE? , 1990 .

[31]  M. Charleston,et al.  Jungles: a new solution to the host/parasite phylogeny reconciliation problem. , 1998, Mathematical biosciences.

[32]  Roderic D. M. Page,et al.  PARALLEL PHYLOGENIES: RECONSTRUCTING THE HISTORY OF HOST‐PARASITE ASSEMBLAGES , 1994 .

[33]  Rob DeSalle,et al.  The Widespread Colonization Island of Actinobacillus actinomycetemcomitans , 2003, Nature Genetics.

[34]  D. Brooks.  Macroevolutionary Comparisons Of Host And Parpsite Phylogenies , 1988 .

[35]  D. Brooks,et al.  Revision and phylogenetic analysis of the amphilinidea poche, 1922 (Platyhelminthes: Cercomeria: Cercomeromorpha) , 1987 .

[36]  Fredrik Ronquist,et al.  Parsimony analysis of coevolving species associa-tions , 2002 .

[37]  Daniel R. Brooks,et al.  Macroevolutionary Comparisons of Host and Parasite Phylogenies , 1988 .

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

[39]  R. Page,et al.  Trees within trees: phylogeny and historical associations. , 1998, Trends in ecology & evolution.

[40]  J. S. Rogers,et al.  Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. , 2001, Systematic biology.

[41]  Diego Pol,et al.  Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10-Taxon Case , 2001 .

[42]  W. Hennig.  Phylogenetic Systematics , 2002 .

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

[44]  J. Morrone,et al.  IN SEARCH OF A METHOD FOR CLADISTIC BIOGEOGRAPHY: AN EMPIRICAL COMPARISON OF COMPONENT ANALYSIS, BROOKS PARSIMONY ANALYSIS, AND THREE‐AREA STATEMENTS , 1994 .

[45]  Roderic D. M. Page,et al.  Tangled trees : phylogeny, cospeciation, and coevolution , 2003 .

[46]  J. Farris,et al.  Regular ArticlePARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING , 1996 .

[47]  M. Siddall,et al.  Long‐Branch Abstractions , 1999 .

[48]  R. Page.  Parasites, phylogeny and cospeciation , 1993 .

[49]  P. Hovenkamp.  Vicariance Events, not Areas, Should be Used in Biogeographical Analysis , 1997, Cladistics : the international journal of the Willi Hennig Society.

[50]  Marco G. P. Van Veller,et al.  Methods in Vicariance Biogeography: Assessment of the Implementations of Assumptions 0, 1, and 2 , 2000 .

[51]  O. A. Sæther,et al.  THE MYTH OF OBJECTIVITY—POST‐HENNIGIAN DEVIATIONS , 1986 .

[52]  Daniel R. Brooks,et al.  Testing the Context and Extent of Host-Parasite Coevolution , 1979 .

[53]  J. Cracraft.  Deep-history Biogeography: Retrieving the Historical Pattern of Evolving Continental Biotas , 1988 .

[54]  Daniel R. Brooks,et al.  Parsimony Analysis in Historical Biogeography and Coevolution: Methodological and Theoretical Update , 1990 .

[55]  M. Siddall,et al.  The AIDS Pandemic is New, but is HIVNotNew?☆☆☆ , 1997 .

[56]  M. Siddall,et al.  Probabilism and Phylogenetic Inference , 1997, Cladistics : the international journal of the Willi Hennig Society.

[57]  David P. Mindell,et al.  THE AIDS PANDEMIC IS NEW, BUT IS HIV NEW ? , 1995 .

[58]  E. Hoberg,et al.  Phylogeny, historical biogeography, and ecology of Anophryocephalus spp. (Eucestoda: Tetrabothriidae) among pinnipeds of the Holarctic during the late Tertiary and Pleistocene , 1992 .

[59]  J. Huelsenbeck,et al.  SUCCESS OF PHYLOGENETIC METHODS IN THE FOUR-TAXON CASE , 1993 .