ON CONSENSUS, CONFIDENCE, AND “TOTAL EVIDENCE”

The issue of whether it is best to combine separate data sets (“total evidence”), or to combine trees (“taxonomic congruence”) has received considerable attention in the recent literature (e.g. Kluge, 1989; Barrett et al. 1991; Kluge and Wolf, 1993; Miyamoto and Fitch, 1995). In this note I discuss some recent arguments that have been made regarding this issue, starting with Barrett et al.’s (1991) argument against consensus methods. I then touch on bootstrapping and the problem of confidence sets of trees (Sanderson, 1989), before considering the implication of the difference between gene trees and species trees for the concept of total evidence. The common theme underlying these topics is the role of consensus in systematics. Consensus trees are very useful tools, but they have their limits. However, the nature of these limits is still being explored.

[1]  Michael M. Miyamoto,et al.  TESTING SPECIES PHYLOGENIES AND PHYLOGENETIC METHODS WITH CONGRUENCE , 1995 .

[2]  Mike Steel,et al.  The complexity of the median procedure for binary trees , 1994 .

[3]  D. Penny,et al.  The Use of Tree Comparison Metrics , 1985 .

[4]  M. Steel,et al.  Distributions of Tree Comparison Metrics—Some New Results , 1993 .

[5]  R. Page,et al.  COMMENTS ON COMPONENT‐COMPATIBILITY IN HISTORICAL BIOGEOGRAPHY , 1989 .

[6]  J. Doyle,et al.  Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy , 1992 .

[7]  F. McMorris,et al.  The median procedure for n-trees , 1986 .

[8]  A. Kluge,et al.  CLADISTICS: WHAT'S IN A WORD? , 1993, Cladistics : the international journal of the Willi Hennig Society.

[9]  A. Kluge,et al.  Regular ArticleCladistics: What's in a Word? , 1993 .

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

[11]  J. Patton,et al.  Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (Genus Thomomys) , 1994 .

[12]  D. Swofford.  When are phylogeny estimates from molecular and morphological data incongruent , 1991 .

[13]  Michael J. Sanderson1.  CONFIDENCE LIMITS ON PHYLOGENIES: THE BOOTSTRAP REVISITED , 1989 .

[14]  A. Queiroz.  For Consensus (Sometimes) , 1993 .

[15]  Gareth Nelson,et al.  Systematics and Biogeography: Cladistics and Vicariance , 1981 .

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

[17]  Fred R. McMorris,et al.  Consensusn-trees , 1981 .

[18]  D. A. Neumann,et al.  Consensus functions defined on trees , 1983 .

[19]  J. Bull,et al.  Partitioning and combining data in phylogenetic analysis , 1993 .

[20]  Edward N. AdamsIII.  N-trees as nestings: Complexity, similarity, and consensus , 1986 .

[21]  D. Swofford,et al.  Inferring Evolutionary Trees from Gene Frequency Data Under the Principle of Maximum Parsimony , 1987 .

[22]  Allen G. Rodrigo,et al.  A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree , 1993 .

[23]  Robert R. Sokal,et al.  Advances in Cladistics, Proceedings of the First Meeting of the Willi Hennig Society , 1982 .

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

[25]  Michael J Sanderson,et al.  CONFIDENCE LIMITS ON PHYLOGENIES: THE BOOTSTRAP REVISITED , 1989, Cladistics : the international journal of the Willi Hennig Society.

[26]  A. Kluge.  A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes) , 1989 .

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

[28]  David M. Williams,et al.  Congruence Between Molecular and Morphological Phylogenies , 1993 .

[29]  D. Ord,et al.  PAUP:Phylogenetic analysis using parsi-mony , 1993 .

[30]  Daniel R. Brooks,et al.  Phylogeny, Ecology, and Behavior , 1992 .

[31]  B. Baum.  Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees , 1992 .

[32]  D. Hillis.  Approaches for Assessing Phylogenetic Accuracy , 1995 .