Garbage in, Garbage out

As in conventional phylogenetic analyses, issues surrounding the source data are paramount in the supertree construction, but have received insufficient attention. In supertree construction, however, the source data represent phylogenetic trees rather than primary character data. This presents several supertree-specific problems. In this paper, we examine several key data issues for supertree construction, including data set non-independence, taxonomy of terminal taxa, and the question of what constitutes a valid source tree. Throughout, we present our suggested protocol for source tree collection and manipulation based on our experiences in building a supertree of mammals. Other protocols and decisions are naturally possible. What is important is that all collection protocols are presented explicitly and address minimally the issues that we have identified.

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

[2]  Olaf R. P. Bininda-Emonds,et al.  The adaptive significance of coloration in lagomorphs , 2003 .

[3]  Michael J Benton,et al.  A genus-level supertree of the Dinosauria , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[4]  M. Ragan.  Phylogenetic inference based on matrix representation of trees. , 1992, Molecular phylogenetics and evolution.

[5]  Junhyong Kim,et al.  Separate Versus Combined Analysis of Phylogenetic Evidence , 1995 .

[6]  O. Bininda-Emonds,et al.  Factors influencing phylogenetic inference: a case study using the mammalian carnivores. , 2000, Molecular phylogenetics and evolution.

[7]  M. Springer,et al.  A Critique of Matrix Representation with Parsimony Supertrees , 2004 .

[8]  G Perrière,et al.  Bacterial molecular phylogeny using supertree approach. , 2001, Genome informatics. International Conference on Genome Informatics.

[9]  Mark A. Ragan,et al.  The MRP Method , 2004 .

[10]  Roderic D. M. Page,et al.  Taxonomy, Supertrees, and the Tree of Life , 2004 .

[11]  M J Sanderson,et al.  Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. , 2001, Systematic biology.

[12]  Marc W Allard,et al.  The misleading effects of composite taxa in supermatrices. , 2003, Molecular phylogenetics and evolution.

[13]  W. Maddison.  Gene Trees in Species Trees , 1997 .

[14]  Andy Purvis,et al.  A Modification to Baum and Ragan's Method for Combining Phylogenetic Trees , 1995 .

[15]  R. Jenner.  Bilaterian phylogeny and uncritical recycling of morphological data sets. , 2001, Systematic biology.

[16]  M. Kennedy,et al.  SEABIRD SUPERTREES: COMBINING PARTIAL ESTIMATES OF PROCELLARIIFORM PHYLOGENY , 2002 .

[17]  Michael M. Miyamoto,et al.  Molecular and Morphological Supertrees for Eutherian (Placental) Mammals , 2001, Science.

[18]  John J. Flynn,et al.  A Phylogenetic Analysis and Definition of the Carnivora , 1993 .

[19]  Mark S. Springer,et al.  Which Mammalian Supertree to Bark Up? , 2001, Science.

[20]  Rob DeSalle,et al.  Resolution of a supertree/supermatrix paradox. , 2002, Systematic biology.

[21]  A. Purvis,et al.  A phylogenetic supertree of the bats (Mammalia: Chiroptera) , 2002, Biological reviews of the Cambridge Philosophical Society.

[22]  Charles Semple,et al.  Supertree Algorithms for Nested Taxa , 2004 .

[23]  J. L. Gittleman,et al.  The (Super)Tree of Life: Procedures, Problems, and Prospects , 2002 .

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

[25]  James O. McInerney,et al.  Some Desiderata for Liberal Supertrees , 2004 .

[26]  O. Bininda-Emonds,et al.  Properties of matrix representation with parsimony analyses. , 1998, Systematic biology.

[27]  A. Purvis.  A composite estimate of primate phylogeny. , 1995, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[28]  J. L. Gittleman,et al.  Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia) , 1999, Biological reviews of the Cambridge Philosophical Society.

[29]  M. Gouy,et al.  A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. , 2002, Genome research.

[30]  Kate E. Jones,et al.  Supertrees are a necessary not-so-evil: a comment on Gatesy et al. , 2003, Systematic biology.