The supermatrix approach to systematics

doi:10.1016/j.tree.2006.10.002

Trends in Ecology & Evolution

Volume 22, Issue 1, January 2007, Pages 34-41

https://doi.org/10.1016/j.tree.2006.10.002 Get rights and content

Recent reviews of the construction of large phylogenies have focused on supertree methods that involve separate analyses of data sets and subsequent integration of the resulting trees. Here, we consider the alternative method of analyzing all character data simultaneously. Such ‘supermatrix’ analyses use information from each character directly and enable straightforward incorporation of diverse kinds of data, including characters from fossils. The approach has been extended by the development of new methods, including model-based techniques for analyzing heterogeneous data and hierarchical methods for constructing extremely large trees. Recent work also suggests that the problem of missing data in supermatrix analyses has been overstated. Although the supermatrix approach is not suited for all cases, we suggest that its inherent strengths will ensure that it will continue to have a central role in inferring large phylogenetic trees from diverse data.

Section snippets

Building ever-larger trees

In The Origin of Species [1], Charles Darwin established that descent with modification explains the similarities and differences among all organisms: from bacteria to orchids to humans, we are all connected in a single Tree of Life. Until recently, taxonomic specialists were restricted to reconstructing phylogenetic relationships among relatively few species using small numbers of characters. However, recent advances now enable phylogenetic analyses of thousands of taxa or characters (e.g. 2, 3

Basic strengths of the supermatrix approach

The supermatrix approach is defined by the direct, simultaneous use of all the character evidence from all included taxa (Figure 1). A basic advantage of the approach is simply that it uses this character evidence more fully in estimating the tree than do supertree methods; in supertree analyses, some of the character information within data sets is lost when sets of characters are summarized as trees 6, 13. This advantage of the supermatrix approach is so fundamental (more information is

The gene tree–species tree problem

The standard supermatrix approach implicitly assumes that all characters have experienced the same branching history. It is now well known that this assumption is not always valid. In particular, the gene tree for copies of a gene in different species might not match the species tree (the history of splitting of species lineages) because of hybridization, horizontal gene transfer, gene duplication and sorting of genetic polymorphisms among species lineages (lineage sorting) [22]. This ‘gene

New supermatrix methods

An equally weighted parsimony approach has been perhaps the most common mode of analysis in supermatrix studies (e.g. 18, 29). Proponents of parsimony seek maximally general explanations for similarities among taxa as results of inheritance from a common ancestor; the criterion of generality entails choosing a tree that minimizes the number of character-state changes required to explain character similarities [30]. Here, we describe several new methods that extend the capabilities of

Supermatrices and the Tree of Life

The Tree of Life as we know it includes ∼1.5 million living species [48] plus many thousands of extinct species. Despite the continuing development of methods that increase the speed of phylogenetic analyses (e.g. 40, 49, 50, 51, 52), it might never be possible to estimate the entire Tree of Life reliably using a single, standard supermatrix analysis [53]. Nonetheless, current methods used to construct very large trees suggest that a supermatrix approach can have a central role in assembling

Supermatrices for the future

The supermatrix approach has proven to be a powerful method of combining diverse data to infer phylogenetic relationships. The approach directly uses the evidence provided by each character, often revealing emergent support that is hidden in separate analyses of data partitions, and easily accommodates different classes of character data. Regarding the latter point, molecular systematists sometimes forget that a tree of all known life must include many fossil taxa and, thus, must be derived in

Acknowledgements

We thank C. Hayashi, J. Kim, K. de Queiroz and three anonymous reviewers for discussion or comments on the article, and M. O’Leary and G. Giribet for providing the MorphoBank figure. J.G. was funded by NSF EAR0228629, DEB–0213171 and DEB–0212572.

Glossary

Bayesian phylogenetic method: any method that uses Bayesian inference in phylogenetic estimation. In Bayesian phylogenetic inference, the posterior probability of a tree (which, given certain assumptions, is the probability that the tree is correct) is a function of the product of the tree's prior probability and its likelihood. The most commonly used Bayesian phylogenetic method uses a Markov Chain Monte Carlo technique designed to visit different tree topologies with a frequency proportional to

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Trends in Ecology & Evolution

ReviewThe supermatrix approach to systematics

Section snippets

Building ever-larger trees

Basic strengths of the supermatrix approach

The gene tree–species tree problem

New supermatrix methods

Supermatrices and the Tree of Life

Supermatrices for the future

Acknowledgements

Glossary

Trends Ecol. Evol.

Trends Ecol. Evol.

Cladistics

Trends Genet.

Mol. Phylog. Evol.

Mol. Phylog. Evol

Cladistics

Org. Diversity Evol.

Mol. Phylog. Evol.

Bull. Math. Biol.

Curr. Biol.

Cladistics

Cladistics

Math. Biosci.

J. Biomed. Inform.

Cladistics

On the Origin of Species

Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants, and flowering plants

Plant Syst. Evol.

Genome-scale approaches to resolving incongruence in molecular phylogenies

Nature

A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes)

Syst. Zool.

Prospects for building the Tree of Life from large sequence databases

Science

Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia

Syst. Biol.

Molecular evidence and marine snake origins

Biol. Lett.

Relationships of endemic African mammals and their fossil relatives based on morphological and molecular evidence

J. Mamm. Evol.

Phylogenetic relationships of extinct cetartiodactyls: results of simultaneous analyses of molecular, morphological, and stratigraphic data

J. Mamm. Evol.

Phylogenomics and the reconstruction of the tree of life

Nat. Rev. Genet.

Separate versus combined analysis of phylogenetic evidence

Annu. Rev. Ecol. Syst.

Against consensus

Syst. Zool.

Combining data in phylogenetic systematics: an empirical approach using three molecular data sets in the Solanaceae

Syst. Biol.

Partitioned Bremer support localizes significant conflict in bee flies (Diptera: Bombyliidae: Anthracinae)

Invertebr. Syst.

Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

Proc. R. Soc. B

Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets

Syst. Biol.

Taxonomic sampling, phylogenetic accuracy, and investigator bias

Syst. Biol.

Increased taxon sampling greatly reduces phylogenetic error

Syst. Biol.

Gene trees in species trees

Syst. Biol.

Inferring phylogeny despite incomplete lineage sorting

Syst. Biol.

Review
The supermatrix approach to systematics