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Systematic Biology Advance Access originally published online on September 17, 2009
Systematic Biology 2009 58(5):463-467; doi:10.1093/sysbio/syp061
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© The Author(s) 2009. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

L. Lacey Knowles*

Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA

* Correspondence to be sent to: Museum of Zoology, 1109 Geddes Avenue, University of Michigan, Ann Arbor, MI 48109-1079, USA; E-mail: knowlesl@umich.edu.

The first 150 words of the full text of this article appear below.

Discord among the gene trees of multilocus data has motivated the development of phylogenetic approaches that account for gene-tree heterogeneity in the estimation procedure. Rather than equating a gene tree with the phylogenetic history, the new approaches explicitly consider the relationships between gene trees and the underlying history of species divergence, providing direct estimates of species trees (Fig. 1). The inherent appeal of these approaches is 2-fold. Incorporating information contained in the distribution of gene trees not only extracts phylogenetic signal, but modeling the relationship between the gene trees embedded in a species tree also reveals the biological processes that have influenced the diversification history and shaped organismal genomes. In contrast, ignoring the variance in genealogical histories (e.g., concatenating loci into a single supermatrix) disregards an inescapable biological reality—gene trees differ for a variety of reasons (reviewed in Maddison 1997; Degnan and Rosenberg 2009). As such, when the . . . [Full Text of this Article]


   CONCEPTUAL BASIS FOR SPECIES-TREE ESTIMATION
 
Species-Tree Inference Procedures
Need for a Paradigm Shift?

   THE SYMPOSIUM
 

   PROSPECTS FOR THE FUTURE
 

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