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Systematic Biology Advance Access originally published online on July 9, 2009
Systematic Biology 2009 58(4):452-460; doi:10.1093/sysbio/syp034
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© Society of Systematic Biologists

Phylogenetic Analysis in the Anomaly Zone

Liang Liu* and Scott V. Edwards

Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; E-mail: sedwards@fas.harvard.edu

* Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; E-mail: lliu@oeb.harvard.edu.

Received October 7, 2008; Revised December 17, 2008; Accepted April 6, 2009
The first 150 words of the full text of this article appear below.

The concatenation method has been widely used as a means of combining data to estimate phylogenetic trees (Huelsenbeck et al. 1996a, 1996b; Glazko and Nei 2003). However, simulation studies have shown that the maximum likelihood (ML) estimate of the species tree for concatenated sequences may be statistically inconsistent if the gene trees are highly heterogeneous (Kolaczkowski and Thornton 2004; Kubatko and Degnan 2007). Recently, Degnan and Rosenberg (2006) defined an "anomaly zone"—a set of short internal branches in species trees that will generate gene trees that are discordant with the species tree more often than gene trees that are concordant. Kubatko and Degnan (2007) went on to show that when DNA sequences are generated from gene trees simulated from species trees in the anomaly zone, as well as from species trees slightly outside this zone but still with short internal branches, the ML . . . [Full Text of this Article]


   THEORETICAL RESULTS
 
Expected Coalescence Time of Alleles Sampled from 2 Species in a Multispecies Tree
Ancestral Order of Populations and Species Tree Estimation
Simulations and Phylogenetic Analysis of Concatenated Sequences under Coalescence

   DISCUSSION
 

   FUNDING
 

   APPENDIX 1
 
Proof.

   APPENDIX 2
 
Proof:

   APPENDIX 3
 
Proof.

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