May 2006 | Volume 2 | Issue 5 | e68 | James H. Degnan, Noah A. Rosenberg
The paper by Degnan and Rosenberg explores the phenomenon of gene tree discordance with species trees, particularly focusing on the case where the number of species is five or more. They find that for any species tree topology with five or more species, there exist branch lengths for which the most likely gene tree topology differs from the species tree topology. This means that using the most frequently observed gene tree topology to estimate the species tree can lead to incorrect inferences as the number of genes increases. The authors introduce the concept of "anomalous gene trees" (AGTs) and demonstrate that these AGTs can occur for species tree topologies with four taxa as well, but only for asymmetric topologies. They provide mathematical proofs and examples to illustrate these findings, highlighting the importance of considering AGTs in phylogenetic studies to avoid misleading inferences. The paper concludes with suggestions for overcoming this challenge, such as using multiple individuals per species and combining data from multiple genes.The paper by Degnan and Rosenberg explores the phenomenon of gene tree discordance with species trees, particularly focusing on the case where the number of species is five or more. They find that for any species tree topology with five or more species, there exist branch lengths for which the most likely gene tree topology differs from the species tree topology. This means that using the most frequently observed gene tree topology to estimate the species tree can lead to incorrect inferences as the number of genes increases. The authors introduce the concept of "anomalous gene trees" (AGTs) and demonstrate that these AGTs can occur for species tree topologies with four taxa as well, but only for asymmetric topologies. They provide mathematical proofs and examples to illustrate these findings, highlighting the importance of considering AGTs in phylogenetic studies to avoid misleading inferences. The paper concludes with suggestions for overcoming this challenge, such as using multiple individuals per species and combining data from multiple genes.