title: In the light of deep coalescence: revisiting trees within networks.
abstract: BACKGROUND
  Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A salient concept underlying a great majority of these developments has been the notion that a network displays a set of trees and those trees can be used to infer, analyze, and study the network.
  
  
  RESULTS
  In this paper, we show that in the presence of coalescence effects, the set of displayed trees is not sufficient to capture the network. We formally define the set of parental trees of a network and make three contributions based on this definition. First, we extend the notion of anomaly zone to phylogenetic networks and report on anomaly results for different networks. Second, we demonstrate how coalescence events could negatively affect the ability to infer a species tree that could be augmented into the correct network. Third, we demonstrate how a phylogenetic network can be viewed as a mixture model that lends itself to a novel inference approach via gene tree clustering.
  
  
  CONCLUSIONS
  Our results demonstrate the limitations of focusing on the set of trees displayed by a network when analyzing and inferring the network. Our findings can form the basis for achieving higher accuracy when inferring phylogenetic networks and open up new venues for research in this area, including new problem formulations based on the notion of a network's parental trees.
authors.affiliation: Department of Computer Science, Rice University, Houston, 77005, Texas, USA.
authors.forename: Jiafan
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Department of Computer Science, Rice University, Houston, 77005, Texas, USA.
authors.forename: Yun
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Department of Computer Science, Rice University, Houston, 77005, Texas, USA. nakhleh@rice.edu.|Department of BioSciences, Rice University, Houston, 77005, Texas, USA. nakhleh@rice.edu.
authors.forename: Luay
authors.initials: L
authors.lastname: Nakhleh
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D008957:Models, Genetic; D010802:Phylogeny