On the Number of Ranked Species Trees Producing Anomalous Ranked Gene Trees

Analysis of probability distributions conditional on species trees has demonstrated the existence of anomalous ranked gene trees (ARGTs), ranked gene trees that are more probable than the ranked gene tree that accords with the ranked species tree. Here, to improve the characterization of ARGTs, we study enumerative and probabilistic properties of two classes of ranked labeled species trees, focusing on the presence or avoidance of certain subtree patterns associated with the production of ARGTs. We provide exact enumerations and asymptotic estimates for cardinalities of these sets of trees, showing that as the number of species increases without bound, the fraction of all ranked labeled species trees that are ARGT-producing approaches 1. This result extends beyond earlier existence results to provide a probabilistic claim about the frequency of ARGTs.

• Publication year

  2014

• Venue

  IEEE/ACM Transactions on Computational Biology & Bioinformatics

• Publication date

  2014-07-10

• Fields of study

  Biology, Mathematics, Medicine, Computer Science

• Identifiers
  DOI 10.1109/TCBB.2014.2343977arXiv 1407.2976PMID 26357058
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle

  2013cited by this paper
• Yule-generated trees constrained by node imbalance.

  2013cited by this paper
• Anomalous unrooted gene trees.

  2013cited by this paper
• The probability distribution of ranked gene trees on a species tree.

  2012cited by this paper
• A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

  2012cited by this paper
• COALESCENT‐BASED SPECIES TREE INFERENCE FROM GENE TREE TOPOLOGIES UNDER INCOMPLETE LINEAGE SORTING BY MAXIMUM LIKELIHOOD

  2012cited by this paper
• A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees

  2012cited by this paper
• Determining species tree topologies from clade probabilities under the coalescent.

  2011cited by this paper
• Gene tree discordance, phylogenetic inference and the multispecies coalescent.

  2009cited by this paper
• Analytic Combinatorics

  2009cited by this paper
• Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent

  2009cited by this paper
• Properties of consensus methods for inferring species trees from gene trees.

  2008cited by this paper
• Discordance of species trees with their most likely gene trees: the case of five taxa.

  2008cited by this paper
• Coalescent Theory: An Introduction

  2008cited by this paper
• Discordance of Species Trees with Their Most Likely Gene Trees

  2006cited by this paper
• Properties of Subtree-Prune-and-Regraft Operations on Totally-Ordered Phylogenetic Trees

  2006cited by this paper
• The Mean and Variance of the Numbers of r-Pronged Nodes and r-Caterpillars in Yule-Generated Genealogical Trees

  2006cited by this paper
• GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS

  2005cited by this paper
• Gene Genealogies, Variation and Evolution - A Primer in Coalescent Theory

  2004cited by this paper
• The probability of topological concordance of gene trees and species trees.

  2002cited by this paper
• Properties of phylogenetic trees generated by Yule-type speciation models.

  2001cited by this paper
• From Gene Trees to Species Trees

  2000cited by this paper
• A Dictionary of Inequalities

  1998influential reference
• Probabilities of Evolutionary Trees

  1994cited by this paper
• RANDOM DENDROGRAMS AND NULL HYPOTHESES IN CLADISTIC BIOGEOGRAPHY

  1991cited by this paper
• Relationships between gene trees and species trees.

  1988cited by this paper
• Evolutionary relationship of DNA sequences in finite populations.

  1983cited by this paper
• The probabilities of rooted tree-shapes generated by random bifurcation

  1971cited by this paper
• Estimation of the Branch Points of a Branching Diffusion Process

  1970cited by this paper
• A Mathematical Theory of Evolution Based on the Conclusions of Dr. J. C. Willis, F.R.S.

  1925cited by this paper
• Variation and Evolution.

  1893cited by this paper
• A Mathematical Theory of Evolution, Based on the Conclusions of Dr. J. C. Willis, F.R.S.

  year unknowncited by this paper

• Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

  2022cites this paper
• Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

  2019cites this paper
• On the unranked topology of maximally probable ranked gene tree topologies

  2019cites this paper
• Probabilities of unranked and ranked anomaly zones under birth-death models.

  2019cites this paper
• Bijective Diameters of Gene Tree Parsimony Costs

  2018cites this paper
• There are no caterpillars in a wicked forest.

  2015cites this paper