Inconsistency of Species Tree Methods under Gene Flow

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

A maximum pseudo-likelihood approach for phylogenetic networks

(2015) Yun Yu et al.   BMC GENOMICS

Disentangling the Relationship of the Australian Marsupial Orders Using Retrotransposon and Evolutionary Network Analyses

(2015) Susanne Gallus et al.   Genome Biology and Evolution

Conundrum of jumbled mosquito genomes

(2015) A. G. Clark et al.   SCIENCE

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable

(2015) Fabio Pardi et al.   PLoS Computational Biology

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Quartet-based methods to reconstruct phylogenetic networks

(2014) Jialiang Yang et al.   BMC Systems Biology

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speciation with gene flow in equids despite extensive chromosomal plasticity

(2014) Hákon Jónsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical binning enables an accurate coalescent-based estimation of the avian tree

(2014) S. Mirarab et al.   SCIENCE

Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics?

(2014) David A. Morrison   SYSTEMATIC BIOLOGY

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Systematic inference of highways of horizontal gene transfer in prokaryotes

(2013) Mukul S. Bansal et al.   BIOINFORMATICS

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES

(2013) Rongfeng Cui et al.   EVOLUTION

SuperQ: Computing Supernetworks from Quartets

(2013) Stefan Grunewald et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Lateral Gene Transfer from the Dead

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Anomalous Unrooted Gene Trees

(2013) James H. Degnan   SYSTEMATIC BIOLOGY

The Tree of Life: Metaphor, Model, and Heuristic Device

(2013) David P. Mindell   SYSTEMATIC BIOLOGY

Networks: expanding evolutionary thinking

(2013) Eric Bapteste et al.   TRENDS IN GENETICS

Unified modeling of gene duplication, loss, and coalescence using a locus tree

(2012) M. D. Rasmussen et al.   GENOME RESEARCH

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

(2012) G. J. Szollosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is Recombination a Problem for Species-Tree Analyses?

(2012) Hayley C. Lanier et al.   SYSTEMATIC BIOLOGY

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

(2011) David Gerard et al.   BMC EVOLUTIONARY BIOLOGY

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

(2011) Yujin Chung et al.   SYSTEMATIC BIOLOGY

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

(2010) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees

(2008) M. Slatkin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY