Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The gene tree delusion

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

New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

(2016) Greg W. Rouse et al.   NATURE

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

(2015) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Impact of Missing Data on Species Tree Estimation

(2015) Zhenxiang Xi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

(2015) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

(2015) Jeffrey W. Streicher et al.   SYSTEMATIC BIOLOGY

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

(2015) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

(2015) Diego Mallo et al.   SYSTEMATIC BIOLOGY

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

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

Ultra-large alignments using phylogeny-aware profiles

(2015) Nam-phuong D. Nguyen et al.   GENOME BIOLOGY

Best practices in insect genome sequencing: what works and what doesn’t

(2015) Stephen Richards et al.   Current Opinion in Insect Science

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

(2015) Md Shamsuzzoha Bayzid et al.   PLoS One

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

BBCA: Improving the scalability of *BEAST using random binning

(2014) Théo Zimmermann et al.   BMC GENOMICS

Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting

(2014) L. Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses

(2014) Mark P. Simmons   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

(2014) Bastien Boussau et al.   PLoS One

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

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

(2014) S. Mirarab et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Land plant origins and coalescence confusion

(2014) Mark S. Springer et al.   TRENDS IN PLANT SCIENCE

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Effects of missing data on species tree estimation under the coalescent

(2013) Rasmus Hovmöller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Insect phylogenomics: new insights on the relationships of lower neopteran orders (Polyneoptera)

(2013) HARALD LETSCH et al.   SYSTEMATIC ENTOMOLOGY

Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera

(2012) Oliver Niehuis et al.   CURRENT BIOLOGY

Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence

(2012) MD. Shamsuzzoha Bayzid et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic Insights into the Cambrian Explosion, the Colonization of Land and the Evolution of Flight in Arthropoda

(2012) Christopher W. Wheat et al.   SYSTEMATIC BIOLOGY

Advances in Insect Phylogeny at the Dawn of the Postgenomic Era

(2011) Michelle D. Trautwein et al.   Annual Review of Entomology

Misleading results of likelihood-based phylogenetic analyses in the presence of missing data

(2011) Mark P. Simmons   CLADISTICS

Evolution of the hymenopteran megaradiation

(2011) John Heraty et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

(2011) Kevin Liu et al.   PLoS One

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia

(2011) BENJAMIN WIPFLER et al.   SYSTEMATIC ENTOMOLOGY

Monophyletic Polyneoptera recovered by wing base structure

(2011) KAZUNORI YOSHIZAWA   SYSTEMATIC ENTOMOLOGY

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola

(2010) Rolf G. Beutel et al.   CLADISTICS

The phylogeny of hexapod “orders”. A critical review of recent accounts

(2010) N. P. Kristensen   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences

(2010) Keisuke Ishiwata et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

(2010) Jerome C. Regier et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

9-Genes Reinforce the Phylogeny of Holometabola and Yield Alternate Views on the Phylogenetic Placement of Strepsiptera

(2010) Duane D. McKenna et al.   PLoS One

Resolving insect phylogeny: The significance of cephalic structures of the Nannomecoptera in understanding endopterygote relationships

(2009) Rolf G. Beutel et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

400 million years on six legs: On the origin and early evolution of Hexapoda

(2009) David A. Grimaldi   ARTHROPOD STRUCTURE & DEVELOPMENT

Single-copy nuclear genes resolve the phylogeny of the holometabolous insects

(2009) Brian M Wiegmann et al.   BMC BIOLOGY

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION