Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae)

New methods to calculate concordance factors for phylogenomic datasets

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)

(2020) Kin Onn Chan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Model selection may not be a mandatory step for phylogeny reconstruction

(2019) Shiran Abadi et al.   Nature Communications

Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics.

(2019) Karen Siu-Ting et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

(2019) Alison Cloutier et al.   SYSTEMATIC BIOLOGY

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

(2019) Emily J Roycroft et al.   SYSTEMATIC BIOLOGY

Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships

(2019) Frank T Burbrink et al.   SYSTEMATIC BIOLOGY

An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

(2019) Jin-Min Chen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution

(2018) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

DiscoVista: Interpretable visualizations of gene tree discordance

(2018) Erfan Sayyari et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comprehensive multi-locus phylogeny of Old World tree frogs (Anura: Rhacophoridae) reveals taxonomic uncertainties and potential cases of over- and underestimation of species diversity

(2018) Kin Onn Chan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees

(2018) Ziheng Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

(2018) et al.   Genes

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

(2017) Kin Onn Chan et al.   MOLECULAR ECOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

(2017) Yan-Jie Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC BIOLOGY

Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics

(2017) Étienne Léveillé-Bourret et al.   SYSTEMATIC BIOLOGY

Why Concatenation Fails Near the Anomaly Zone

(2017) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats

(2017) Roy N Platt et al.   SYSTEMATIC BIOLOGY

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

(2017) Sushma Reddy et al.   SYSTEMATIC BIOLOGY

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

(2016) Charles W. Linkem et al.   SYSTEMATIC BIOLOGY

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

(2016) Kelly A. Meiklejohn et al.   SYSTEMATIC BIOLOGY

A new small-sized Theloderma (Anura: Rhacophoridae) from Laos

(2016) NIANE SIVONGXAY et al.   ZOOTAXA

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

(2015) Jed Chou et al.   BMC GENOMICS

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

Mitochondrial phylogeny of an Asian tree frog genus Theloderma (Anura: Rhacophoridae)

(2015) Tao Thien Nguyen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

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

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

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

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

Patterns of reproductive-mode evolution in Old World tree frogs (Anura, Rhacophoridae)

(2015) Madhava Meegaskumbura et al.   ZOOLOGICA SCRIPTA

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) E. D. Jarvis et al.   SCIENCE

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

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

(2013) N. A. Rosenberg   MOLECULAR BIOLOGY AND EVOLUTION

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

(2013) Emiliano Dell’Ampio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversification in a biodiversity hotspot – The evolution of Southeast Asian rhacophorid tree frogs on Borneo (Amphibia: Anura: Rhacophoridae)

(2013) Stefan T. Hertwig et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

(2013) Torsten H. Struck   PLoS One

Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene

(2013) Jia-Tang Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

(2011) R. Alexander Pyron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent

(2010) Elizabeth S. Allman et al.   JOURNAL OF MATHEMATICAL BIOLOGY

What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?

(2009) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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