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

When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

(2015) Shea M. Lambert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Coalescent methods for estimating species trees from phylogenomic data

(2015) Liang Liu et al.   Journal of Systematics and Evolution

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)

(2014) R. Alexander Pyron et al.   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

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

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang 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

Land plant origins and coalescence confusion

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

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

(2013) R Pyron et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Anomalous Unrooted Gene Trees

(2013) James H. Degnan   SYSTEMATIC BIOLOGY

Conserved Genes, Sampling Error, and Phylogenomic Inference

(2013) Ricardo Betancur-R. et al.   SYSTEMATIC BIOLOGY

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

(2012) J. J. Wiens et al.   Biology Letters

A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees

(2012) James H. Degnan et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles

(2012) Daniel G. Mulcahy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

The phylogenetic systematics of blue-tailed skinks (Plestiodon) and the family Scincidae

(2012) MATTHEW C. BRANDLEY et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

Lygosomine phylogeny and the origins of Australian scincid lizards

(2011) Adam Skinner et al.   JOURNAL OF BIOGEOGRAPHY

The probability distribution of ranked gene trees on a species tree

(2011) James H. Degnan et al.   MATHEMATICAL BIOSCIENCES

Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveals underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification

(2011) Cameron D. Siler et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships

(2011) CHARLES W. LINKEM et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Bayesian species delimitation using multilocus sequence data

(2010) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coalescent histories for discordant gene trees and species trees

(2010) Noah A. Rosenberg et al.   THEORETICAL POPULATION BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Maximum tree: a consistent estimator of the species tree

(2009) Liang Liu et al.   JOURNAL OF MATHEMATICAL BIOLOGY

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

(2009) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design

(2009) John E. McCormack et al.   SYSTEMATIC BIOLOGY

Phylogenetic Analysis in the Anomaly Zone

(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

Rapid and repeated limb loss in a clade of scincid lizards

(2008) Adam Skinner et al.   BMC EVOLUTIONARY BIOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors

(2008) Ralph Burgess et al.   MOLECULAR BIOLOGY AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Discordance of Species Trees with Their Most Likely Gene Trees: The Case of Five Taxa

(2008) Noah A. Rosenberg et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Supertrees

(2008) Mike Steel et al.   SYSTEMATIC BIOLOGY

Analysis of 142 genes resolves the rapid diversification of the rice genus

(2008) Xin-Hui Zou et al.   GENOME BIOLOGY