Addressing Gene Tree Discordance and Non-Stationarity to Resolve a Multi-Locus Phylogeny of the Flatfishes (Teleostei: Pleuronectiformes)

Osteology of †Heteronectes chaneti(Acanthomorpha, Pleuronectiformes), an Eocene stem flatfish, with a discussion of flatfish sister-group relationships

(2012) Matt Friedman   JOURNAL OF VERTEBRATE PALEONTOLOGY

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study

(2012) Omar Rota-Stabelli et al.   SYSTEMATIC BIOLOGY

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

(2011) Béatrice Roure et al.   BMC EVOLUTIONARY BIOLOGY

PhyDesign: an online application for profiling phylogenetic informativeness

(2011) Francesc López-Giráldez et al.   BMC EVOLUTIONARY BIOLOGY

COALESCENT-BASED SPECIES TREE INFERENCE FROM GENE TREE TOPOLOGIES UNDER INCOMPLETE LINEAGE SORTING BY MAXIMUM LIKELIHOOD

(2011) Yufeng Wu   EVOLUTION

Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria

(2011) Apurva Narechania et al.   Genome Biology and Evolution

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

Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics

(2011) B. Nabholz et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Monophyly and interrelationships of Snook and Barramundi (Centropomidae sensu Greenwood) and five new markers for fish phylogenetics

(2011) Chenhong Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Generalized Mixture Models for Molecular Phylogenetic Estimation

(2011) Jason Evans et al.   SYSTEMATIC BIOLOGY

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Data Sets

(2010) N. M. Evans et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary affinity of billfishes (Xiphiidae and Istiophoridae) and flatfishes (Plueronectiformes): Independent and trans-subordinal origins of endothermy in teleost fishes

(2010) A.G. Little et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The phylogenetic placement of sinipercid fishes (“Perciformes”) revealed by 11 nuclear loci

(2010) Chenhong Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

(2010) C. T. Hittinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Species Delimitation Using a Combined Coalescent and Information-Theoretic Approach: An Example from North American Myotis Bats

(2010) Bryan C. Carstens et al.   SYSTEMATIC BIOLOGY

When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics

(2010) HOJUN SONG et al.   SYSTEMATIC ENTOMOLOGY

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Bayesian Inference of Species Trees from Multilocus Data

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

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics

(2009) Nathan C. Sheffield 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

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Phylogenetic analysis of the order Pleuronectiformes (Teleostei) based on sequences of 12S and 16S mitochondrial genes

(2008) Marisa F.C. Azevedo et al.   GENETICS AND MOLECULAR BIOLOGY

New insights into the organization and evolution of vertebrate IRBP genes and utility of IRBP gene sequences for the phylogenetic study of the Acanthomorpha (Actinopterygii: Teleostei)

(2008) Agnès Dettaï et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RNF213, a new nuclear marker for acanthomorph phylogeny

(2008) Blaise Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The evolutionary origin of flatfish asymmetry

(2008) Matt Friedman   NATURE

Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci

(2008) Chenhong Li et al.   SYSTEMATIC BIOLOGY

Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts

(2007) Ryouka Kawahara et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION