Conserved Genes, Sampling Error, and Phylogenomic Inference

Capturing protein-coding genes across highly divergent species

(2016) Chenhong Li et al.   BIOTECHNIQUES

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

(2013) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

(2013) Jenna Morgan Lang et al.   PLoS One

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

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

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

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

Accuracy and Precision of Species Trees: Effects of Locus, Individual, and Base Pair Sampling on Inference of Species Trees in Lizards of the Liolaemus darwinii Group (Squamata, Liolaemidae)

(2011) Arley Camargo et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS 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

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

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

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

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Dealing with incongruence in phylogenomic analyses

(2008) N. Galtier et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence

(2008) Jerome C. Regier et al.   SYSTEMATIC BIOLOGY

Resolving an Ancient, Rapid Radiation in Saxifragales

(2008) Shuguang Jian et al.   SYSTEMATIC BIOLOGY

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

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

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

(2008) Chenhong Li et al.   SYSTEMATIC BIOLOGY