Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction
Authors
Keywords
-
Journal
SYSTEMATIC BIOLOGY
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-07-31
DOI
10.1093/sysbio/syaa063
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects
- (2019) Benjamin Wipfler et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization
- (2019) John Yin et al. BIOINFORMATICS
- Statistical binning leads to profound model violation due to gene tree error incurred by trying to avoid gene tree error
- (2019) Richard H. Adams et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores)
- (2019) Noor D. White 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
- TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees
- (2018) Uyen Mai et al. BMC GENOMICS
- Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life
- (2018) Rosa Fernández et al. CURRENT BIOLOGY
- Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements
- (2018) Princess S. Gilbert et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- On the universality of target-enrichment baits for phylogenomic research
- (2018) Silas Bossert et al. Methods in Ecology and Evolution
- Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization
- (2018) Ruth B. McCole et al. Cell Reports
- Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary
- (2018) Michael E. Alfaro et al. Nature Ecology & Evolution
- Advancing mite phylogenomics: Designing ultraconserved elements for acari phylogeny
- (2018) Matthew H. Van Dam et al. Molecular Ecology Resources
- Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae
- (2018) Silas Bossert et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event
- (2018) Kevin Winker et al. PeerJ
- Ultraconserved Sequences Associated with HoxD Cluster Have Strong Repression Activity
- (2017) Gopal Kushawah et al. Genome Biology and Evolution
- Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements
- (2017) Jacob A. Esselstyn et al. Genome Biology and Evolution
- On the independent gene trees assumption in phylogenomic studies
- (2017) W. Bryan Jennings MOLECULAR ECOLOGY
- Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems
- (2017) Andrea M. Quattrini et al. Molecular Ecology Resources
- De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
- (2017) Olga Dudchenko et al. SCIENCE
- To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
- (2017) Erin K Molloy et al. SYSTEMATIC BIOLOGY
- Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics
- (2017) Scott V. Edwards et al. SYSTEMATIC BIOLOGY
- Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils
- (2017) Matthew H. Van Dam et al. PLoS One
- Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye
- (2016) Richard C. Harrington et al. BMC EVOLUTIONARY BIOLOGY
- Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
- (2016) Erfan Sayyari et al. MOLECULAR BIOLOGY AND EVOLUTION
- An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)
- (2016) Daniel M. Portik et al. Molecular Ecology Resources
- Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
- (2016) Scott V. Edwards et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Tectonic collision and uplift of Wallacea triggered the global songbird radiation
- (2016) Robert G. Moyle et al. Nature Communications
- RPANDA: an R package for macroevolutionary analyses on phylogenetic trees
- (2016) Hélène Morlon et al. Methods in Ecology and Evolution
- A New Chicken Genome Assembly Provides Insight into Avian Genome Structure
- (2016) Wesley C. Warren et al. G3-Genes Genomes Genetics
- Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens
- (2016) Bonnie B. Blaimer et al. PLoS One
- Estimating phylogenetic trees from genome-scale data
- (2015) Liang Liu et al. Annals of the New York Academy of Sciences
- ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
- (2015) Siavash Mirarab et al. BIOINFORMATICS
- PHYLUCE is a software package for the analysis of conserved genomic loci
- (2015) Brant C. Faircloth BIOINFORMATICS
- Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa
- (2015) Marek L. Borowiec et al. BMC GENOMICS
- Characterizing and Comparing Phylogenies from their Laplacian Spectrum
- (2015) Eric Lewitus et al. SYSTEMATIC BIOLOGY
- SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees
- (2015) Diego Mallo et al. SYSTEMATIC BIOLOGY
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)
- (2014) Gong-Hua Lin et al. BMC GENOMICS
- Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
- (2014) Brant C. Faircloth et al. Molecular Ecology Resources
- 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
- The Inference of Gene Trees with Species Trees
- (2014) Gergely J. Szöllősi et al. SYSTEMATIC BIOLOGY
- Abnormal Dosage of Ultraconserved Elements Is Highly Disfavored in Healthy Cells but Not Cancer Cells
- (2014) Ruth B. McCole et al. PLoS Genetics
- Naive binning improves phylogenomic analyses
- (2013) Md Shamsuzzoha Bayzid et al. BIOINFORMATICS
- Unlocking the vault: next-generation museum population genomics
- (2013) Ke Bi et al. MOLECULAR ECOLOGY
- A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)
- (2013) Brant C. Faircloth et al. PLoS One
- Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements
- (2012) S. Dimitrieva et al. BIOINFORMATICS
- PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
- (2012) R. Lanfear et al. MOLECULAR BIOLOGY AND EVOLUTION
- Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
- (2012) Alan R. Lemmon et al. SYSTEMATIC BIOLOGY
- Is Recombination a Problem for Species-Tree Analyses?
- (2012) Hayley C. Lanier et al. SYSTEMATIC BIOLOGY
- Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
- (2012) Brant C. Faircloth et al. SYSTEMATIC BIOLOGY
- The Many Landscapes of Recombination in Drosophila melanogaster
- (2012) Josep M. Comeron et al. PLoS Genetics
- 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
- phangorn: phylogenetic analysis in R
- (2010) Klaus Peter Schliep BIOINFORMATICS
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- The earliest beetle identified
- (2009) Olivier Béthoux JOURNAL OF PALEONTOLOGY
- Bootstrap Support Is Not First-Order Correct
- (2009) Edward Susko SYSTEMATIC BIOLOGY
- Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data
- (2008) T.-K. Seo MOLECULAR BIOLOGY AND EVOLUTION
Become a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get StartedAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started