Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling
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Title
Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling
Authors
Keywords
-
Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 40, Issue 8, Pages -
Publisher
Oxford University Press (OUP)
Online
2023-08-09
DOI
10.1093/molbev/msad175
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Note: Only part of the references are listed.- Ancient gene linkages support ctenophores as sister to other animals
- (2023) Darrin T. Schultz et al. NATURE
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- (2022) Harris A. Lewin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Deeply conserved synteny and the evolution of metazoan chromosomes
- (2022) Oleg Simakov et al. Science Advances
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- (2022) Megan L. Smith et al. MOLECULAR BIOLOGY AND EVOLUTION
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- (2022) Christoph G. Höpel et al. ZOOLOGICA SCRIPTA
- Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods
- (2022) Emily A Ellis et al. SYSTEMATIC BIOLOGY
- Resolving tricky nodes in the tree of life through amino acid recoding
- (2022) Mattia Giacomelli et al. iScience
- PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
- (2021) Jacob L Steenwyk et al. BIOINFORMATICS
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- (2021) Nicolás Mongiardino Koch MOLECULAR BIOLOGY AND EVOLUTION
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- (2021) Yuanning Li et al. MOLECULAR BIOLOGY AND EVOLUTION
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- (2021) Cassandra Koga et al. Diversity-Basel
- The dynamics of stem and crown groups
- (2020) Graham E. Budd et al. Science Advances
- Hemiptera phylogenomic resources: tree‐based orthology prediction and conserved exon identification
- (2020) Christopher L. Owen et al. Molecular Ecology Resources
- A Cambrian–Ordovician Terrestrialization of Arachnids
- (2020) Jesus Lozano-Fernandez et al. Frontiers in Genetics
- Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks
- (2020) Graham E. Budd et al. Interface Focus
- New Approaches for Inferring Phylogenies in the Presence of Paralogs
- (2020) Megan L. Smith et al. TRENDS IN GENETICS
- The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
- (2020) Benny K K Chan et al. ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
- A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
- (2019) Joanna M. Wolfe et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees
- (2019) Mark N Puttick BIOINFORMATICS
- Pancrustacean evolution illuminated by taxon-rich genomic-scale data sets with an expanded remipede sampling
- (2019) Jesus Lozano-Fernandez et al. Genome Biology and Evolution
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- (2019) Christopher E. Laumer et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Exceptional preservation of comma shrimp from a mid-Cretaceous Lagerstätte of Colombia, and the origins of crown Cumacea
- (2019) Javier Luque et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
- (2018) Chao Zhang et al. BMC BIOINFORMATICS
- Earth BioGenome Project: Sequencing life for the future of life
- (2018) Harris A. Lewin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Early fossil record of Euarthropoda and the Cambrian Explosion
- (2018) Allison C. Daley et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The biomass distribution on Earth
- (2018) Yinon M. Bar-On et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics
- (2018) Martin Schwentner et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Three-Dimensionally Preserved Appendages in an Early Cambrian Stem-Group Pancrustacean
- (2018) Dayou Zhai et al. CURRENT BIOLOGY
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- (2018) Ricardo Betancur‐R. et al. EVOLUTION
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- (2017) Joanna M. Wolfe INTEGRATIVE AND COMPARATIVE BIOLOGY
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- (2017) Thibaut Jombart et al. Molecular Ecology Resources
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- (2017) Jose Barba-Montoya et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
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- (2017) Joseph W Brown et al. SYSTEMATIC BIOLOGY
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- (2014) Lam-Tung Nguyen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Statistical binning enables an accurate coalescent-based estimation of the avian tree
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- (2014) Siavash Mirarab et al. SYSTEMATIC BIOLOGY
- Naive binning improves phylogenomic analyses
- (2013) Md Shamsuzzoha Bayzid et al. BIOINFORMATICS
- Agalma: an automated phylogenomics workflow
- (2013) Casey W Dunn et al. BMC BIOINFORMATICS
- Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages
- (2013) Joanna M. Wolfe et al. CLADISTICS
- Molecular Timetrees Reveal a Cambrian Colonization of Land and a New Scenario for Ecdysozoan Evolution
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- (2013) Michael S.Y. Lee et al. CURRENT BIOLOGY
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- (2013) Alexandra S. Petrunina et al. JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
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- Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees
- (2013) Michael DeGiorgio et al. SYSTEMATIC BIOLOGY
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- (2013) Nicolas Lartillot et al. SYSTEMATIC BIOLOGY
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- (2012) Limin Fu et al. BIOINFORMATICS
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- (2012) Todd H. Oakley et al. MOLECULAR BIOLOGY AND EVOLUTION
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- (2011) Jørgen Olesen et al. ARTHROPOD STRUCTURE & DEVELOPMENT
- A new view of insect–crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics
- (2011) David R. Andrew ARTHROPOD STRUCTURE & DEVELOPMENT
- Exploring uncertainty in the calibration of the molecular clock
- (2011) R. C. M. Warnock et al. Biology Letters
- The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
- (2011) A. R. Nabhan et al. BRIEFINGS IN BIOINFORMATICS
- Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda
- (2011) B. M. von Reumont et al. MOLECULAR BIOLOGY AND EVOLUTION
- Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
- (2011) M. d. Reis et al. MOLECULAR BIOLOGY AND EVOLUTION
- Resolving the evolutionary relationships of molluscs with phylogenomic tools
- (2011) Stephen A. Smith et al. NATURE
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- (2011) Manfred G Grabherr et al. NATURE BIOTECHNOLOGY
- Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
- (2010) Jerome C. Regier et al. NATURE
- OMA 2011: orthology inference among 1000 complete genomes
- (2010) A. M. Altenhoff et al. NUCLEIC ACIDS RESEARCH
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- 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
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
- (2009) Adrian M. Altenhoff et al. PLoS Computational Biology
- First maxillae suction discs in Branchiura (Crustacea): Development and evolution in light of the first molecular phylogeny of Branchiura, Pentastomida, and other “Maxillopoda”
- (2008) O.S. Møller et al. ARTHROPOD STRUCTURE & DEVELOPMENT
- Phyutility: a phyloinformatics tool for trees, alignments and molecular data
- (2008) S. A. Smith et al. BIOINFORMATICS
- Empirical profile mixture models for phylogenetic reconstruction
- (2008) Le Si Quang et al. BIOINFORMATICS
- Broad phylogenomic sampling improves resolution of the animal tree of life
- (2008) Casey W. Dunn et al. NATURE
- Graph Clustering Via a Discrete Uncoupling Process
- (2008) Stijn Van Dongen SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS
- Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence
- (2008) Jerome C. Regier et al. SYSTEMATIC BIOLOGY
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