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Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/bf00182392openalex-snapshot
Substitutional bias confounds inference of cyanelle origins from sequence data
inferredcites →https://doi.org/10.1007/bf01215182openalex-snapshot
Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes
inferredcites →https://doi.org/10.1007/bf02101990openalex-snapshot
A new method for calculating evolutionary substitution rates
inferredcites →https://doi.org/10.1007/pl00006145openalex-snapshot
Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria
inferredcites →https://doi.org/10.1007/pl00006471openalex-snapshot
Compositional Bias May Affect Both DNA-Based and Protein-Based Phylogenetic Reconstructions
inferredcites →https://doi.org/10.1016/j.tig.2006.02.003openalex-snapshot
Phylogenomics: the beginning of incongruence?
inferredcites →https://doi.org/10.1016/j.ympev.2006.03.020openalex-snapshot
Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
inferredcites →https://doi.org/10.1016/j.ympev.2006.04.021openalex-snapshot
Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch
inferredcites →https://doi.org/10.1016/j.ympev.2009.01.011openalex-snapshot
MtZoa: A general mitochondrial amino acid substitutions model for animal evolutionary studies
inferredcites →https://doi.org/10.1016/s0378-1119(99)00270-xopenalex-snapshot
Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system
inferredcites →https://doi.org/10.1016/s0723-2020(11)80247-xopenalex-snapshot
Reduced Thermophilic Bias in the 16S rDNA Sequence from Thermus ruber Provides Further Support for a Relationship Between Thermus and Deinococcus
inferredcites →https://doi.org/10.1016/s0723-2020(11)80311-5openalex-snapshot
Archaeal Phylogeny: Reexamination of the Phylogenetic Position of Archaeoglohus fulgidus in Light of Certain Composition-induced Artifacts
inferredcites →https://doi.org/10.1038/nature03149openalex-snapshot
Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I
inferredcites →https://doi.org/10.1038/nature08742openalex-snapshot
Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
inferredcites →https://doi.org/10.1073/pnas.0306212101openalex-snapshot
The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships
inferredcites →https://doi.org/10.1073/pnas.0910915107openalex-snapshot
Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles
inferredcites →https://doi.org/10.1073/pnas.1105499108openalex-snapshot
MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda
inferredcites →https://doi.org/10.1073/pnas.92.24.11317openalex-snapshot
Inferring phylogenies from DNA sequences of unequal base compositions.
inferredcites →https://doi.org/10.1080/10635150490445779openalex-snapshot
Modeling Compositional Heterogeneity
inferredcites →https://doi.org/10.1080/10635150490468648openalex-snapshot
The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated
inferredcites →https://doi.org/10.1080/10635150490468756openalex-snapshot
Phylogenetic Artifacts Can be Caused by Leucine, Serine, and Arginine Codon Usage Heterogeneity: Dinoflagellate Plastid Origins as a Case Study
inferredcites →https://doi.org/10.1080/10635150701397643openalex-snapshot
Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
inferredcites →https://doi.org/10.1080/10635150802570791openalex-snapshot
Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence
inferredcites →https://doi.org/10.1093/bioinformatics/14.4.372openalex-snapshot
GCUA: general codon usage analysis.
inferredcites →https://doi.org/10.1093/bioinformatics/8.3.275openalex-snapshot
The rapid generation of mutation data matrices from protein sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btg427openalex-snapshot
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
inferredcites →https://doi.org/10.1093/bioinformatics/btl446openalex-snapshot
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/btp368openalex-snapshot
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
inferredcites →https://doi.org/10.1093/gbe/evq030openalex-snapshot
Ecdysozoan Mitogenomics: Evidence for a Common Origin of the Legged Invertebrates, the Panarthropoda
inferredcites →https://doi.org/10.1093/molbev/msh112openalex-snapshot
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
inferredcites →https://doi.org/10.1093/molbev/msi012openalex-snapshot
A Comprehensive Analysis of Mammalian Mitochondrial Genome Base Composition and Improved Phylogenetic Methods
inferredcites →https://doi.org/10.1093/molbev/msn018openalex-snapshot
A Site- and Time-Heterogeneous Model of Amino Acid Replacement
inferredcites →https://doi.org/10.1093/molbev/msn067openalex-snapshot
An Improved General Amino Acid Replacement Matrix
inferredcites →https://doi.org/10.1093/molbev/msp186openalex-snapshot
Hemocyanin Suggests a Close Relationship of Remipedia and Hexapoda
inferredcites →https://doi.org/10.1093/molbev/msq130openalex-snapshot
A Phylogenomic Approach to Resolve the Arthropod Tree of Life
inferredcites →https://doi.org/10.1093/molbev/msr270openalex-snapshot
Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025888openalex-snapshot
Models of amino acid substitution and applications to mitochondrial protein evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026166openalex-snapshot
Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040220openalex-snapshot
On the use of nucleic acid sequences to infer early branchings in the tree of life.
inferredcites →https://doi.org/10.1093/sysbio/syp015openalex-snapshot
Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences
inferredcites →https://doi.org/10.1093/sysbio/syr064openalex-snapshot
A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases
inferredcites →https://doi.org/10.1098/rspb.2004.2917openalex-snapshot
Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic
inferredcites →https://doi.org/10.1098/rspb.2004.3042openalex-snapshot
Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic
inferredcites →https://doi.org/10.1098/rspb.2010.0590openalex-snapshot
A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata
inferredcites →https://doi.org/10.1098/rstb.2008.0162openalex-snapshot
Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes
inferredcites →https://doi.org/10.1098/rstb.2009.0034openalex-snapshot
The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods
inferredcites →https://doi.org/10.1111/j.2517-6161.1974.tb00994.xopenalex-snapshot
Cross-Validatory Choice and Assessment of Statistical Predictions
inferredcites →https://doi.org/10.1126/science.287.5456.1283openalex-snapshot
Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions
inferredcites →https://doi.org/10.1186/1471-2148-9-119openalex-snapshot
Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships
inferredcites →https://doi.org/10.1371/journal.pone.0023408openalex-snapshot
Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods
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Origins and early evolution of arthropods
inferred← citeshttps://doi.org/10.1111/syen.12115openalex-snapshot
A new extant family of primitive moths from K angaroo I sland, A ustralia, and its significance for understanding early L epidoptera evolution
inferred← citeshttps://doi.org/10.1111/syen.12257openalex-snapshot
Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles ( C erambycidae)
inferred← citeshttps://doi.org/10.1111/syen.12569openalex-snapshot
A genome‐wide phylogeny and the diversification of genus Liriomyza (Diptera: Agromyzidae) inferred from anchored phylogenomics
inferred← citeshttps://doi.org/10.1111/syen.12573openalex-snapshot
Systematics and evolution of predatory flower flies (Diptera: Syrphidae) based on exon‐capture sequencing
inferred← citeshttps://doi.org/10.1111/syen.12582openalex-snapshot
Phylogeny of the flea beetles (Galerucinae: Alticini) and the position of Aulacothorax elucidated through anchored phylogenomics (Coleoptera: Chrysomelidae: Alticini)
inferred← citeshttps://doi.org/10.1111/syen.12684openalex-snapshot
Inconsistent performance of multi‐type genomic data in phylogenomics of neuropteridan insects, with solutions toward conflicting results
inferred← citeshttps://doi.org/10.1111/zsc.12246openalex-snapshot
Gene rearrangement and sequence analysis of mitogenomes suggest polyphyly of Archaeobalanid and Balanid barnacles (Cirripedia: Balanomorpha)
inferred← citeshttps://doi.org/10.1111/zsc.12412openalex-snapshot
Mitogenomic phylogeny of the Naticidae (Gastropoda: Littorinimorpha) reveals monophyly of the Polinicinae
inferred← citeshttps://doi.org/10.1146/annurev-ecolsys-120213-091824openalex-snapshot
The Phylogeny and Evolution of Ants
inferred← citeshttps://doi.org/10.1155/jzs/8718127openalex-snapshot
Cryptic Diversity in the Slender Walking Catfish Inferred From Mitogenomes and DNA Barcodes Reveals a Clarias nieuhofii Species Complex Across Sundaland
inferred← citeshttps://doi.org/10.1177/1176934320903735openalex-snapshot
Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates
inferred← citeshttps://doi.org/10.1186/1471-2105-15-183openalex-snapshot
L.U.St: a tool for approximated maximum likelihood supertree reconstruction
inferred← citeshttps://doi.org/10.1186/1471-2105-15-s2-s8openalex-snapshot
Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics
inferred← citeshttps://doi.org/10.1186/1471-2148-13-5openalex-snapshot
Cnidarian phylogenetic relationships as revealed by mitogenomics
inferred← citeshttps://doi.org/10.1186/1471-2148-14-44openalex-snapshot
Evolutionary relationships of the Critically Endangered frog Ericabatrachus baleensisLargen, 1991 with notes on incorporating previously unsampled taxa into large-scale phylogenetic analyses
inferred← citeshttps://doi.org/10.1186/1471-2164-15-857openalex-snapshot
Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species
inferred← citeshttps://doi.org/10.1186/s12862-014-0211-2openalex-snapshot
Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae
inferred← citeshttps://doi.org/10.1186/s12864-018-4650-9openalex-snapshot
Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera)
inferred← citeshttps://doi.org/10.1186/s12864-026-12794-9openalex-snapshot
Chromosome-level genome assembly of the common tenrec, Tenrec ecaudatus (Schreber, 1778), a new model for early placental mammal evolution
inferred← citeshttps://doi.org/10.1371/journal.pbio.2005359openalex-snapshot
Comparative genomics and the nature of placozoan species
inferred← citeshttps://doi.org/10.1371/journal.pone.0107709openalex-snapshot
Strepsiptera, Phylogenomics and the Long Branch Attraction Problem
inferred← citeshttps://doi.org/10.1371/journal.pone.0123331openalex-snapshot
Phylogenetic Signal Dissection Identifies the Root of Starfishes
inferred← citeshttps://doi.org/10.1371/journal.pone.0333693openalex-snapshot
Complete mitogenomes of two major dengue vectors Aedes aegypti and Aedes albopictus from Bangladesh: Insights from comparative genomics with global mitogenome diversity and phylogenetics
inferred← citeshttps://doi.org/10.15298/arthsel.30.1.04openalex-snapshot
Low support values and lack of reproducibility of molecular phylogenetic analysis of Copepoda orders
inferred← citeshttps://doi.org/10.19004/taxa.51.0_42openalex-snapshot
カイアシ類の高次分類群の系統に関するコメント：Khodami et al. (2017) の分子系統に関する論文取り下げを受けて
inferred← citeshttps://doi.org/10.2216/14-002.1openalex-snapshot
Molecular phylogeny of the Cymbellales (Bacillariophyceae, Heterokontophyta) with a comparison of models for accommodating rate variation across sites
inferred← citeshttps://doi.org/10.3389/fevo.2024.1243221openalex-snapshot
Incomplete lineage sorting and long-branch attraction confound phylogenomic inference of Pancrustacea
inferred← citeshttps://doi.org/10.3389/fmars.2021.681966openalex-snapshot
Glycogen Synthase Kinase 3 Gene Is Important in Growth and Molting of the Pacific White Shrimp Litopenaeus vannamei
inferred← citeshttps://doi.org/10.3389/fmars.2024.1425922openalex-snapshot
Phylogenetic relationships and lineage-specific mitochondrial gene rearrangement in Ophiuroidea: insights from mitochondrial genomes
inferred← citeshttps://doi.org/10.3390/biology11101516openalex-snapshot
Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization
inferred← citeshttps://doi.org/10.3390/cimb45020054openalex-snapshot
Conflicts in Mitochondrial Phylogenomics of Branchiopoda, with the First Complete Mitogenome of Laevicaudata (Crustacea: Branchiopoda)
inferred← citeshttps://doi.org/10.3390/genes10100820openalex-snapshot
The Complete Mitogenome of Pyrrhocoris tibialis (Hemiptera: Pyrrhocoridae) and Phylogenetic Implications
inferred← citeshttps://doi.org/10.3390/life10090171openalex-snapshot
Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration
inferred← citeshttps://doi.org/10.48550/arxiv.1307.1586openalex-snapshot
Evaluating strategies of phylogenetic analyses by the coherence of their results
inferred← citeshttps://doi.org/10.5539/jas.v9n9p56openalex-snapshot
Codon Usage Bias of the Wheat Flower Development Gene WAG-2 and Other AGAMOUS Group Genes
inferred← citeshttps://doi.org/10.58837/chula.the.2018.5openalex-snapshot
Functional characterization of heat shock proteins during stress response in pacific white shrimp Penaeus vannamei and brine shrimp Artemia franciscana
inferred← citeshttps://doi.org/10.70675/0c4cc8b0z8e9az4885zbf8cz03721e8218aeopenalex-snapshot
Une fenêtre évolutive sur la terrestrialisation des arthropodes : étude des Myriapodes du gisement à préservation exceptionnelle de Montceau-les-Mines (Carbonifère, 305 Ma)
inferred← citeshttps://doi.org/10.7287/peerj.10312v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10312v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10312v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10312v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.10312v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.10312v0.3/reviews/2openalex-snapshot
Peer Review #2 of "Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect (v0.3)"
inferred← citeshttps://doi.org/10.7287/peerj.10312v0.3/reviews/3openalex-snapshot
Peer Review #3 of "Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect (v0.3)"
inferred← citeshttps://doi.org/10.7287/peerj.10312v0.4/reviews/2openalex-snapshot
Peer Review #2 of "Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect (v0.4)"
inferred← citeshttps://doi.org/10.7287/peerj.2982v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.2982v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.2982v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.2982v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.2982v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.2982v0.2/reviews/3openalex-snapshot
Peer Review #3 of "Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda) (v0.2)"
inferred← citeshttps://doi.org/10.7554/elife.36278openalex-snapshot
Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
inferred← citeshttps://doi.org/10.7717/peerj.10312openalex-snapshot
Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect
inferred← citeshttps://doi.org/10.7717/peerj.2982openalex-snapshot
Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda)
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