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Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria

https://doi.org/10.1007/pl00006145
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Codon bias in actin multigene families and effects on the reconstruction of phylogenetic relationships
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Substitutional bias confounds inference of cyanelle origins from sequence data
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Silent nucleotide substitutions and G+C content of some mitochondrial and bacterial genes
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Correlation between codon usage, regional genomic nucleotide composition, and amino acid composition in the cytochrome P-450 gene superfamily
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Ribosomal RNA trees misleading?
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Confidence in evolutionary trees from biological sequence data
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The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins
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Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia.
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Evidence from Analyses of Intergenic Regions for Strand-specific Directional Mutation Pressure in Metazoan Mitochondrial DNA
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Phylogenetic place of mitochondrion-lacking protozoan, Giardia lamblia, inferred from amino acid sequences of elongation factor 2.
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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Nucleotide Bias Causes a Genomewide Bias in the Amino Acid Composition of Proteins
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An Unusual Form of Purifying Selection in a Sperm Protein
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026360openalex-snapshot
The Complete Mitochondrial DNA Sequence of the Horseshoe Crab Limulus polyphemus
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026366openalex-snapshot
The Complete Sequence of the Mitochondrial Genome of the Crustacean Penaeus monodon: Are Malacostracan Crustaceans More Closely Related to Insects than to Branchiopods?
inferred← citeshttps://doi.org/10.1093/sysbio/syaa075openalex-snapshot
Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets
inferred← citeshttps://doi.org/10.1093/sysbio/syad013openalex-snapshot
Compositionally Constrained Sites Drive Long-Branch Attraction
inferred← citeshttps://doi.org/10.1093/sysbio/syad036openalex-snapshot
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies
inferred← citeshttps://doi.org/10.1093/sysbio/sys042openalex-snapshot
Is the General Time-Reversible Model Bad for Molecular Phylogenetics?
inferred← citeshttps://doi.org/10.1093/sysbio/sys077openalex-snapshot
Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study
inferred← citeshttps://doi.org/10.1099/mic.0.26381-0openalex-snapshot
Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia
inferred← citeshttps://doi.org/10.1101/2022.03.03.482715openalex-snapshot
Compositionally Constrained Sites Drive Long Branch Attraction
inferred← citeshttps://doi.org/10.1101/2025.07.14.663642openalex-snapshot
WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
inferred← citeshttps://doi.org/10.1111/1744-7917.12326openalex-snapshot
The complete mitochondrial genome ofAnopheles minimus(Diptera: Culicidae) and the phylogenetics of knownAnophelesmitogenomes
inferred← citeshttps://doi.org/10.1111/1755-0998.13160openalex-snapshot
MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics
inferred← citeshttps://doi.org/10.1111/cla.12396openalex-snapshot
Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales
inferred← citeshttps://doi.org/10.1111/imb.12838openalex-snapshot
Evolution of mitogenomic gene order in Orthoptera
inferred← citeshttps://doi.org/10.1111/j.1095-8312.2004.00396.xopenalex-snapshot
The gall-inducing habit has evolved multiple times among the eriococcid scale insects (Sternorrhyncha: Coccoidea: Eriococcidae)
inferred← citeshttps://doi.org/10.1111/nph.19099openalex-snapshot
Compositional shifts associated with major evolutionary transitions in plants
inferred← citeshttps://doi.org/10.1139/g2012-005openalex-snapshot
The first mitochondrial genome for the wasp superfamily Platygastroidea: the egg parasitoidTrissolcus basalis
inferred← citeshttps://doi.org/10.1139/gen-2014-0158openalex-snapshot
The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium
inferred← citeshttps://doi.org/10.1159/000297715openalex-snapshot
From Reptilian Phylogenomics to Reptilian Genomes: Analyses of c-Jun and DJ-1 Proto-Oncogenes
inferred← citeshttps://doi.org/10.11606/d.41.2002.tde-06052002-110339openalex-snapshot
Seqüenciamento e análise do genoma mitocondrial de Melipona bicolor (Hymenoptera, Apidae, Meliponini).
inferred← citeshttps://doi.org/10.11646/zootaxa.3995.1.4openalex-snapshot
Antonbruunia sociabilis sp. nov. (Annelida: Antonbruunidae) associated with the chemosynthetic deep-sea bivalve Thyasira scotiae Oliver & Drewery, 2014, and a re-examination of the systematic affinities of Antonbruunidae
inferred← citeshttps://doi.org/10.1186/1471-2148-14-139openalex-snapshot
Molecular evolution of NASP and conserved histone H3/H4 transport pathway
inferred← citeshttps://doi.org/10.1186/1471-2148-7-16openalex-snapshot
Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus
inferred← citeshttps://doi.org/10.1186/1471-2148-8-108openalex-snapshot
Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria
inferred← citeshttps://doi.org/10.1186/1471-2148-8-165openalex-snapshot
Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: Evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection
inferred← citeshttps://doi.org/10.1186/1471-2148-8-255openalex-snapshot
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
inferred← citeshttps://doi.org/10.1186/1471-2164-12-572openalex-snapshot
The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships
inferred← citeshttps://doi.org/10.1186/1745-6150-5-63openalex-snapshot
Modeling compositional dynamics based on GC and purine contents of protein-coding sequences
inferred← citeshttps://doi.org/10.1186/gb-2001-2-4-research0010openalex-snapshot
A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
inferred← citeshttps://doi.org/10.1186/gb-2004-5-10-117openalex-snapshot
Genomic and proteomic adaptations to growth at high temperature.
inferred← citeshttps://doi.org/10.1186/gb-2005-6-11-r91openalex-snapshot
Do universal codon-usage patterns minimize the effects of mutation and translation error?
inferred← citeshttps://doi.org/10.1186/s12870-015-0543-0openalex-snapshot
Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events
inferred← citeshttps://doi.org/10.12692/ijb/3.9.248-258openalex-snapshot
Genetic diversity of Tribolium castaneum (Herbst) population in storage infrastructures and agro ecological zones in Senegal
inferred← citeshttps://doi.org/10.1371/journal.pbio.3002577openalex-snapshot
How do bacterial endosymbionts work with so few genes?
inferred← citeshttps://doi.org/10.1371/journal.pone.0019449openalex-snapshot
Systematic and Evolutionary Insights Derived from mtDNA COI Barcode Diversity in the Decapoda (Crustacea: Malacostraca)
inferred← citeshttps://doi.org/10.1371/journal.pone.0030520openalex-snapshot
The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria
inferred← citeshttps://doi.org/10.1371/journal.pone.0056642openalex-snapshot
Causes and Implications of Codon Usage Bias in RNA Viruses
inferred← citeshttps://doi.org/10.1371/journal.pone.0068005openalex-snapshot
Arthropod Phylogenetics in Light of Three Novel Millipede (Myriapoda: Diplopoda) Mitochondrial Genomes with Comments on the Appropriateness of Mitochondrial Genome Sequence Data for Inferring Deep Level Relationships
inferred← citeshttps://doi.org/10.1371/journal.pone.0109140openalex-snapshot
Comparative Analysis of the Mitochondrial Genomes of Callitettixini Spittlebugs (Hemiptera: Cercopidae) Confirms the Overall High Evolutionary Speed of the AT-Rich Region but Reveals the Presence of Short Conservative Elements at the Tribal Level
inferred← citeshttps://doi.org/10.1371/journal.pone.0110381openalex-snapshot
Hydrophobicity and Aromaticity Are Primary Factors Shaping Variation in Amino Acid Usage of Chicken Proteome
inferred← citeshttps://doi.org/10.13918/j.issn.2095-8137.2014.6.537openalex-snapshot
Complete mitochondrial genome of yellow meal worm (Tenebrio molitor).
inferred← citeshttps://doi.org/10.1575/1912/108openalex-snapshot
North Brazil current rings experiment: mooring S1 data report, November 1998-June 2000
inferred← citeshttps://doi.org/10.1590/s0074-02762010000400027openalex-snapshot
Phylogenetic analysis of Biomphalaria tenagophila (Orbigny, 1835) (Mollusca: Gastropoda)
inferred← citeshttps://doi.org/10.1590/s1415-47572008000300010openalex-snapshot
The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini): sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini
inferred← citeshttps://doi.org/10.2108/zsj.30.570openalex-snapshot
Complete Coding Region of the Mitochondrial Genome ofMonochamus alternatusHope (Coleoptera: Cerambycidae)
inferred← citeshttps://doi.org/10.2200/s00360ed1v01y201105bme041openalex-snapshot
Computational Genomic Signatures
inferred← citeshttps://doi.org/10.3233/jad-231083openalex-snapshot
Molecular Dissection of Herpes Simplex Virus Type 1 to Elucidate Molecular Mechanisms Behind Latency and Comparison of Its Codon Usage Patterns with Genes Modulated During Alzheimer’s Disease as a Part of Host-Pathogen Interaction
inferred← citeshttps://doi.org/10.32920/14638440openalex-snapshot
Molecular evolution of NASP and conserved histone H3/H4 transport pathway
inferred← citeshttps://doi.org/10.32920/14638440.v1openalex-snapshot
Molecular evolution of NASP and conserved histone H3/H4 transport pathway
inferred← citeshttps://doi.org/10.32920/14638440.v2openalex-snapshot
Molecular evolution of NASP and conserved histone H3/H4 transport pathway
inferred← citeshttps://doi.org/10.32920/ryerson.14668284openalex-snapshot
Characterization of major chromatin assembly proteins in tetrahymena thermophile using proeomic and molecular evolutionary analyses
inferred← citeshttps://doi.org/10.32920/ryerson.14668284.v1openalex-snapshot
Characterization of major chromatin assembly proteins in tetrahymena thermophile using proeomic and molecular evolutionary analyses
inferred← citeshttps://doi.org/10.3389/fevo.2026.1774703openalex-snapshot
The amino acid composition of mammalian mitochondrial proteins correlates with generation time
inferred← citeshttps://doi.org/10.3389/fimmu.2019.01558openalex-snapshot
Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons
inferred← citeshttps://doi.org/10.3389/fpls.2022.873788openalex-snapshot
Nucleotide Evolution, Domestication Selection, and Genetic Relationships of Chloroplast Genomes in the Economically Important Crop Genus Gossypium
inferred← citeshttps://doi.org/10.3390/ani13121985openalex-snapshot
Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea)
inferred← citeshttps://doi.org/10.3390/ani13243841openalex-snapshot
Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae
inferred← citeshttps://doi.org/10.3390/ani14101454openalex-snapshot
Characterization of the Mitogenome of the Genus Dendrocerus Ratzeburg (Hymenoptera: Megaspilidae) with the Specific Designed Primers
inferred← citeshttps://doi.org/10.3390/biom12020171openalex-snapshot
Determination of the Amino Acid Recruitment Order in Early Life by Genome-Wide Analysis of Amino Acid Usage Bias
inferred← citeshttps://doi.org/10.3390/d18070430openalex-snapshot
DNA Barcoding of Flesh Flies (Diptera: Sarcophagidae) in Jamaica: A Preliminary Assessment
inferred← citeshttps://doi.org/10.3390/microorganisms11071833openalex-snapshot
Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa
inferred← citeshttps://doi.org/10.35537/10915/26202openalex-snapshot
Inferencia filogeográfica aplicada a la conservación de hembras partenogenéticas del género Aylacostoma Spix, 1827: especies amenazadas del río Paraná
inferred← citeshttps://doi.org/10.3724/sp.j.1002.2008.08016openalex-snapshot
Taxon sampling and the accuracy of phylogenetic analyses
inferred← citeshttps://doi.org/10.4238/2015.november.18.27openalex-snapshot
Short Communication Complete mitochondrial genome and codon usage of the Nepalese whiskered bat Myotis muricola (Vespertilionidae)
inferred← citeshttps://doi.org/10.4238/gmr16019300openalex-snapshot
Complete mitochondrial genome of the Amur hedgehog Erinaceus amurensis (Erinaceidae) and higher phylogeny of the family Erinaceidae
inferred← citeshttps://doi.org/10.6084/m9.figshare.40550openalex-snapshot
Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites and -2
inferred← citeshttps://doi.org/10.70675/088f0755z4f29z434czb21fze696e294b023openalex-snapshot
Functional exploration of the Plasmodium tRNA import machinery
inferred← citeshttps://doi.org/10.70675/0b3fded9z0768z4976z9f7cz8b7e4a9f1114openalex-snapshot
Phylogenomics and comparative genomics in ant-eating mammals
inferred← citeshttps://doi.org/10.7287/peerj.6131v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.6131v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.6131v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7633v0.1/reviews/1openalex-snapshot
Peer Review #1 of "The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7633v0.1/reviews/2openalex-snapshot
Peer Review #2 of "The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7633v0.1/reviews/3openalex-snapshot
Peer Review #3 of "The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7853v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.7853v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.7853v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.7853v0.3/reviews/1openalex-snapshot
Peer Review #1 of "Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China (v0.3)"
inferred← citeshttps://doi.org/10.7287/peerj.7853v0.3/reviews/2openalex-snapshot
Peer Review #2 of "Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China (v0.3)"
inferred← citeshttps://doi.org/10.7287/peerj.7853v0.4/reviews/1openalex-snapshot
Peer Review #1 of "Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China (v0.4)"
inferred← citeshttps://doi.org/10.7287/peerj.7853v0.4/reviews/2openalex-snapshot
Peer Review #2 of "Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China (v0.4)"
inferred← citeshttps://doi.org/10.7717/peerj.6131openalex-snapshot
Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae)
inferred← citeshttps://doi.org/10.7717/peerj.7633openalex-snapshot
The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae
inferred← citeshttps://doi.org/10.7717/peerj.9740openalex-snapshot
Six complete mitochondrial genomes of mayflies from three genera of Ephemerellidae (Insecta: Ephemeroptera) with inversion and translocation oftrnIrearrangement and their phylogenetic relationships
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.