Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Codon usage patterns in cytochrome oxidase I across multiple insect orders.

Joshua T Herbeck1, John Novembre

  • 1Division of Insect Biology, University of California, Berkeley, Berkeley, CA 94720, USA. herbeck@mbl.edu

Journal of Molecular Evolution
|August 13, 2003
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

FRAME: Fine-Resolution Asymmetric Migration Estimation.

Nature communications·2026
Same author

Germline genetic testing and privacy concerns in patients with mesothelioma.

Genetics in medicine : official journal of the American College of Medical Genetics·2026
Same author

Reduced cyclin D3 expression in erythroid cells protects against malaria.

Nature·2026
Same author

When migration leaves a clean trace: Decoupling migration from coalescence in the structured serial coalescent.

bioRxiv : the preprint server for biology·2025
Same author

Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance.

PLoS genetics·2025
Same author

HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.

BMC bioinformatics·2025

Synonymous codon usage bias in insect mitochondrial DNA (mtDNA) varies greatly, with few clear phylogenetic patterns. Major codon preferences also shift, but these changes are often phylogenetically conservative.

Area of Science:

  • Evolutionary Biology
  • Genomics
  • Molecular Biology

Background:

  • Synonymous codon usage bias is shaped by mutation, translational selection, and genetic drift.
  • Understanding codon bias in mitochondrial DNA (mtDNA) is crucial for evolutionary studies.

Purpose of the Study:

  • To analyze codon usage patterns across 88 insect species.
  • To determine the variability of codon bias levels and major codon preferences.
  • To investigate phylogenetic constraints on codon bias and preference in insect mtDNA.

Main Methods:

  • A likelihood-based method was used to estimate codon bias levels and major codon preferences.
  • This method accounts for and removes biases from genome nucleotide composition.
  • Phylogenetic analysis was performed across 12 insect orders.

Related Experiment Videos

Main Results:

  • High variation in codon bias levels was observed among the 88 insect taxa, with limited apparent phylogenetic patterns.
  • Shifts in major codon preference occurred across the phylogeny for multiple amino acids.
  • Changes in codon preference primarily involved double-preference models and were phylogenetically conservative.

Conclusions:

  • Codon bias in insect mtDNA is highly variable and not strictly dictated by phylogeny.
  • Population size effects may influence bias level shifts, as seen in the genus Papilio.
  • While major codon preferences shift, these changes exhibit phylogenetic conservatism, especially within double-preference models.