Jove
Visualize
Contact Us

Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

You might also read

Related Articles

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

Sort by
Same author

Systemic Acquired Resistance signaling molecule N-hydroxypipecolic acid is involved in Age-Related Resistance in Arabidopsis thaliana.

Plant physiology·2026
Same author

Ankh-Score Produces Better Sequence Alignments Than AlphaFold3.

Proteins·2026
Same author

Protein embeddings and local alignments.

Computational and structural biotechnology journal·2026
Same author

Diverse N<sub>2</sub> Functionalization Enabled by an Unsymmetric Dititanium Complex.

Journal of the American Chemical Society·2026
Same author

Component puzzle protein-protein interaction prediction.

Briefings in bioinformatics·2025
Same author

Development of a deep learning model for guiding treatment decisions of acute variceal bleeding in patients with cirrhosis.

World journal of gastroenterology·2025
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 Video

Updated: May 27, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Inferring sequence regions under functional divergence in duplicate genes.

Yi-Fei Huang1, G Brian Golding

  • 1Department of Biology, McMaster University, Hamilton, ON, Canada.

Bioinformatics (Oxford, England)
|November 29, 2011
PubMed
Summary

This study introduces HMMDiverge, a new phylogenetic hidden Markov model to identify functional divergence in duplicate genes. The tool successfully pinpoints protein regions with divergent substitution rates, aiding in understanding evolutionary changes.

More Related Videos

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp
10:44

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

Related Experiment Videos

Last Updated: May 27, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
06:40

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp
10:44

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

Area of Science:

  • Evolutionary Biology
  • Genomics
  • Bioinformatics

Background:

  • Existing phylogenetic methods for detecting functional divergence in duplicate genes often fail to model substitution rate autocorrelation.
  • This limitation reduces their power in identifying specific protein regions undergoing functional divergence.

Purpose of the Study:

  • To develop a novel phylogenetic hidden Markov model (HMM) to accurately identify protein regions associated with type-I functional divergence.
  • To create a computational tool, HMMDiverge, for estimating model parameters and detecting these divergence regions.

Main Methods:

  • Designed a phylogenetic hidden Markov model incorporating sequence autocorrelation.
  • Developed the HMMDiverge software in C++ for parameter estimation and region identification.
  • Validated the method through simulations and application to animal G protein α subunits.

Main Results:

  • HMMDiverge effectively identifies protein regions under type-I functional divergence, particularly when substitution rate discrepancies are significant and regions are sufficiently long.
  • Analysis of G protein α subunits revealed a novel candidate region (α-4 helix and α4-β6 loop) with divergent substitution rates, distinct from previous findings.
  • This identified region is implicated in receptor-G protein interaction specificity.

Conclusions:

  • HMMDiverge is a powerful and useful tool for identifying type-I functional divergence regions after gene duplication.
  • The findings suggest that functional divergence in G protein α subunits may be linked to altered receptor-G protein specificity.
  • The identified regions provide insights into the molecular mechanisms of evolutionary adaptation in G proteins.