Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Gene Evolution - Fast or Slow?

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?

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...

Hardy-Weinberg Principle

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.In the early 20th century,...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Test for Homogeneity

Test for Homogeneity

The goodness–of–fit test can be used to decide whether a population fits a given distribution, but it will not suffice to decide whether two populations follow the same unknown distribution. A different test, called the test for homogeneity, can be used to conclude whether two populations have the same distribution. To calculate the test statistic for a test for homogeneity, follow the same procedure as with the test of independence. The hypotheses for the test for homogeneity can be stated as...

Evolutionary Relationships through Genome Comparisons

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...

You might also read

Related Articles

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

Sort by

Same author

GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics.

bioRxiv : the preprint server for biology·2026

Same author

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026

Same author

IQ-TREE 3: phylogenomic inference software using complex evolutionary models.

Molecular biology and evolution·2026

Same author

Comparing partition and mixture models with akaike information criteria.

Systematic biology·2026

Same author

The LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature - a critical evaluation of Akiyoshi, 2025.

Journal of cell science·2026

Same author

Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes.

Current biology : CB·2025

Search research articles

Related Experiment Video

Updated: Jun 4, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

Fast statistical tests for detecting heterotachy in protein evolution.

Huai-Chun Wang¹, Edward Susko, Andrew J Roger

¹Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada. hcwang@mathstat.dal.ca.

Molecular Biology and Evolution

|February 24, 2011

Summary

The w statistic and its modified versions (w' and correlation tests) can detect heterotachy (evolutionary rate variation) in protein sequences. However, their effectiveness varies with data size, substitution rates, and specific heterotachy models, sometimes requiring careful taxon selection.

More Related Videos

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on ¹⁵N Metabolic Labeling and Quantitative Mass Spectrometry

Published on: March 13, 2014

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Related Experiment Videos

Last Updated: Jun 4, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry

A New Approach for the Comparative Analysis of Multiprotein Complexes Based on ¹⁵N Metabolic Labeling and Quantitative Mass Spectrometry

Published on: March 13, 2014

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Evolutionary biology
Molecular evolution
Bioinformatics

Background:

Heterotachy, or variation in evolutionary rates across sites or lineages, is a significant challenge in phylogenetic inference.
The w statistic was developed to detect heterotachy by comparing amino acid substitution patterns between monophyletic groups.
Existing methods have limitations, particularly with small datasets or low substitution rates.

Purpose of the Study:

To evaluate the effectiveness of the w statistic in detecting heterotachy under various conditions.
To develop and assess improved statistical tests for heterotachy detection.
To compare the power of different statistical tests for identifying various modes of heterotachy.

Main Methods:

Simulations were used to test the performance of the w statistic with varying dataset sizes and substitution rates.
A modified statistic, w', was developed using site entropy to enhance sensitivity to heterotachy.
Pearson's correlation of site entropies between groups was employed as an alternative heterotachy detection method.

Main Results:

The w statistic is effective for small datasets and low substitution rates but struggles under other conditions.
The w' statistic and the Pearson correlation test demonstrate increased power in detecting covarion and bivariate rate shift heterotachy, especially in large, variable datasets.
All tested methods (w, w', correlation) can fail to detect heterotachy in data simulated under a branch length mixture model, sometimes necessitating strategic taxon selection.

Conclusions:

The w' statistic and correlation test offer improved detection of certain heterotachy types compared to the original w statistic.
No single statistical test is universally effective; performance depends on data characteristics and the specific mode of heterotachy.
Further investigation into lineage-specific changes in site variability is warranted, and taxon sampling can influence heterotachy detection.