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

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Cis-regulatory Sequences

Cis-regulatory Sequences

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Frequency-dependent Selection

Frequency-dependent Selection

When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.

Multi-species Conserved Sequences

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...

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...

You might also read

Related Articles

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

Sort by

Same author

de novo assembly of 5 highly contiguous Heliconius butterfly genomes with long-read sequencing alone.

Genome biology and evolution·2026

Same author

Structures of DnaA domain I reveal a dimer conserved across Actinomycetes.

Nucleic acids research·2026

Same author

Wnt dynamics at the blastopore and stomodeum during sea urchin gastrulation.

Development (Cambridge, England)·2026

Same author

Genetically tractable embryonic cell lines from sea urchins Lytechinus variegatus and Strongylocentrotus purpuratus.

Communications biology·2025

Same author

Head start: fossil clues about how bodies evolved from two-fold to five-fold symmetry.

Nature·2025

Same author

Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies.

PLoS biology·2025

Search research articles

Related Experiment Video

Updated: Dec 21, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.

Alejandro Berrio¹, Ralph Haygood², Gregory A Wray³

¹Department of Biology, Duke University, Biological Sciences Building, 124 Science Drive, Durham, NC, 27708, USA. alebesc@gmail.com.

|May 15, 2020

Summary

A new method, adaptiPhy, enhances the detection of adaptive evolution in noncoding DNA. It improves the identification of positive selection in human accelerated elements, revealing that a quarter of these elements evolve under positive selection.

Keywords:

Adaptation Analytical method Neutral Positive selection Proxy adaptiPhy

More Related Videos

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

Published on: March 29, 2019

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: Dec 21, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

Published on: March 29, 2019

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
Genomics
Bioinformatics

Background:

Adaptive changes in cis-regulatory elements are key to evolution by natural selection.
Identifying functional noncoding DNA is crucial for linking genotype to phenotype.

Purpose of the Study:

To introduce adaptiPhy, a method for improved detection of directional selection in noncoding DNA.
To provide a more sensitive and targeted characterization of selection across the genome.

Main Methods:

Utilized ENCODE annotations for proxy neutral sequences.
Applied adaptiPhy to human accelerated elements and open chromatin regions.
Evaluated the impact of sequence length and branch count on test performance.

Main Results:

adaptiPhy demonstrated utility in identifying selection in noncoding elements.
Optimal lengths for query (150 bp–1 kb) and reference (3 kb) alignments were determined.
The method successfully distinguished positive selection from neutral evolution and relaxation of constraint.
Confirmed that 25% of non-coding Human Accelerated Elements show evidence of positive selection.

Conclusions:

adaptiPhy offers significant improvements for detecting branch-specific directional selection in noncoding sequences.
The method enhances the characterization of directional selection and neutral evolution genome-wide.