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

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...

Microbial Phylogeny

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

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...

Phylogenetic Trees

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

Phylogenetic Trees

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

Phylogeny

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

You might also read

Related Articles

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

Sort by

Same author

Linking land use to the likely origins of third-generation cephalosporin-resistant Enterobacterales in freshwater.

Applied and environmental microbiology·2026

Same author

Evolutionary and Structural Analysis Reveals the Gradual Establishment and High Conservation of Auxin Pathways from Algae to Land Plants.

Plant physiology·2026

Same author

Insights into the phylogenetic, structural and functional evolution of <i>LHC</i> superfamily in photosynthetic organisms.

Plant diversity·2026

Same author

Adaptive evolutionary shifts in de novo birth and fixation strategy of lineage-specific genes during plant terrestrialization.

The Plant journal : for cell and molecular biology·2026

Same author

Functional evolution and rewiring of the UVR8-BES1/BIM1 module underpin the refinement of UV-B responses during plant terrestrialization.

Plant communications·2026

Same author

The evolutionary path of widespread IR heteroplasmy of chloroplast genomes in the context of Rhodophyta phylogeny.

Journal of molecular evolution·2026

Same journal

Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.

Genome biology and evolution·2026

Same journal

Genome-wide analysis of an endangered axolotl endemic to Mexico reveals genomic variation associated with body condition, environment and infection by a pathogenic fungus.

Genome biology and evolution·2026

Same journal

Conservation of IAMT preference for indole acetic acid methylation across 250 million years of seed plant divergence, with only one recent evolutionary switch in Ocimum.

Genome biology and evolution·2026

Same journal

Regulatory logic and transposable element dynamics in Caenorhabditis genomes.

Genome biology and evolution·2026

Same journal

Interchromosomal translocations and large deletions drive the evolution of the outlier chromosome in the smallest photosynthetic eukaryote.

Genome biology and evolution·2026

Same journal

Chromosome-scale genome assemblies of duckweeds provide insights into genomic plasticity, aquatic adaptation and morphological reduction.

Genome biology and evolution·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 28, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Systematic error in seed plant phylogenomics.

Bojian Zhong¹, Oliver Deusch, Vadim V Goremykin

¹Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand. bjzhong@gmail.com

Genome Biology and Evolution

|October 22, 2011

Summary

This summary is machine-generated.

Phylogenetic analysis of seed plants reveals that Gnetales are closely related to Pinaceae, challenging previous assumptions. This finding, based on chloroplast DNA, refines our understanding of conifer evolution.

More Related Videos

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

Published on: January 21, 2020

Related Experiment Videos

Last Updated: May 28, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

Published on: January 21, 2020

Area of Science:

Evolutionary Biology
Phylogenetics
Molecular Systematics

Background:

The evolutionary relationships of Gnetales, a group of gymnosperms, remain poorly understood due to significant divergence from related taxa.
Previous phylogenetic studies have faced challenges in resolving the precise placement of Gnetales within seed plant evolution.

Purpose of the Study:

To investigate the evolutionary properties of conifer chloroplast DNA sequences.
To improve taxon sampling of Cupressophyta (non-Pinaceae conifers) for more robust phylogenetic analysis.
To resolve the enigmatic phylogenetic position of Gnetales within seed plants.

Main Methods:

Sequencing of three new chloroplast (cp) genomes from Southern Hemisphere conifers to enhance Cupressophyta sampling.
Application of a site pattern sorting criterion to assess compositional heterogeneity and heterotachy in cp genome sequences.
Evaluation of the fit of conifer chloroplast genome sequences to a general time reversible + G substitution model.

Main Results:

Non-time reversible properties in aligned chloroplast genome sequences of Gnetales were found to mislead phylogenetic reconstruction.
Exclusion of the 2,250 most variable sites from the concatenated alignment led to phylogenetic analyses supporting a close relationship between Gnetales and Pinaceae (the Gnepine hypothesis).
The study demonstrates the critical importance of the goodness of fit between substitution models and sequence data in phylogenomic analyses.

Conclusions:

The Gnepine hypothesis, suggesting a close evolutionary link between Gnetales and Pinaceae, is supported by analyses that account for sequence heterogeneity.
The developed analytical protocol offers a robust method for assessing the reliability of phylogenomic inferences.
Accurate phylogenetic reconstruction of seed plants necessitates careful consideration of substitution model adequacy and data characteristics.