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...

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...

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...

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,...

The Tree of Life - Bacteria, Archaea, Eukaryotes

The Tree of Life - Bacteria, Archaea, Eukaryotes

The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both extant and...

You might also read

Related Articles

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

Sort by

Same author

Infrared radiation is an ancient pollination signal.

Science (New York, N.Y.)·2025

Same author

Low genetic differentiation among morphologically distinct Cycas species informs the delineation of conservation management units.

Annals of botany·2025

Same author

Correction: Global Impacts Dataset of Invasive Alien Species (GIDIAS).

Scientific data·2025

Same author

Resolving relationships in the radiation of Australia's largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing.

Annals of botany·2025

Same author

Global Impacts Dataset of Invasive Alien Species (GIDIAS).

Scientific data·2025

Same author

Distinct and redundant roles of the Arabidopsis OCTOPUS gene family in plant growth beyond phloem development.

Journal of experimental botany·2025

Search research articles

Related Experiment Video

Updated: Jun 2, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

A comprehensive phylogenomic framework for cycads (Cycadales).

Michael Calonje¹, James A R Clugston^1,2, Mario Coiro³

¹Montgomery Botanical Center, Coral Gables, Florida, USA SENCKENBERG - Leibniz Institution for Biodiversity and Earth System Research (SGN), Senckenberg Research Institute and Natural History Museum Frankfurt Frankfurt am Main Germany https://ror.org/00xmqmx64.

|June 1, 2026

Summary

This study presents a comprehensive time-calibrated phylogeny for cycads, revealing a robust evolutionary framework. The research provides crucial insights into cycad taxonomy and intergeneric relationships, essential for understanding their evolutionary history.

Keywords:

Cycadales divergence times gene concordance factors molecular dating phylogenomics site concordance factors timetree transcriptomics

More Related Videos

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Related Experiment Videos

Last Updated: Jun 2, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

Botany
Evolutionary Biology
Phylogenetics

Background:

Cycads represent an ancient lineage of seed plants with significant evolutionary history.
A comprehensive understanding of cycad phylogeny is crucial for taxonomy and conservation.
Previous phylogenetic studies have been limited in scope and data.

Purpose of the Study:

To construct a time-calibrated phylogeny for cycads using a large phylogenomic dataset.
To resolve intergeneric relationships and confirm generic monophyly within cycads.
To provide an accessible phylogenomic framework for cycad evolutionary studies.

Main Methods:

Inferred phylogeny from 1,409 single-copy nuclear loci (411,345 amino acid sites) from transcriptome and genome data.
Utilized maximum likelihood analysis with partitioned data and assessed branch support using ultrafast bootstrap (UFBoot2).
Estimated divergence times using penalized likelihood (TreePL) with 12 calibration constraints and bootstrap replicates.

Main Results:

Developed a time-calibrated phylogeny covering approximately 86% of known cycad species across all 10 genera.
Recovered a strongly supported generic backbone and confirmed the monophyly of all cycad genera.
Observed high bootstrap support but low gene concordance factors, indicating limited phylogenetic signal per locus.

Conclusions:

The study provides the first broadly accessible phylogenomic framework for cycad taxonomy and evolutionary history.
The resolved phylogeny clarifies intergeneric relationships and supports the monophyly of all extant cycad genera.
The data generated will facilitate future research on cycad evolution, biogeography, and conservation.