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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.

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 kingdom.

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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...

Export of Mitochondrial and Chloroplast Genes

Export of Mitochondrial and Chloroplast Genes

A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...

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Related Experiment Video

Updated: Jun 24, 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

Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data.

Shuangbin Xu¹, Lin Li¹, Xiao Luo¹

¹Department of Bioinformatics, School of Basic Medical Sciences Southern Medical University Guangzhou China.

|June 13, 2024

Summary

The ggtree object enhances phylogenetic data reusability by integrating tree structures, associated data, and visualization directives into a single, extractable graphic object, improving analytical reproducibility.

Keywords:

annotation data data structure ggtree phylogenetic tree visualization

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Related Experiment Videos

Last Updated: Jun 24, 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

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Phylogenetic trees are crucial for understanding evolutionary relationships.
Current methods for publishing phylogenetic data often hinder reusability due to image-only formats and incompatible data storage.
This limits data synthesis, comparative studies, and analytical reproducibility.

Purpose of the Study:

To introduce the ggtree object as a novel data structure for phylogenetic information.
To enhance the reproducibility and reusability of phylogenetic data.
To facilitate integrative and comparative analyses in evolutionary biology.

Main Methods:

Development of the ggtree object, a graphic object designed to store phylogenetic trees and associated data.
The ggtree object integrates visualization directives alongside the tree and data.
Enables extraction of input tree and associated data from the graphic object for further analysis.

Main Results:

The ggtree object serves as a unified structure for publishing phylogenetic trees, associated data, and visualization information.
It allows for the direct extraction of underlying data, overcoming limitations of image-only formats.
Facilitates seamless reuse of phylogenetic data in subsequent studies.

Conclusions:

The ggtree object significantly improves the reusability and reproducibility of phylogenetic data.
It provides an ideal data structure for publishing comprehensive phylogenetic information.
Promotes advancements in integrative and comparative evolutionary studies.