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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.

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...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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...

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

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Updated: May 21, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics.

Niema Moshiri¹

¹Department of Computer Science & Engineering, UC San Diego, La Jolla, CA 92093, USA.

Gigabyte (Hong Kong, China)

|March 20, 2025

Summary

This summary is machine-generated.

Existing tree libraries struggle with large phylogenies. CompactTree, a new C++ library with a Python wrapper, efficiently handles ultra-large phylogenetic trees, offering significant speed and memory improvements for viral and bacterial species studies.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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The ITS2 Database

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Published on: March 12, 2012

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Last Updated: May 21, 2025

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

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Area of Science:

Computational Biology
Bioinformatics
Phylogenetics

Background:

Analyzing viral and bacterial species necessitates handling extremely large phylogenetic trees with millions of tips.
Current tree-handling software often fails to scale efficiently to these massive datasets.

Purpose of the Study:

To introduce CompactTree, a novel C++ library designed for efficient traversal of ultra-large phylogenies.
To provide a user-friendly Python wrapper for seamless integration into existing bioinformatics workflows.

Main Methods:

Development of a lightweight, header-only C++ library named CompactTree.
Implementation of a Python wrapper to enhance usability and accessibility.
Performance benchmarking against existing phylogenetic tree libraries.

Main Results:

CompactTree demonstrates orders of magnitude improvement in speed compared to existing solutions.
CompactTree requires significantly less memory, making it suitable for large-scale phylogenetic analysis.
The library is easily integrated into other computational tools.

Conclusions:

CompactTree offers a scalable and efficient solution for navigating ultra-large phylogenetic trees.
This advancement facilitates more comprehensive studies of viral and bacterial diversity.
The open-source availability promotes wider adoption and further development in bioinformatics.