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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...

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.

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.

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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Related Experiment Video

Updated: Oct 17, 2025

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

Fast and accurate distance-based phylogenetic placement using divide and conquer.

Metin Balaban¹, Yueyu Jiang², Daniel Roush³

¹Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.

Molecular Ecology Resources

|October 13, 2021

Summary

APPLES-2 is a new phylogenetic placement method that accurately and efficiently places microbial genomes on large evolutionary trees. This advance improves molecular ecology analyses, especially for microbiome environmental sampling.

Keywords:

distance-based methods metagenomics microbiome phylogenetic placement

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Related Experiment Videos

Last Updated: Oct 17, 2025

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

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

Molecular Ecology
Bioinformatics
Phylogenetics

Background:

Phylogenetic placement is crucial for molecular ecology, aiding sample identification and microbiome analysis.
Increasingly large reference trees necessitate accurate and scalable placement methods.
Distance-based methods offer scalability for analyzing diverse environmental samples.

Purpose of the Study:

Introduce APPLES-2, a novel distance-based phylogenetic placement method.
Evaluate APPLES-2's accuracy and scalability compared to existing methods.
Demonstrate APPLES-2's utility for placing microbial genomes and metagenomic scaffolds on ultra-large trees.

Main Methods:

Developed APPLES-2, a distance-based phylogenetic placement tool.
Utilized a divide-and-conquer strategy to optimize distance calculations and placement.
Tested APPLES-2 on a dataset of 10,575 microbial species using marker genes.

Main Results:

APPLES-2 demonstrates superior accuracy and scalability over existing distance-based and some maximum-likelihood methods.
Achieved high accuracy, placing 97% of query genomes within three branches of the optimal position using 50 marker genes.
Successfully placed metagenomic scaffolds on ultra-large trees with high accuracy when tens of marker genes were present.

Conclusions:

APPLES-2 offers a significant advancement in phylogenetic placement accuracy and scalability.
The method is effective for analyzing microbial genomes and metagenomic data on massive phylogenetic trees.
APPLES-2 facilitates broader and more efficient applications of phylogenetic placement in molecular ecology.