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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...

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.

Gene Flow

Gene Flow

Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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...

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Related Experiment Video

Updated: Jan 5, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Inferring putative transmission clusters with Phydelity.

Alvin X Han^1,2,3, Edyth Parker^3,4, Sebastian Maurer-Stroh^1,5

¹Protein Sequence Analysis Group, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, 138671 Singapore.

Virus Evolution

|October 17, 2019

Summary

Phydelity identifies pathogen transmission clusters using a novel, statistically principled framework that avoids arbitrary genetic distance thresholds. This new method improves cluster accuracy and aids in identifying direct transmission events across various pathogens.

Keywords:

molecular epidemiology phylogenetic clustering transmission

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Last Updated: Jan 5, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Published on: December 7, 2021

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

Area of Science:

* Phylogenetics
* Computational Biology
* Epidemiology

Background:

* Current phylogenetic clustering methods for pathogen transmission rely on arbitrary genetic distance thresholds, hindering standardization.
* Lack of knowledge on pathogen dynamics makes threshold selection an ad hoc process.
* Existing methods face challenges in accurately identifying transmission clusters.

Purpose of the Study:

* Introduce Phydelity, a novel tool for identifying transmission clusters in pathogen phylogenies.
* Develop a statistically principled and phylogeny-informed framework that eliminates arbitrary distance thresholds.
* Enhance the accuracy and reliability of transmission cluster identification.

Main Methods:

* Phydelity identifies sequence groups more closely related than the phylogeny's ensemble distribution.
* Employs a statistically principled and phylogeny-informed framework.
* Does not require arbitrary distance thresholds or parameter calibration.

Main Results:

* Phydelity demonstrated higher cluster purity and lower misclassification rates in simulated phylogenies compared to threshold- and model-based methods.
* Applied to Hepatitis B and C virus datasets, Phydelity identified clusters with superior correspondence to likely transmission events.
* Outperformed widely used non-parametric phylogenetic clustering methods without parameter calibration.

Conclusions:

* Phydelity offers a robust, standardized approach to pathogen transmission cluster identification.
* The tool is generalizable to any pathogen, facilitating the detection of direct transmission events.
* Phydelity provides a more accurate and reliable alternative to existing phylogenetic clustering methods.