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Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

Gene Duplication and Divergence

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

Synteny and Evolution

Synteny and Evolution

John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...

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...

Exon Recombination

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...

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Updated: May 26, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Evolution of orthologous tandemly arrayed gene clusters.

Olivier Tremblay Savard¹, Denis Bertrand, Nadia El-Mabrouk

¹Department of Computer Science (DIRO), University of Montreal, Montreal, Quebec, Canada. olivier.tremblay-savard@umontreal.ca

BMC Bioinformatics

|December 14, 2011

Summary

This study extends the DILTAG algorithm to analyze the evolutionary history of Tandemly Arrayed Gene (TAG) clusters across multiple species. The enhanced method accurately infers gene duplication events but faces challenges with multiple gene deletions.

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Area of Science:

Genomics
Evolutionary Biology
Bioinformatics

Background:

Tandemly Arrayed Gene (TAG) clusters are paralogous genes found adjacently on chromosomes, crucial in eukaryotes.
TAG cluster evolution involves tandem duplications, inversions, and deletions affecting gene order and orientation.
The DILTAG algorithm previously inferred evolutionary histories for single TAG clusters.

Purpose of the Study:

To develop a generalized methodology extending DILTAG for analyzing orthologous TAG clusters across multiple species.
To incorporate speciation events alongside gene duplication, deletion, and inversion events in evolutionary history inference.

Main Methods:

An extension of the DILTAG algorithm was developed for multi-species TAG cluster analysis.
The methodology accounts for speciation, tandem duplications (simple/multiple, direct/inverted), deletions (simple/multiple), and inversions.
Algorithm performance was evaluated using simulated datasets and applied to human, chimpanzee, mouse, and rat protocadherin gene clusters.

Main Results:

The extended algorithm demonstrated good performance in inferring the total number and size distribution of gene duplication events from simulated data.
Application to protocadherin gene clusters provided insights into their evolutionary history across the studied species.

Conclusions:

The developed methodology effectively infers evolutionary histories of orthologous TAG clusters across species.
A limitation exists in handling multiple gene deletions due to the algorithm's high computational complexity.
Further refinement is needed to address the intractability of multiple deletion events in evolutionary inference.