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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

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...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Synteny and Evolution02:31

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...
Phylogeny01:23

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.
Gene Families01:57

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 Families01:57

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...

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Updated: May 31, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

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Published on: December 7, 2021

Positional orthology: putting genomic evolutionary relationships into context.

Colin N Dewey1

  • 1Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, 5785 Medical Sciences Center, 1300 University Ave, Madison, WI 53706, USA. cdewey@biostat.wisc.edu

Briefings in Bioinformatics
|June 28, 2011
PubMed
Summary

Orthology refines homology for genome evolution and gene function. Toporthology, a new term for positional orthology, considers genomic position, offering a more precise understanding of gene evolution and function.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Orthology is a key concept for understanding genome evolution and gene function.
  • Traditional orthology lacks consideration of genomic position, limiting its descriptive power for equivalent gene roles across genomes.
  • The concept of positional orthology addresses this limitation by focusing on genes retaining ancestral genomic positions.

Purpose of the Study:

  • To formally define positional orthology and introduce the term 'toporthology'.
  • To highlight the biological significance of distinguishing between orthology and toporthology.
  • To review methods for inferring toporthology using genomic context.

Main Methods:

  • Formal definition of toporthology based on ancestral evolutionary events.
  • Discussion of recent studies on genomic context's role in gene evolution.
  • Review of orthology prediction methods incorporating genomic context.

Main Results:

  • The distinction between orthology and toporthology is biologically significant.
  • Genomic context plays a crucial role in gene evolution.
  • Several orthology prediction methods can be adapted to infer toporthology.

Conclusions:

  • Toporthology provides a more refined understanding of gene evolution than traditional orthology.
  • Considering genomic position is essential for accurately describing gene function and evolution.
  • Further development and application of toporthology prediction methods are warranted.