Related Experiment Video
Updated: May 26, 2026
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Opsin gene duplication and divergence in ray-finned fish
Diana J Rennison1, Gregory L Owens, John S Taylor
1University of Victoria, Department of Biology, Station CSC, Victoria, BC, Canada V8W 3N5.
Molecular Phylogenetics and Evolution
|December 20, 2011
Summary
Ray-finned fishes possess large opsin gene repertoires due to extensive gene duplication and divergence. This process, primarily driven by tandem duplication, relaxes evolutionary constraints on opsin sequences.
Area of Science:
- Evolutionary biology
- Genomics
- Molecular biology
Background:
- Opsin gene sequences were first identified in the 1980s to understand human color vision.
- Early research hypothesized opsins formed a single gene family, with variations in color vision linked to gene mutations.
- Subsequent studies revealed extensive opsin gene repertoires in ray-finned fishes (Actinopterygii).
Purpose of the Study:
- To review the duplication and divergence events responsible for large opsin gene repertoires in ray-finned fishes.
- To analyze the evolutionary mechanisms driving opsin gene family expansion in fishes.
- To investigate the impact of gene duplication on opsin sequence evolution.
Main Methods:
- Phylogenetic analyses of opsin gene sequences.
- Examination of data from whole genome sequencing projects and large-insert clones.
- Mapping of amino acid substitutions at key sites onto phylogenies.
- Calculation of dN/dS ratios to assess evolutionary constraints.
Main Results:
- Large opsin gene repertoires in fish result from gene duplication and divergence throughout ray-finned fish evolution.
- Tandem duplication is the predominant mechanism for opsin gene family expansion in fishes.
- Gene conversion between tandem duplicates can complicate evolutionary relationship assessments.
- Amino acid substitutions at key sites show numerous examples of convergence.
- Higher dN/dS values after gene duplication suggest relaxed evolutionary constraints compared to speciation events.
Conclusions:
- Gene duplication and divergence are key drivers of opsin gene repertoire diversity in ray-finned fishes.
- Tandem duplication is the primary mode of opsin gene expansion, with relaxed evolutionary constraints post-duplication.
- Despite extensive gene duplication, clear links between opsin repertoires and environmental or life history traits remain elusive.
Related Concept Videos
02:37Gene 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.
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.
01:57Gene 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...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
01:54Convergent Evolution
Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
02:32Exon 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...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
02:55The Evidence for Evolution
Genetic variations accumulating within populations over generations give rise to biological evolution. Evolutionary changes can result in the formation of novel varieties and entire new species. These changes are responsible for the diverse forms of life inhabiting the planet. The evidence for evolution suggests that all living organisms descended from common ancestors.
01:07Speciation Rates
Overview