Related Experiment Video
Updated: Jul 14, 2026
09:45
Mosaic Zebrafish Transgenesis for Functional Genomic Analysis of Candidate Cooperative Genes in Tumor Pathogenesis
Published on: March 31, 2015
Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish.
Paula M Mabee1, Gloria Arratia, Miles Coburn
1Department of Biology, University of South Dakota, Vermillion, South Dakota 57069, USA. pmabee@usd.edu
Summary
This study connects evolutionary anatomy databases with the Zebrafish Information Network using ontologies. This approach enhances the analysis of gene mutation effects on phenotype for evolutionary studies.
Area of Science:
- Developmental Biology
- Evolutionary Biology
- Bioinformatics
Background:
- Understanding gene regulation in development is crucial.
- Phenotypic effects of gene mutation are studied in model organisms like zebrafish.
- Morphological phylogenies are inferred from evolutionary characters.
Purpose of the Study:
- To connect the Cypriniformes Tree of Life project's evolutionary anatomy and image database with the Zebrafish Information Network (zfin.org) database.
- To utilize ontologies for integrating disparate biological databases.
- To facilitate computational analysis and exploration of evolutionary character data.
Main Methods:
- Development and application of shared ontologies for homologous phenotypic modules.
- Recoding free-form text descriptors of anatomical characters into a structured format.
- Linking evolutionary anatomy data with the Zebrafish Information Network.
Main Results:
- Demonstrated the utility of ontologies in connecting evolutionary anatomy and image databases.
- Enabled easier computation, exploration, and mining of evolutionary character data.
- Provided a framework for addressing evolutionary questions through integrated databases.
Conclusions:
- Shared ontologies are essential for connecting biological databases.
- This approach enhances the study of gene function and evolutionary processes.
- The presented method offers broad utility for evolutionary and developmental biology research.
Related Concept Videos
02:54Evolutionary 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...
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.The structures that arise from convergent evolution are called analogous structures. They are similar in function even if they are dissimilar in structure. Further, structures can be analogous while also...
02:31Synteny 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...
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...
02:32Osmoregulation in Fishes
When cells are placed in a hypotonic (low-salt) fluid, they can swell and burst. Meanwhile, cells in a hypertonic solution—with a higher salt concentration—can shrivel and die. How do fish cells avoid these gruesome fates in hypotonic freshwater or hypertonic seawater environments?
02:16Genetics of Speciation
Speciation is the evolutionary process resulting in the formation of new, distinct species—groups of reproductively isolated populations.The genetics of speciation involves the different traits or isolating mechanisms preventing gene exchange, leading to reproductive isolation. Reproductive isolation can be due to reproductive barriers that have effects either before or after the formation of a zygote. Pre-zygotic mechanisms prevent fertilization from occurring, and post-zygotic mechanisms...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...