ArticleMolecular biology and evolution2016
Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 50 citations in OpenAlex.
- Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework.Yeast (Chichester, England) · 2024Review
- GallOnt: An ontology for plant gall phenotypes.Biodiversity data journal · 2024Article
- Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae).Biodiversity data journal · 2024Article
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- Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research.Journal of biomedical semantics · 2022Article
- STOREFISH 2.0: a database on the reproductive strategies of teleost fishes.Database : the journal of biological databases and curation · 2020Article
- Transforming the study of organisms: Phenomic data models and knowledge bases.PLoS computational biology · 2020Review
- Open Science principles for accelerating trait-based science across the Tree of Life.Nature ecology & evolution · 2020Review
- A Logical Model of Homology for Comparative Biology.Systematic biology · 2020Article
- A database of functional traits for spiders from native forests of the Iberian Peninsula and Macaronesia.Biodiversity data journal · 2020Article
- Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Organizing phenotypic data-a semantic data model for anatomy.Journal of biomedical semantics · 2019Article
- Article
- The anatomy of phenotype ontologies: principles, properties and applications.Briefings in bioinformatics · 2018Article
- Incentivising use of structured language in biological descriptions: Author-driven phenotype data and ontology production.Biodiversity data journal · 2018Article
- Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes.PLoS genetics · 2017Article
- Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae).BMC genomics · 2017Article
- Novel Candidate Genes Underlying Extreme Trophic Specialization in Caribbean Pupfishes.Molecular biology and evolution · 2017Article
- Identification and Expression Analysis of the Complete Family of ZebrafishFrontiers in cell and developmental biology · 2017Article
- Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences.Molecular biology and evolution · 2016Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
Abstract
Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.