Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.
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.
Institute of Neuroscience, University of Oregon.
Richard C
RC
Edmunds
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University.
Baofeng
B
Su
National Evolutionary Synthesis Center, Durham, NC.
James P
JP
Balhoff
Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada.
B Frank
BF
Eames
National Evolutionary Synthesis Center, Durham, NC Department of Biology, University of South Dakota.
Wasila M
WM
Dahdul
National Evolutionary Synthesis Center, Durham, NC.
Hilmar
H
Lapp
Department of Ichthyology, The Academy of Natural Sciences, Philadelphia, Philadelphia, PA.
John G
JG
Lundberg
National Evolutionary Synthesis Center, Durham, NC Department of Biology, University of North Carolina, Chapel Hill.
Todd J
TJ
Vision
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University.
Rex A
RA
Dunham
Department of Biology, University of South Dakota.
Paula M
PM
Mabee
Institute of Neuroscience, University of Oregon monte@uoneuro.uoregon.edu.
Monte
M
Westerfield
D000818:Animals; D002397:Catfishes / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D015870:Gene Expression / Q000235:genetics / Q000502:physiology; D008957:Models, Genetic; D010641:Phenotype; D012984:Software
catfish; evolutionary phenotypes; gene expression; molecular evolution; nonmodel organism