Driving Research Questions

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Motivation

Driving biological research questions for this project (also called "use-cases") are meant to push the current limits of inferring knowledge or generating hypotheses about the origin and forces behind phenotypic changes, as well as the developmental processes that are involved in these.

These research questions will in turn drive the development of our database and web-based interfaces to ensure that the system we are developing, and the data that we are collecting, will allow the research community to obtain answers to those questions.

Examples

For illustration, we have identified three initial use-cases as depicted below.

Identifying candidate genes for a particular evolutionary phenotype

One focus of developmental biology is to understand how genes regulate development, and therefore examining the phenotypic effects of single gene mutations is a major emphasis in studies of zebrafish and other model organisms. Genetic change underlies alterations in evolutionary characters as well, but the connection between specific genes and most evolutionary changes has not been made. Thus, one of the first steps in investigating the developmental basis for a particular evolutionary change in morphology is to hypothesize a relationship between that morphology and a set of candidate genes.

Identifying evolutionary changes that match the phenotype of a zebrafish mutant

With the rise of evo-devo, developmental biologists have become more interested in exploring the covariation of developmental and evolutionary traits. A common question is simply whether a particular trait varies in evolution and if so, what the pattern of evolution has been.

Compare genetically and evolutionarily correlated characters

Determining whether morphological characters are independent or genetically/developmentally correlated has been a longstanding and intractable question in phylogenetics. Often the correlation between two (or more) characters is difficult to ascertain, particularly when the characters involved are linked together at the molecular level. However, if evolutionary character changes could be matched to mutant developmental and morphological phenotypes, single-gene mutant phenotype data from zebrafish would allow a detailed analysis of this issue for any evolutionary characters of interest.