Needs Analysis Workshop/Breakout group 1

Break-out Group 1: Developmental genetics of morphology

Examples for driving research questions:

• Which genes are known to be expressed in the development of a particular morphological structure?
• Is there a model organism mutant that has a phenotype similar to a human disease?

Characters

GW - describe natural units - not necessarily arbitrary - can phenotype be decomposed into natural mechanistic units

CK - could ontology hold you back from describing some things

GW - can lead to confusion

EJ - this database can be a way of discovering these units

GW - would database be like GenBank - I could describe a fish and deposit my phenotypes - structure of data would be fluid

PM - data is representation of current knowledge - can change over time

GW - how is change in knowledge, like of orthology statements, handled in genome databases

Manually updated, typically

MW - We should move above mechanics and focus on biological questions

EJ - how can we use data to identify discrete modules of variation within evolution

GW - taxonomic work in mammals often involves tooth characters - usually cusps are individualized - actually character identity should be attached to tooth type rather than cusp as unit character - resolves many homology issues

Question: See same tooth type evolving again and again. Developmentally, cusps don't come and go individually. - see covariance within mutants query for mutants that affect cusp X - always see that other cusp is affected

GW - Homology and analogy - often too "yes or no" - instead could have "character model" - contain kind of cells within, location in body, relation to other characters, what kind of states can it assume - represent variational tendencies of a chunk of the body - avoid simplifying biological reality - open-ended structure

CK - can you really ask question like "what are modules of evolution" from database - is that too big

PM and MW - hope to draw such conclusions from database

EJ - quantify levels of covariation across clade as well as across experimental phenotypes

Question: Paired appendages in vertebrates - fins and limbs etc. Homologous, but endoskeletons are not comparable though Do fish have digits (digit homolog)? Is there a skeletal structure that is historically continuous with digits? Are there mutants in the mouse that affect phalanges? Are there similar zebrafish mutants that affect radials? Position, shape, cell type of skeletal elements? Similar gene expression patterns? Does it support continuity of developmental identity? Evidence that there are intermediate forms - continuity - require fossil data

1. Are there mutants that affect phalanges?
2. What genes are involved?
3. Are there mutants in "similar" structures affected by any of those genes?
   • Point you to best candidates in terms of phenotypic similarity, membership in pathway

Compare in database?

Question: Comparative catalog of cell types