Needs Analysis Workshop/Correlation Breakout
Arhat Abzhanov, Todd Vision, Elizabeth Jockusch, Hopi Hoekstra, Jim Balhoff
Notes
AA - Important to note difference in naming conventions between genetic terminology and diversity terminology
TV - Ontologies are meant to solve this problem - can map synonym terms to each other
EJ - many natural phenotypes are much more subtle than genetic mutants
TV - that is an advantage of relationships in ontology - can tell that phenotypes are related to the same morphology
AA - only some phenotypes will overlap - the types of variation are different
TV - but at least both may be annotated as affecting the same part of morphology
AA - user may want to be able to see traits at various levels within ontology - see everything within the tail or just one vertebra
TV - Covariance matrix can provide table of co-occurring changes in entities on tree
EJ - there are many complicated ways for doing character reconstruction - user will probably want to get data and run themselves
HH - especially in the case of parsimony, can't always treat transition probabilities as equal
HH & EJ - maybe provide some default methods, such as parsimony, maybe allowing specifying of transition models
EJ - co-ocurrrence table will be useful for eyeballing interesting groupings
EJ - also want to see which traits are related to the same genes
HH - this should be either location of expression in both entities, or same type of effect in both entities
On the branches where trait 1 changes, how many also have change in trait 2? Of the genes affecting trait 1, how many also affect trait 2?
- View these in two matrices - are there correlations in these two matrices?
Should we allow the user to specify the entity-quality combinations they want in their matrix?
In mayflies, does having a particular gill morphology, increase diversity in habitat? Is gregariousness more likely to evolve in aposematically colored lineages?
I see these two traits covarying - how does the system tell you that?
- table output (matrix) lets you visually scan for for co-occurrence
- click on cell, bring up tree with covarying branches highlighted
- or click on multiple cells and limit tree to those
- further information on how the character changed...
2 approaches - interested in investigating a particular branch vs. interested in trait correlation across independent changes across tree
Gene can affect multiple tissues/structures
What genes affects all x structures? See results on anatomy view, separated into developmental series / developmental modules
- See list of genes, click on gene, see mutant phenotypes, then see links to similar evolutionary phenotypes
- See matrix of co-ocurring mutant phenotypes in two entities/ developmental regions
See colored indication on anatomy view of co-occurrence showing shared genetic bases
Find minimum number of genetic changes which can account for a particular compound evolutionary change (multiple phenotypes)
