Phenoscape use cases

Identify candidate genes for a particular evolutionary phenotype

Motivation

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.

Example

Extensive variation in the size, shape, presence and absence of bones characterizes the course of vertebrate evolution, and such variation is commonly used in phylogenetic analysis in fishes. An evolutionary biologist observes variation in the size of a particular bone, ceratobranchial 5, among Ostariophysi (Siebert, '87). The person queries the evolutionary phenotype database for matching mutant zebrafish phenotypes by using terms from shared ontologies: Entity = Ceratobranchial 5 [from TAO] and all qualities pertaining to attribute ‘size’ [from the PATO]. The response will be a list of zebrafish mutants and their phenotypes, along with the associated genes, and possibly gene expression images. sox9a is shown to have a role in size reduction in ceratobranchial 5 in the mutant line sox9ahi1134 (Yan et al., '05). The evolutionary biologist would hypothesize that the regulation or sequence of sox9a has been altered during evolution to result in the enlargement of this bone in two lineages, and they would pursue the appropriate developmental genetic work to test this hypothesis. They might further explore the function of the gene in other model organisms.

Input

A phenotype search specification: entity, quality, etc. Option to match exactly or to match descendant terms (as in quality "size", above).

Output

A list of ZFIN mutant identifiers with matching phenotype of each, associated gene, perhaps gene expression images (or links to).

Identify evolutionary changes that match the phenotype of a zebrafish mutant

Motivation

With the rise of evo-devo, developmental biologists have become more interested in exploring the co- variation 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.

Example

A developmental biologist observes a reduction in number of branchiostegal rays (bones in the gill membrane) in a zebrafish mutant due to changes in endothelin-1. The user wants to know whether branchiostegal ray number is variable among fish species, and if so, they want to see the pattern of change across fish evolution. They query the evolutionary phenotype database using terms from shared ontologies: Entity = Branchiostegal rays [from TAO] and all qualities pertaining to attribute ‘count’ [from the PATO]. The response will be a list of taxa and their matching evolutionary character changes or states. The user would see that all cypriniforms, including zebrafish, have three branchiostegal rays, but other fishes, including close ostariophysan relatives, have higher and lower numbers (McAllister, '68).

Input

A phenotype search specification: entity, quality, etc. Option to match exactly or to match descendant terms (as in quality "count", above).

Output

A list of matching evolutionary phenotypes and the taxon for each.

Compare genetically and evolutionarily correlated characters

Motivation

Determining whether morphological characters are independent or genetically/developmentally correlated has been a long- standing and intractable question in phylogenetic systematics (Sneath and Sokal, '73; Wiley, '81; Farris, '83; O'Keefe and Wagner, '01). 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.

Example

On a phylogenetic tree of the Ostariophysi, an evolutionary biologist observes a suite of the characters that support the monophyly of a particular clade. These characters, however, are all marked by changes in size of the dentary, maxilla, ceratohyal, and opercle bones. The user wants to know whether the size modification of each of these bones represents independent support for this phylogenetic hypothesis, or whether the changes are correlated due to a common genetic or developmental basis. Querying the zebrafish mutant phenotype descriptions in EQ syntax with the above anatomical terms would show that in sox9ahi1134 mutants, the dentary, opercle, and maxilla bones are reduced in size relative to wild-type zebrafish, whereas other bones are relatively unaffected (Yan et al., '05). This suggests that the size of the dentary, opercle, and maxilla might be co-regulated in part by sox9a, and we would conclude that support for the monophyly of this clade is not as strong as previously proposed.

Input

Multiple phenotype search specifications: entity, quality, etc., representing the evolutionary character changes. Option to match exactly or to match descendant terms (as in quality "count", above).

Output

A list of ZFIN mutant identifiers and associated genes which are associated with phenotypes matching all, or perhaps just more than one, of the search criteria.

Map changes of an evolutionary character on a phylogeny

Motivation

After observing variation of a trait in evolution (as found in use case #Identify evolutionary changes that match the phenotype of a zebrafish mutant, a biologist may further want to know what the pattern of evolution of this trait has been. This can lead to hypotheses relating to how often this trait changes in evolution, such as whether such changes occur in parallel at many places on the evolutionary tree.

Example

A biologist observes in number of branchiostegal rays across taxa in the database (such as in the results of #Identify evolutionary changes that match the phenotype of a zebrafish mutant). The biologist maps the character changes on a phylogeny, and sees that all cypriniforms, including zebrafish, have three branchiostegal rays, but other fishes, including close ostariophysan relatives, have higher and lower numbers (McAllister, '68). Specifically, reduction in number has occurred multiple times; solenostomids and syngnathids (ghost pipefishes and pipefishes), giganturids, and saccopharyngoid (gulper and swallower) eels have the fewest branchiostegal rays (McAllister, '68).

Input

A list of taxa and their phenotypes for a previously searched character specification. A phylogenetic tree including the taxa of interest.

Output

A graphical representation of a phylogenetic tree (cladogram). The branches are colored to represent reconstructed ancestral states of the given character values (or ambiguity). The state reconstruction is performed using a standard algorithm such as parsimony or a maximum likelihood method.

View values for a particular character for a set of species with some value for another character

Motivation

A particular phenotype change may have evolutionary consequences for another aspect of phenotype. This may be because they are linked via developmental or physical constraints, or are related through their effect on natural selection.

Example

A biologist observes a number of species missing the parietal bone. It appears that these species are also generally small in size. The biologist searches for all species in the database which lack the parietal bone. He then requests the body length value for all those species.

Input

A phenotype search specification for the phenotype to match. A second phenotype search specification for the attribute for which to search for values.

Output

A table containing a list of taxa matching the first entered phenotype. A second column in the table presenting the value of each taxon for the second entered character.

View all species with multiple phenotypes matching a condition

Example

A biologist wants to list all the species that have lost more than one bone. O more specifically, all species that have lost more than one bone in the head.

Input

A phenotype search specification, with constraints on the entity term such as "is_a term1" and "part_of term2". The threshold number of annotations matching the phenotype required to include a taxon.

Output

A list of taxa and their phenotypes matching the input criteria.

View every change in an anatomical structure mapped on a tree

Motivation

A biologist may be interested in how a particular structure has evolved, without knowing what types of changes have occurred in that structure. It would be useful to view the pattern of evolution of all phenotypes involving that structure, visualized on a phylogeny as in #Map changes of an evolutionary character on a phylogeny.

Example

A biologist is interested in the parietal bone. She chooses this term from the anatomy ontology and then views a phylogeny displaying all reconstructed character transitions involving the parietal as an entity.

Input

An anatomical term from an anatomy ontology. A phylogeny containing the species of interest.

Output

A listing of all phenotypes for each species which contain the entered term as an entity. A display of the phylogeny mapping changes for each phenotypic character.