Bioma as a graph

Graphs for taxonomical history

The first issue in Biodiversity Data Management is to proper record taxonomical data. Without proper identification, samples and specimens are of nearly no value for any biodiversity study. Taxonomic names change with time as a consequence of updates in the classification of organisms. These updates need to be tracked so that a given specimen now referred to as, say, Constrictotermes cyphergaster, can be quickly realized to belong to the same species as those specimens referred to in the old literature as Eutermes (Constrictotermes) cyphergaster or even as Eutermes cyphergaster.

There are several types of taxonomic changes, here exemplified for the case of species names, but which can equally be applied to any taxonomic rank. Everything starts from the first assertion of a Latin binomial to a new species and then its history develops as exemplified below for a termite species.

1. Silvestri finds a new species in 1901 and creates a new taxonomic entity giving it the epithet cyphergaster and placing it under the genus Eutermes, which as previously described by Heer.
2. Latter on, in 1903, Silvestri redescribes Eutermes cyphergaster based on a better series of specimens.
3. Desneux in 1904 realocates Silvestri's Eutermes cyphergaster into the genus Termes which had been already described by Linnaeus in 1758.
4. Holmgren in 1910 creates Constrictotermes as a subgenus of Eutermes (no type-species was asserted to it initially).
5. Emerson in 1925 realocates Holmgren's Constrictotermes as a subgenus of Nasutitermes which was already described by Dudley.
6. Snyder voids Deusneux's and Silvestri's assertions moving Eutermes cyphergaster from Linnaeus' Termes and places 'cyphergaster' under Emerson's Nasutitermes (Constrictotermes), creating Nasutitermes (Constrictotermes) cyphergaster
7. Mathews in 1977 redescribes Constrictotermes erecting it to generic status, creating Constrictotermes cyphergaster

A graph representation of this whole story is presented below.

Practical instructions on building taxonomic history as a graph

Simple taxonomic assertions

It is not always straightforward to build taxonomic histories as a graph. The basic strategy is to consider each new proposition (such as descriptions of new species, changes of taxonomic rank, etc,) as an independent node of the type (or "Class") TaxonomicAssertion. Taxonomic names should also be placed as nodes of the type "TaxonName", so that they can be reused attached to several Taxonomic Assertion nodes. Another node type, "Person" is reserved for authors of Taxonomic Assertions. Additional nodes type can be attached later, such as "Bibliography" to hold bibliographic data, and "Morfology" to hold morfological traits of the individuals used in the taxonomic description. These additional nodes can also be in fact entire new domains.

Start from the type-species of that genus; the first node will hold the taxonomic assertion which first described that species, even if this Latin binomial is not valid any more. To do so, create a TaxonomicAssertion node to represent the first description of this species. Link this node to one TaxonName node holding the specific epithet. Do the same for the generic name (a TaxonomicAssertion and its respective TaxonName node). Then link the epithet, as below:

From this point on, follow the chronology of changes, always linking a new TaxonomicAssertion node to an existing TaxonomicAssertion node. so that the graph keeps the historical flux correctly.

Multiple taxonomic assertions

Sometimes, both the genus and the specific epithet are created in the same publication by a given author. For instance:

1. Fontes finds a new species in 1979 and creates a new taxonomic entity giving it the epithet guarinim.
2. realizing that this new species also represents a new genus, Fontes creates a another taxonomic entity, Atlantitermes, to which link guarinim as a child.

This does not change the general modelling presented above, under "Simple taxonomic assertions": you simply create two independent nodes of the type TaxonomicAssertion and proceed as usual:

Simultaneous taxonomic changes

Use blank nodes to group together Taxonomic Assertions which were simultaneously changed, as in Desneux's propostion to place Eutermes cyphergaster under Termes (i.e., turning Eutermes a subgenus of Termes while keeping cyphergaster affiliation to Eutermes).