Open access links to online versions of the paper are given below:

Wasila M. Dahdul; John G. Lundberg; Peter E. Midford; James P. Balhoff; Hilmar Lapp; Todd J. Vision; Melissa A. Haendel; Monte Westerfield; Paula M. Mabee.  2010.  The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age.  Systematic Biology.  View full text or download PDF.

A recent publication on Megapiranha paranensis from Phenoscape curators Wasila Dahdul and John Lundberg is in the news!

DURHAM, N.C. — How did piranhas — the legendary freshwater fish with the razor bite — get their telltale teeth? Researchers from Argentina, the United States and Venezuela have uncovered the jawbone of a striking transitional fossil that sheds light on this question. Named Megapiranha paranensis, this previously unknown fossil fish bridges the evolutionary gap between flesh-eating piranhas and their plant-eating cousins.

Present-day piranhas have a single row of triangular teeth, like the blade on a saw, explained the researchers. But their closest relatives — a group of fishes commonly known as pacus — have two rows of square teeth, presumably for crushing fruits and seeds. “In modern piranhas the teeth are arranged in a single file,” said Wasila Dahdul, a visiting scientist at the National Evolutionary Synthesis Center in North Carolina. “But in the relatives of piranhas — which tend to be herbivorous fishes — the teeth are in two rows,” said Dahdul.

Megapiranha shows an intermediate pattern: it’s teeth are arranged in a zig-zag row. This suggests that the two rows in pacus were compressed to form a single row in piranhas. “It almost looks like the teeth are migrating from the second row into the first row,” said John Lundberg, curator at the Academy of Natural Sciences in Philadelphia and a co-author of the study.

If this is so, Megapiranha may be an intermediate step in the long process that produced the piranha’s distinctive bite. To find out where Megapiranha falls in the evolutionary tree for these fishes, Dahdul examined hundreds of specimens of modern piranhas and their relatives. “What’s cool about this group of fish is their teeth have really distinctive features. A single tooth can tell you a lot about what species it is and what other fishes they’re related to,” said Dahdul. Her phylogenetic analysis confirms their hunch — Megapiranha seems to fit between piranhas and pacus in the fish family tree.

The Megapiranha fossil was originally collected in a riverside cliff in northeastern Argentina in the early 1900s, but remained unstudied until paleontologist Alberto Cione of Argentina’s La Plata Museum rediscovered the startling specimen — an upper jaw with three unusually large and pointed teeth — in the 1980s in a museum drawer.

Cione’s find suggests that Megapiranha lived between 8-10 million years ago in a South American river system known as the Parana. But you wouldn’t want to meet one today. If the jawbone of this fossil is any indication, Megapiranha was a big fish. By comparing the teeth and jaw to the same bones in present-day species, the researchers estimate that Megapiranha was up to 1 meter (3 feet) in length. That’s at least four times as long as modern piranhas. Although no one is sure what Megapiranha ate, it probably had a diverse diet, said Cione.

Other riddles remain, however. “Piranhas have six teeth, but Megapiranha had seven,” said Dahdul. “So what happened to the seventh tooth?”

“One of the teeth may have been lost,” said Lundberg. “Or two of the original seven may have fused together over evolutionary time. It’s an unanswered question. Maybe someday we’ll find out.”

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The team’s findings were published in the June 2009 issue of the Journal of Vertebrate Paleontology.

CITATION: Cione, A., W. Dahdul, J. Lundberg, and A. Machado-Allison. (2009). “Megapiranha paranensis, a new genus and species of Serrasalmidae (Characiformes, Teleostei) from the upper Miocene of Argentina.” Journal of Vertebrate Paleontology 29(2): 350-358.

Image Credits:
Artwork by Ray Troll, 2005

The other good update from the Bioportal development is that terms can now be found by their synonyms as well. For example, try searching TAO for the ‘dermosphenotic’, which at present isn’t the name of a term in the ontology. Instead, you get the ‘infraorbital 5‘, for which dermosphenotic is a synonym.

Fish morphologists will note that this is actually problematic, since in reality the dermosphenotic is the synonym for the last infraorbital bone. In zebrafish, with which we seeded the TAO, this is indeed the 5th in the series of infraorbitals, but in other clades of teleosts it is the 6th or yet another one. But that’s another story, which we’ll highlight in a forthcoming post on building the TAO.

What’s in the TTO?

The TTO contains slightly over 35,000 terms, of which 30,385 are species, 5045 are genera, and 542 are families. The ontology is organized as a traditional taxonomy, which is also refered to a class hierarchy – thus the species Danio rerio is a subclass of the genus Danio, which is a subclass of the family Cyprinidae. In addition to terms from the Catalog of Fish (CoF), we have added a small number of ‘higher level’ taxa, which allow the TTO to have Craniata as its root.

The TTO also contains a set of taxonomic rank terms – ‘genus’, ‘family’, ‘order’, etc. Most of the taxa named in the ontology are tagged with one of these rank terms, using a property called ‘has_rank.’ This structure is virtually identical to the NCBI taxonomy ontology that is periodically generated by Chris Mungall. The current structure is diagrammed in the figure below. I have constructed a separate ontology of rank terms, which will be submitted to the OBO community in the near future.

The TTO also contains over 38,000 taxonomic synonyms, mostly at the species level, but there are also some at the level of genera.

We have also consulted with taxonomic experts for several Ostariophysian families, including Siluriforms, Characiforms, and Cypriniforms. One benefit of the contributions from area experts is the addition of several fossil taxa, particularly for Siluriforms. Although fossil taxa are not included in the CoF or in the NCBI taxonomy, which focuses on taxa which have molecular data, inclusion of fossil taxa is consistent with the use of this ontology to support annotation of morphological characters. For taxa that have not entered the TTO as an entry in the CoF, we try to include a doi or similar identifier as a database cross reference.

For taxa that are mentioned, but are not actually described in a publication (e.g. Abramites sp. appearing in Fink and Fink (1981)), we include the source publication as part of the name, for example: “Abramites sp. (Fink and Fink 1981).”

There is a Wiki page that lists all the changes we have made relative to the last version directly generated from the CoF. This is currently from November 2007, though we will be generating an update from the January 2008 CoF in the near future.

Constructing the TTO

The TTO was constructed from a database dump of the Catalog of Fish that was very generously made available to us by Bill Eschmeyer and Stan Blum. The dump consisted of three tables: species, genera, and lineages. Each table consisted of rows of names, with the status of each name and, if appropriate, whether the name was currently valid or a synonym. Each row also indicated the higher level group that subsumes each term. I constructed a tool ‘TTOUpdate’ to build the OBO format ontology from these three tables.

The tool is currently capable of doing limited updates from tables in a special format. Otherwise, updates are currently done by hand, though the next version of the TTOUpdate tool should be more flexible. The next version will also support generation of ‘intermediate synonyms’ by extracting taxon names from the history comments. Currently only names that appear as either current names (which might however, be marked as synonyms) or original names will be extracted from the CoF into the TTO (as either valid term names or synonyms).

Browsing the TTO

We do not have a tool specifically for browsing the TTO, however, there are several options for doing so. The TTO is available on NCBO’s bioportal, though we have been having some difficultly with that site. However, the TTO is available as a text file (OBO format), can be visualized as a tree, and can be searched from here.

If you are familiar with OBOEdit, you can download the text version from any of the usual OBO respositories (e.g., the source forge cvs ). The cvs browser will also let you see another view of the changes to the TTO, in terms of tracker items and other requests that each change addresses (I do try to write meaningful commit comments).

The ontologies were deposited into the OBO versioning system already in November, but a database loading problem prevented their functioning in the BioPortal browser earlier.