New taxon Dipnotetrapodomorpha in NCBI taxonomy

For the annotation of homologies in Bgee, we are presently curating in Uberon the taxonomic level at which each homologous relation is correct. For example, muscle is homologous accross Metazoa, while placenta is only homologous among Mammalia. For this, we use NCBI taxonomy IDs.

In the process, we ran into a problem: many structures are homologous between tetrapods and lungfish, but not shared by coelacanths. And there is no NCBI ID for the grouping of tetrapods and lungfish.

lungfishAfter checking the literature, we found (i) the taxon Rhipidistia in Wikipedia, but which seems mostly used for fossils, and (ii) the taxon Dipnotetrapodomorpha introduced in the latest edition of Fishes of the World (Nelson 2006), exactly for the purpose we needed.

We thus wrote the following email to NCBI:

In the NCBI taxonomy, at present, Sarcopterygii (8287) is divided in three groups which are not further clustered.But the literature now strongly supports the position of Dipnoi (7878) as sister group to Tetrapoda (32523) to the exclusion of Coelacanthimorpha (118072), e.g.:

http://www.nature.com/nature/journal/v496/n7445/full/nature12027.html

http://mbe.oxfordjournals.org/content/early/2013/05/13/molbev.mst072.full

The standard reference book for fish taxonomy has suggested the term Dipnotetrapodomorpha for this grouping of Dipnoi and Tetrapoda (Nelson 2006, p. 461):

http://books.google.ch/books?id=exTV-GLnCB4C&lpg=PA461&ots=aW0gNAETbp&dq=dipnotetrapodomorpha&pg=PA461#v=onepage&q=dipnotetrapodomorpha&f=false

This term has started to be used by the phylogenetic community, e.g.:

http://currents.plos.org/treeoflife/article/the-tree-of-life-and-a-new-classification-of-bony-fishes/ (Figure 1)

We use NCBI taxonomy to annotate computationally homology of anatomy between animals, in the context of Bgee (http://bgee.unil.ch/) and of Uberon (http://uberon.org/), and there are many anatomical structures which are homologous between lungfishes and tetrapodes, to the exclusion of coelacanths. Thus an NCBI identifier for this grouping would be extremely useful.

We thus request the introduction of the term Dipnotetrapodomorpha in the NCBI taxonomy, designing the grouping of Dipnoi and Tetrapoda.

The NCBI taxonomy team has been very reactive, and four days after our request the term has been added:

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1338369

So next time you look at the long string of taxonomic terms linking Homo sapiens to the root of the tree of life in NCBI, you know whom you have to blame for having yet another term in that list.

And all our thanks go out to the wonderfully reactive NCBI taxonomy team!

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About bgeedb

This is the blog of the database of gene expression evolution Bgee, at University of Lausanne and Swiss Institute of Bioinformatics. http://www.bgee.org/
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2 Responses to New taxon Dipnotetrapodomorpha in NCBI taxonomy

  1. Pingback: Don’t complain about NCBI taxonomy, improve it! | Marc Robinson-Rechavi

  2. Pingback: Aidez vos enfants à classifier des animaux comme des pro | Tout se passe comme si

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