Tuesday, November 14, 2006

Synonomy and kinds of name

Just wanted to write this example down before I loose it. Browsing Bill Piel's trees in Google Earth, and was looking at Lee et al.'s paper (doi:10.1111/j.1365-294X.2005.02707.x) on Physalaemus pustulosus. Searching in iSpecies.org lead to records in GenBank, whereupon I stumble on the fact that in GenBank it is Engystomops pustulosus (Taxonomy ID: 76066). Following up the reference on the NCBI taxonomy page, I find a
PDF of the paper freely available (although only a URL for an identifier). Browsing the GenBank records (e.g., DQ337249), I find Ron et al. (10.1016/j.ympev.2005.11.022). Among other things, this paper refines the genus Engystomops:

Engystomops, Jiménez de la Espada 1872 (converted clade name). Definition: clade stemming from the most recent common ancestor of E. petersi Jiménez de la Espada 1872, and E. pustulatus (Shreve, 1941).

Then paddling off to HerpNET I query for "Engystomops pustulosus" and get one record, whereas for "Physalaemus pustulosus" I get lots of records (although the geographic range doesn't include all the localities in doi:10.1111/j.1365-294X.2005.02707.x.

My point? Well, don't really have one, except that again we are clicking around different web sites to get a complete picture of what is going on, important data are attached to different names for the same animal, and the nature of those names themselves may vary (for example, Nascimento et al. define Engystomops as a set with a type species (E. petersi), whereas Ron et al. (10.1016/j.ympev.2005.11.022) define Engystomops as a least common ancestor of two taxa on a tree. All of this makes integration a challenge, to say the least.


Nick Isaac said...

You raise an important issue: one of my pet hates, in fact.
Most databases are stuck with the names of a single taxonomy, yet the taxonomy for many clades are in constant flux, both at species level and above.
I've been collating data on primate ecology for the past 4 years. The number of species has doubled recently, which is a recipe for many dark hours working out (using maps and species descriptions) how the name in the study relates to the list of names in my preferred taxonomy.
At the very least, we need to encourage the purveyors of data archives to build in flexibility against future taxonomic change.
(end rant)

sexy said...