Friday, October 12, 2012

Making EZ to ID. More thoughts regarding GUIDs

The BiSciCol team is feeling very prolific!! After several brainstorming sessions in the past several weeks, especially after a short retreat at the Museum of Vertebrate Zoology, UC Berkeley, we feel we really have a plan to propose to the scientific collection community. Find more in our blog.

Saturday, August 25, 2012

News from the BiSciCol team

The BiSciCol project is making great progress and perhaps we nailed down a great way to move forward with assigning globally unique identifiers to digital objects.  Read our latest news update on how we think we can 'GUID'.

Monday, June 4, 2012

Postdoc position available

A 1 year (extendable) Postdoctoral Associate position is available in my lab at the Florida Museum of Natural History, University of Florida starting as soon as possible.  This person will primarily contribute to the BiSciCol project and will work closely with a fantastic group of young developers. We are looking for a highly motivated and creative individual, ideally with experience in UI and RESTful web service development, in addition to Java programming (yes, Java is a must have!).  Please, email me if you wish to have additional information about this opportunity.

Monday, January 16, 2012

Species and Phylogenetic Nomenclature

DISCLAIMER: This post may inflame you if you are not a supporter of phylogenetic nomenclature, so my advise to you before you go on is don't ruin your day and skip reading it.  If you choose to read it, please keep in mind this is not a debate on the validity of the PhyloCode (that's a given to us). However, if you fundamentally share the philosophy at the core of phylogenetic nomenclature, then you may want to know what's going on among us proponents.

Last October, Brent Mishler (University of California, Berkeley), David Baum (University of Wisconsin, Madison) and I submitted a proposal to the International Society for Phylogenetic Nomenclature (ISPN) in order to remove all mention of "species" from the PhyloCode.  We provide justifications for this goal in a supporting paper (Cellinese et al. 2012). The proposal is currently being discussed by the ISPN Committee of Phylogenetic Nomenclature, and given our paper is also in review, this seems to be the right time to stir the pot a little more.

All proponents of phylogenetic nomenclature would agree that the PhyloCode is about naming clades, and removing ranks from nomenclature.  Yet, unfortunately there remain aspects in the current wording of the Code that are not about naming clades and that retain rank considerations.  These aspects all surround the traditional Linnaean rank of species. The PhyloCode currently states that "In this code, the terms "species" and "clade" refer to different kinds of biological entities, not ranks" (note 3.1.1.).  While the concept of species implicitly endorsed by the PhyloCode, that of de Queiroz (2007), does indeed assume that species and clade are distinct entities, this is not universally accepted by any means.  Many different species concepts are currently applied across the different biological domains (Mayden1997).  Some, like de Queiroz (2007) view species as lineages.  Others (e.g. Mishler 1999; Pleijel 1999; Mishler and Theriot 2000 a,b,c; Baum 2009) view species as ranked or unranked clades.  But this disagreement is not relevant to a Code of nomenclature that is (supposedly) rank-agnostic and concerned only with naming clades.  The debate over species concepts does not need to be solved for the purpose of naming clades under the PhyloCode.  Phylogenetic nomenclature can and should remain logically independent from the philosophical debate about species.  Therefore, the PhyloCode need not and should not anoint any particular species concept as the correct one.  By leaving the word “species” out of the entire document it will be clear that the PhyloCode is available to all systematists regardless of their views on the nature of species.

The PhyloCode as currently constructed works under the assumption that species are not clades, yet paradoxically brings species into the naming of clades in a couple of damaging ways.  One is by its current ruling (Article 10.9) that traditional species names should be disallowed for clades.  The current version of the PhyloCode, influenced by Dayrat et al.(2008), effectively applies special rules at the “species” level.  When a clade happens to approximate to a traditional species in content, the PhyloCode now mandates that that clade be given a new name, distinct from the traditional species name.  This is unlike the case when clades approximate in content to genera or families (etc.), in which case the Code strongly encourages the conversion of the traditional name into a clade name.  In this way, the PhyloCode establishes parallel nomenclatural systems for species and species-approximating clades.  We argue that this is illogical; as there are no ranks under the PhyloCode, there should not be an explicit or implicit rank of species.  Phylogenetic nomenclature should accommodate clades whose content is roughly comparable to current species (under whatever species concept).  We propose that the PhyloCode be modified to be neutral about species and thus to accommodate all users, including those who wish to be able to attach appropriate names to clades that approximate taxa at the traditional species level.

Another way in which the current version of the PhyloCode generates problems for itself  is that it allows species to be used as specifiers for clade names (Art. 11), and relegates the governing of species names to the traditional Codes (Art. 21). This means that the PhyloCode is not a freestanding system of nomenclature.  This is unwise; the PhyloCode should be independent and self-contained.  No rules in the PhyloCode should depend on rules in the traditional Codes, including rules for species names.  This is easily solved by requiring that specifiers under the PhyloCode be museum or herbarium specimens (physical reference objects, possibly Linnaean types at the discretion of the taxonomist) at all levels, never Linnaean binomials per se.  Linnaean species binomials are incompatible with phylogenetic taxonomy because they naturally imply the existence of a genus rank, and they are incommensurable with phylogenetic taxa because they are named using only one type (Cellinese et al. 2012).

Since its purpose is to name clades, any mention of ‘species’ in the PhyloCode should be removed.  We propose to streamline the PhyloCode to focus solely on rational procedures for naming clades with uninomials at any level including the traditional species level.  The rules governing names of clades at and around the traditional species level should follow exactly the same rules and recommendations as at higher levels.  To view the original proposals we submitted to ISPN click here. Also see the posting at Phylonames.


Cellinese, N., Baum D.A., Mishler B.D. 2012. Species and Phylogenetic Nomenclature. Syst. Biol. 61: 885-891.

Baum D. A. 2009. Species as ranked taxa. Syst. Biol. 58:74-86.

Dayrat B., Schander C. , Angielczyk, K. D. 2004. Suggestions for a new species nomenclature. Taxon 53:485–591.

Dayrat B., Cantino P.D., Clarke J.A., de Queiroz K. 2008. Species names in the PhyloCode: the approach adopted by the International Society for Phylogenetic Nomenclature. Syst. Biol. 57:507-514.

de Queiroz K. 2007. Species Concepts and Species Delimitation. Syst. Biol. 56:879-886.

Mayden R.L. 1997. A hierarchy of species concepts: The denouement in the saga of the species problem. In: Claridge M.F., Dawah H.A., Wilson M.R., editors. Species: the units of biodiversity. London: Chapman and Hall, p. 381-424.

Mishler B.D. 1999. Getting rid of species? In: Wilson R., editor.  Species: new interdisciplinary essays. Cambridge: MIT Press, p. 307-315.

Mishler B.D., Theriot E.C. 2000a. The phylogenetic species concept (sensu Mishler and Theriot): monophyly, apomorphy, and phylogenetic species concepts. In: Wheeler Q.D., Meier R., editors. Species concepts and phylogenetic theory.  New York: Columbia University Press, p. 44-54.

Mishler B.D., Theriot E.C. 2000b. A critique from the Mishler and Theriot phylogenetic species concept perspective: monophyly, apomorphy, and phylogenetic species concepts. In: Wheeler Q.D., Meier R., editors. Species concepts and phylogenetic theory.  New York: Columbia University Press, p.  119-132.

Mishler B.D., Theriot E.C. 2000c. A defense of the phylogenetic species concept (sensu Mishler and Theriot): monophyly, apomorphy, and phylogenetic species concepts. In:   In: Wheeler Q.D., Meier R., editors. Species concepts and phylogenetic theory.  New York: Columbia University Press, p.  179-184.

Pleijel F. 1999. Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida). Syst. Biol. 48:755-789.