Category Archives: Lizards

Wikispecies – Lets just list them all!

WikiSpecies LogoSince it has been a while since I posted anything I am going to talk about a project I am heavily involved in. Wikispecies. What is it? Well Wikispecies is not Wikipedia for one. So do not go there expecting to see articles on all your topics of interest, some 5 million on the English Wikipedia. No when you arrive at Wikispecies you will see that it is about one thing. Taxonomy and Nomenclature. That is the names of all living things organized by their hierarchies. So I will take you for a tour of the site. A big part of why I am writing this I will conceed is I am looking for more editors for Wikispecies. In particular taxonomists to edit the sections on the species they know. For myself, as I stated I am directly involved in Wikispecies. My user page on Wikimedia Foundation Projects is Faendalimas. The link on my name will take you to my User page on Wikispecies. On there it can be seen that I am a Bureaucrat, a CheckUser, and an Administrator. Basically apart from editing I am involved in a considerable about of policy development and management for the site. On my user page you will notice that my real name, Scott Thomson, is also a link. This is because I have named numerous taxa and hence have a taxonomic authority page which has my various taxonomic publications, category lists to all the taxa I have described etc. I would encourage anyone who has named species to be involved in this. It is a great opportunity to have a say in what goes on your authority page, including links to all your publications. You can make sure your species you have named are all listed, listed correctly, have all the data included.

Elseya rhodini So to walk you all through an example I am going to use a species I have discussed here before. Yes it is one I named, but it is an easy example for me. The southern New Guinea Stream turtle, Elseya rhodini, has its own page and I will explain what is in it (for this article I suggest opening the Wikispecies page for Elseya rhodini and refer to it). So each species has particular information presented. Photo’s are optional on Wikispecies. We put them there when they are available. But are not needed. Wikispecies is about information. The first thing to notice is the hierarchy is presented. Every parent taxon that the species Elseya rhodini belongs to is listed. For example it is a member of the subgenus Hanwarachelys and by clicking on this you can see its sister species, Elseya schultzei and Elseya novaeguineae, next up of course is Elseya, then Chelodininae etc. Each jump up the hierarchy shows more and more related species. Each species page has the type data, the holotype, the type locality, the original reference (often downloadable). Lets imagine you were embarking on a study of the taxonomy of the Elseya. From these pages you can get all the holotype information, all the original references and the current synonymies of every taxon relevant to the Elseya. As Wikispecies develops, it currently has half a million taxa done, you will be able to do this for any living organism on the planet. That is the scope and plan of Wikispecies.

So how do you become involved. Many probably already can. If you have an account on Wikipedia you can make the account global and actually edit as an identified editor on any Wiki Project. If you have no account create one. If you are not logged in your edits will appear as an ip address and these are not viewed favorably. Once you have an account you can start editing. Of course you will need to learn some wiki markup. The language is very simple to use, and not difficult to learn. But we do use templates. If you click on Edit Source you will see the code of the page. In the code near the top for example is {{Elseya (Hanwarachelys)}}, this is a template, and that piece of code contains the entire hierarchy down to the subgenus name. Another template is {{aut|Thomson}} this one makes all the text after the “|” into small caps. That is my name. There are also features such as double square brackets “[[ ]]” which makes the text a link, or ” … ” which makes the text italic. It is easy to learn and if you look around wikipedia you will find plenty of information on wiki-markup language.

If you look around the site you will see what are known as red-links. Links are supposed to be blue (unvisited) or purple (visited) but not red. Red means the link goes to a page not created. Those pages need to be made. Here is my plea. Anyone who has an interest in life, I do not care what species, take an interest. Edit some pages. Edit the pages on the species you like. That is all. You need the references, type data, and most recent synonymy. With that you can create the page. If you need help go to my talk page, see me on IRC in Freenode Channel #Wikispecies. I will help anyone who wants to edit Wikispecies. Please remember one thing. It is not true that anyone can edit the Wikimedia Foundation pages and destroy someone else’s efforts. New users are considered unpatrolled edits. Every edit is checked by editors who patrol these edits. We also have bots that do it. Vandalism, is generally undone (reverted) within minutes of it occurring. People are always asking for a single site that has all the basic taxonomic and nomenclatural data for all species. Well it is being made. Come help make it. It cannot do it by itself or automatically.


To name it? Or not to?

I was recently sent a pdf of a paper that I found both highly interesting but also presented some nomenclatural difficulties on interpretation. The paper is on a new lizard species produced in a lab as a second generation parthenogenic form that was the result of hybridization (Cole et al. 2014). First I think the results are fascinating and the results of the experiments are a worthy addition to science. However, what is not so clear is whether or not this should have been named as a new species. Parthenogenesis is reproduction, effectively cloning, in single sexed populations of an organism. It is rare in vertebrates but a number of reptiles do this. But those results have nothing to do with nomenclature. Here I am just looking at the nomenclatural decision to name it. I must reiterate as I have mentioned before, I cannot make nomenclatural acts in a blog, so I am making no changes to the taxonomy here. That is for those working on these species to do and publish appropriately.

In their paper Cole et al. (2014) cite the Code, Article 1.3.3, as prohibiting the naming of hybrids, and further they refer to Article 17.3, where parthenogenetic forms are not excluded by the code. They use this as justification for the naming of this form. This is correct the code does state this but it states a few other things as well. I am using this as an example of interpretation of the code. It is written in words in both French and English, hence it does take some careful consideration when reading it.

To interpret the code you must look at the entirety of a sentence, and you must follow through its links to other parts of the code. You must also consider all possible sections that may apply to the given situation. For example this form was produced in a lab is it a hypothetical form? If it is article 1.3.1 would apply, also excluding it from being named. However, I think the authors could argue successfully against that and I would agree with them. The main section of the code that does apply to this scenario is article 1.3.3 so we need to look at it in its entirety; there are 7 parts to article 1.3 I will only list the relevant ones. I am presenting both the French and English versions here, some people insist on using both, though to me in this case they read the same.

1.3. Exclusions. Sont exclus des dispositions du Code les noms propsés

1.3.3. pour des spécimens hybrides nommés comme tels; [pour les taxons d’origine hybride, voir Art 17.2;]

1.3. Exclusions. Excluded from the provisions of the Code are names proposed

1.3.3. for hybrid specimens as such (for taxa which are of hybrid origin see Article 17.2);

Basically article 1.3 is dealing with forms that are excluded from nomenclature, that is cannot be named. Article 1.3.3 is including hybrids in this list and forms of hybrid origin. The important words here are hybrid origin. This form is an F2 generation from a hybrid origin. So this would seem to state that because the parthenogenic form arose because of a hybrid cross in its recent lineage that it is precluded from being named. You need to then follow through to article 17.2 of the code which states:

17.2. it is applied to a taxon known, or later found, to be of hybrid origin (see also Article 23.8); or

17.3. it is based on only part of an animal, or one sex, or one stage in the life cycle, or one of several dissimilar generations, or one morph or caste of a polymorphic species, or a parthenogenetic form, or a specimen which is an unusual example of the taxon (for exclusions see Articles 1.3 and 45.6).

Certainly parthenogenic forms can be named as is outlined in 17.3, but this is referring to wild forms of unknown heritage, if hybrid origin is known it is still precluded by 1.3.3. It is quite possible that those species of reptiles that have parthenogenesis in the wild got there by hybridization events in their history, it is also possible there are other factors involved. Each case would have to be tested. But for this case, it is known that it is from hybridization, the offspring, including the clones of the offspring are still hybrids and should be referred to as such.

Although not actually required by the code, though it is a recommendation, this form also has no type locality. How can a form that only occurs in a laboratory have one? My personal view is that much like the process of domestication, human created forms of other species, be it through hybridization or selective breeding or even other means should not be appearing in the zoological record of the species on this planet. That should be reserved for the species that have occurred naturally. Taxonomy and the Nomenclature that supports it are used to conserve, protect etc the species in their natural environments. As I have said I think the experiments that developed this form and what it tells us about evolution etc is brilliant. But it does not need a formal name to do all that.

The Eastern Water Dragon, nomenclatural confusion and poor quality.

For many people the Eastern Water Dragon has long been identified as Physignathus lesueurii a name combination that goes back to John Edward Gray’s work of 1845 (Amey et al., 2012). While in the genus Physignathus it shared that position with the type species of the genus the Chinese Water Dragon (Physignathus concincinus). Andrew Amey, Patrick Couper and Glenn Shea (2012) detail the long nomenclatural history of this species and other relevant species and genera and their paper can be downloaded here. So I will not revisit the entire history. Suffice it to say that with the genus Physignathus being shown to be paraphyletic, and the type species being P. concincinus there is no alternative but to put the Eastern Water Dragon elsewhere.

This particular post is a further demonstration of the type concept, but this time for genera. I am using this example because it would seem to be fairly well resolved now. In my previous post I was largely referring to types for species, in genera there is a type species, again wherever the type goes the name goes. So with P. concincinus being the type species of Physignathus it is the only species that has to go with that name, any species included in the genus alongside it must be related to it and the group must be monophyletic.

This is why various other names listed by Amey et al. (2012) are not available for the Eastern Water Dragon. Genera such as Istiurus originally described by Georges Cuvier in 1829 but for only a single species, I. amboinensis, and that species is hence the type species for Istiurus, by what is known as monotypy. If a genus is described with only one species, that species is its type species. This cannot be changed and since the genus Hydrosaurus was resurrected for the Sailfin Lizard this makes the genus Istiurus a junior synonym of Hydrosaurus, as explained by Amey et al. (2012). So this is another genus that cannot be used for the Eastern Water Dragon.

In the end it comes to the name Intellagama described by Richard Wells and Ross Wellington in 1985 as the oldest available name for the genus containing the Eastern Water Dragon (as Intellagama lesueurii). The difficulty with this name is not that it was not declared or published. Although there have been many criticisms of Wells and Wellington (1985) including a challenge to its validity to the ICZN it is a valid publication. This is because the ICZN deemed the issues with the publication to be taxonomic, not nomenclatural. As I have already pointed out earlier the ICZN only deals with nomenclature. So the publication is to be accepted but not necessarily all the names within it. Amey et al. (2012) point out that this genus has mostly been seen as a junior synonym of Physignathus mainly because it was not diagnosed from the Chinese Water Dragon.

Here is a point on the major difficulty in nomenclature. The types of information presented in a description matters. It is important to name a type species for generic descriptions.  It is true that if the named genus is monotypic then the only species in it is inferred as the type species, but otherwise it must be named. It is also important to diagnose it appropriately with a significant amount of evidence from its related genera. Just as you would with a species. This can be as a revision of previously published work or  done in the description.

The difficulty in the case here was that the genus Intellagama was not diagnosed from the genus containing the Chinese Water Dragon (Physignathus), this did not make the name unavailable but made it unclear how to use it, so it was put in synonymy. It was not until a paper by Townsend et al. (2011) that the usage and justification for the genus was published. It is important to note here that although the name was originally coined by Wells and Wellington (1985) that the evidence that it was actually a genus, and how the name was to be used was not defined until 2011.

It is for this reason that as has been pointed out by many recent authors when discussing a variety of issues in taxonomy and nomenclature that the preferred best practice for the erection of new names is through the peer reviewed journals in this way it can be hoped that mistakes and unclear names can be avoided.