Tag Archives: nomenclature

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.


So why should we care about this system of nomenclature.

Shingleback from South Australia. Photo from Wikipedia.

Shingleback from South Australia. Photo from Wikipedia.

Among the many things I do with taxonomy and systematics is I am a regular follower of a couple of List-Servers that cater to this field. One of those Taxacom has been around for quite some time. I try to be a bit of a back ground viewer and only get involved on occasion. However I do read all the posts. A post was put up the other day entitled “Why defend the code” now that I had to say something about. Some may worry that maybe I should not talk about some of the downsides, but I do so in the hope of bring understanding. I want people to take an interest in the Code, I want people to defend and teach the Code. As this piece is largely a commentary it will have fewer references, so please consider this one an opinion piece, it stems from a discussion I commented on in Taxacom.

But this begs the question, why should we defend this system of nomenclature that we have been using in one way or another since 1756. The Code now in its 4th edition with a 5th in preparation is old, maybe it’s not keeping up to date with the times. Maybe it is being stressed by the speed of advancement in publishing methods, the speed at which new technologies are developing. It was designed in another world. So why should we bother. That is the question today.

One of the reasons is the sheer workload; a 2011 census estimated that there were approximately 7.7 million species of eukaryotes of which a little under 1 million were described with 10000 species added every year. Looking at our area of interest here there are some 10200 odd species of described reptiles in the world. That’s a lot of work and increasing our workload by dumping the system that named what has been done and replacing it with something else seems to be a step backwards. It is clearly going to take many more years of work to describe the rest of these species, and of course I am only talking about eukaryotes here.

Another factor here is that taxonomy and nomenclature are very specific fields, which to be honest most people do not take that much of a thrill from. Your ecologist, manager or medical researcher just wants to know what to call it, they do not care why. This may sound a little callous, and to be fair it’s not true of everyone, but what they are saying is they need this nomenclatural system to be stable. Then they can officially use a name for species X and get on with their science. That is not entirely an unfair point of view from their perspective.

This leads to one of the foundation reasons for the existence of our nomenclatural system in the first place. I have mentioned it before, it’s communication. Common names and scientific names. I grew up knowing a lizard that I called the shingleback, in NSW of Australia that’s what we called them. However I have since learned that they can be called stumpy tails, bobtails depending on where you are from, but they are all Tiliqua rugosa. The common name does not matter in the end, that scientific name is where we can connect all the short-falls of our very fallible language differences over distance. Or worse across language. For example the “Argentinian Snake Neck Turtle” also known as the “Cágado pescoço de cobra” are both names in different languages for the chelid turtle Hydromedusa tectifera. This is the foundation of why we use the system of nomenclature that we do.

Hydromedusa tectifera. Photo from Wikipedia.

Hydromedusa tectifera. Photo from Wikipedia.

So the point was made, why defend the code? Does it need defending? Well yes it does. I find it quite interesting that this document called the Code has been followed for so long. I can think of very few sets of rules that have stood for so long with no requirement to follow them. Yes that is true we follow the ICZN Code voluntarily. There is no law requiring it, no rules that state we must name animals this way, we just do it. The reason for that is it is convenient, it is helpful and by and large it is reasonable. It also provides a stable pillar of how to do this where everyone can be on the same page. The Code is not perfect, it has issues of language that need to be addressed, it needs to be updated for modern technology but by and large it works well. So if it makes so much sense and everyone is mostly happy with it what is the problem?

I have alluded to one of the problems in a previous post where I said that the Code was written under the premise that almost all scientists, almost instinctively, carry out their work according to a set of ethics. They follow a method that other scientists can accept in terms of things such as plagiarism, acceptable levels of evidence and methods (for the time) and in general to treat each other well and not use science as an opportunity to get on a soapbox. The Code instilled these ideals into their appendix on ethics and as such they are not rules within the code, just suggestions, for want of a better word.

Now we have a dilemma, not all people are using the code ethically. Not all are following the principals behind the code and this causes major issues. One of the issues it causes is a considerable amount of tension between individuals. This should not occur but unfortunately it looks bad when people see it. This is not something new, it has happened many times over the years. However, with the modern world and online discussions, twitter, Facebook and e-mail this news gets spread far and wide and quickly. It brings disrepute to the parties involved. Unfortunately it is the case that for some of those involved this disrepute has little effect on, whereas other it will do. We end up with dual nomenclatures, dual taxonomies; i.e. the same species having more than one name or more than one concept. This breaks down the stability this system has had over many years. There are also many insults and libelous claims made, but on International forums these are hard to do anything about. From the outside looking into this world of infighting inside nomenclature it looks petty. It makes people wonder if maybe there is another, maybe better way. So the Code is under attack, from within and from the outside. This system of nomenclature must be defended and there are a number of ways to accomplish this.

People have been in recent years suggesting alternatives to the ICZN code, perhaps the best known is PhyloCode. To be fair to the proponents of PhyloCode they have not taken advantage of the recent issues in ICZN nomenclature they developed their ideas for other reasons. So a difficulty for the ICZN Nomenclatural system is that alternatives have been put on the table. We cannot ignore that and hope the problem will go away.

One of the most important things that can be done for Nomenclature is to teach it. The numbers of professionally trained taxonomists in the world is declining and has been for some time. These taxonomists are also an aging group, which means we are not being replaced. So to the Universities of the world you need to stop saying we need more taxonomists and actually train them. This of course means we need money in those Universities earmarked for the training of taxonomists. Now by taxonomy I mean a lot more than gel jockies. Sorry for the shot at the molecular systematists. The reality though is that we need morphologists too, particularly since we are now using fossils to calibrate molecular trees. Well you cannot do that without morphology. As an integral part of teaching that taxonomy we must teach nomenclature. One of the sad things with nomenclature is that those who are taking advantage of the Code and bringing it into disrepute, in some ways know more about the code than the professionals who try to abide by it.

The next thing we need to do is decide that there is a line that will not be crossed. That may need some tightening in the next version of the Code to make possible, but horrifically unethical behavior is not tolerated anywhere and should not be in taxonomy either. People know what I mean by that, there are lines you do not cross in society with your behavior without consequences it should be the same here. We cannot have material effectively shoved down our throats no matter how it’s presented. Some people have suggested various forms of online voting and analysis by other taxonomists to determine if a name is acceptable. However that is done seems like a good step forward.

The next thing that needs to be done I believe, is the ICZN needs to be visible. They need to be seen by all the different groups. This would probably mean that they need to ensure their membership includes people from a wider range of taxonomic groups. That is just pure politics; people will be more supportive if they see who they are supporting.

Lastly of course, new version of the Code, it’s time for an update, but I will say here they are working on this.

Now I hope that people do not perceive this as a doom and gloom on the ICZN or the Code. It is not. The Code has stood for a long time and we all now need to stand by it. I believe the ICZN and the Code can get through the spate of issues that have come up in recent years. My major plea in all this is to the Universities, teach taxonomy and teach nomenclature and teach them well.

Why nomenclature? A case of history.

Matamata (Chelus fimbriatus) on riverbank, Pacaya Samiria National Park, Peru

Matamata (Chelus fimbriatus) on riverbank, Pacaya Samiria National Park, Peru

One thing I am guessing may be curious is why I a taxonomist and paleontologist, both hard sciences, would be interested in nomenclature. Part of it is of course me and my own interests. It is fair to say that if I had not become a scientist I could easily see myself doing literature I like writing and enjoy books, particularly antique books. I also see it as an important component when studying taxonomy, after all once I determine through scientific methods that a population is a species I do have to decide what it should be called, and sometimes it already has a name, lost and forgotten in synonymy. Unlike much of science where we read the latest findings and older studies are made somewhat redundant by recent advances, the so called cutting edge, nomenclature is the exact opposite with nomenclature we have to start at the beginning.

The ICZN rules determine that the beginning is Linnaeus 1756, the starting point for modern binomial nomenclature. All names prior to that are not available even though Linnaeus copied a number of names from already common usage that go back some even thousands of years, such as Testudo greaca and Chelonia mydas that were used by Aristotle in ancient Greece. In the past I have given historical background for several names here in my discussions of their nomenclatural issues but this time I want to take one further. The Matamata (Chelus fimbriatus) has appeared in the texts of Europe since before Linneaus and  hence has pre-Linnaean names and in this post I am going to trace it back as far as I can go to when it first came to the notice of Europe in its Age of Discovery. It seems the Matamata first came to the attention of European explorers around 1730.

Albertus Seba showing a lizard in the bottle - from Wikipedia.

Albertus Seba showing a lizard in the bottle – from Wikipedia.

In the past I have been told that Albertus Seba (1665-1736) was the first to describe the Matamata in his work “Locupletissimi rerum naturalium thesauri accurata descriptio – Naaukeurige beschryving van het schatryke kabinet der voornaamste seldzaamheden der natuur 1734. However on examining it I find only three turtles from Brazil all described as “Testudo terrestris, Brasiliensis” and figured in Plate 80, figures 2, 3 and 6. Do not mistake this as a binomial name, even if it looks like one, that was not the intent it is in Latin and is meant as the “Forma specifica, locality” That is it is a terrestrial turtle from Brazil. By terrestrial he means its not from the ocean. Figure 2 is a Podocnemis expansa, Figure 3 is a Chelonoidis denticulata and Figure 6 seems to be a Podocnemis unifilis. The Latin descriptions of the specimens in the text would support this by their coloration. Although I have not seen the second edition, published after Seba’s death, it would appear he did not describe a Matamata. This is a very bizare looking turtle its a bit hard to miss.

The first time that the species was however described was by Pierre Barrère (1690-1755) in his work “Essai sur l’histoire naturelle de la France équinoxiale, ou Dénombrement des plantes, des animaux et des minéraux qui se trouvent dans l’isle de Cayenne, les isles de Remire, sur les côtes de la mer et dans le continent de la Guyane”  1741:165.  This Latin text describes the appearance habits of the Matamata that Barrère obtained on his journeys to Guyana and represents the oldest European description I have been able to determine is a genuine Matamata. For those who download it, please note in a PDF reader the appropriate text is on page 181, though this is 165 of the page numbers. He calls it “Testudo terrestris, major putamine echinato, & striato” basically this is saying it is a terrestrial tortoise with an echinate shell that is striated. Again by terrestrial he means not oceanic.

Of course these names are all pre-Linnaean and hence are not available for nomenclature. In Linnaeus’ 1758 edition of Systema Naturae he does mention a Testudo terrestris also as “Testudo terrestris pusilla Worm mus 313” this is not to be confused it is referring to a junior synonym of the Greek Tortoise (Testudo graeca graeca). As may be becoming apparent, quite a few turtles have been called what is effectively “Land Tortoise” over the last 280 years. The link to Linnaeus offered here is a cut-down version with only the turtles in it.

The next description of the species was actually not a bad one, though as I will explain later it cannot be used for nomenclatural purposes. It was the first to describe the Matamata’s infamous facial structures and appendages. This was by Phillipe Fermin (1720-1790) (sorry I can locate no online biography for this person) in a publication called “Histoire naturelle de la Hollande équinoxiale ou description des animaux, plantes, fruits et autres curiosités naturelles, qui se trouvent dans la colonie de Surinam, avec leurs noms différents, tant françois, que latins, hollandois, indiens et nègre-anglois” (1765:51) it is the oldest post-Linnaean name for the species. It was named “Tortue de Terra, en Latin Testudo terrestris, en Indien Raparapa“. He has technically given it the scientific name of Testudo terrestris here and this could technically be the oldest binomial name for the species. It is also the first time the native American name was published. However at a later date this name was dealt with as I shall explain. In Linneaus 1767 and again in 1788 “Testudo terrestris” is mentioned in various combinations that are not relevant to the Matamata. In 1775 Peter Forsskål described the species that is now known as Testudo graeca terrestris a name that was used for many years as either a species or subspecies. The name gained over time what is seen as stability of usage. Being used for the eastern African form of the Spur Thighed Tortoise or Greek Tortoise. It has therefore become destabilising to recognise that this well used name was in fact a junior Homonym to an unused and forgotten name for the Matamata. In nomenclature a homonym is where two names are spelt exactly the same which is not permitted under the Principal of Homonymy, and normally the senior Homonym takes priority.

Johann Gottlob Theaenus Schneider

Johann Gottlob Theaenus Schneider – from Wikipedia

In the meantime back in South America another description of the Matamata had occured. Johann Gottlob Schneider (1750-1822) named the species as we know it today, Testudo fimbriata, now of course in a different genus as Chelus fimbriatus. The spelling change is from what is called the Principal of Coordination, where the gender of the genus and the species names must match. This name also gained long term usage and stability. Interestingly Schneider mentions both Barrère and Fermin in his description of the Matamata and personally I am not entirely convinced he ever saw one. For there is no specimen of the species he had access to at the time, hence there is no holotype. It would seem Schneider’s description is basically based on Fermin and Barrère’s descriptions, in fact he copies part of Fermin’s description word for word. However, it is a binomial name and one of the oldest for the species.  Another description shortly after Schneider was Johann Friedrich Gmelin (1748-1804) who was continuing Linnaeus’ Systema Naturae, I am not really convinced this is a description he called it Testudo fimbria and immediately seems to credit Schneider, it may be a mistake. Interesting to note however he states that Fermin’s specimen came from Surinam, that Barrère’s is from Guyana but makes no mention of any specimen for Schneider.  This one does get listed in synonymies, probably more for safety reasons, ie we cannot be sure.

Figure from Brugiere 1792 of the Mata mata.

Figure from Brugiere 1792 of the Mata mata.

The next description was interesting because this is where we get the common name of Matamata. Jean-Guillaume Bruguière (1750-1798) in a work “Description d’une nouvelle espèce de tortue de Cayenne. Journal d’Histoire Naturelle, Paris 1(7):253–261.” 1792, describes a new species as Testudo matamata, his specimen was sent to Paris and is in all likelihood that later studied by Georges Cuvier. This specimen is from French Guyana. We still do not have a holotype, but I suspect that if Georges Cuvier’s specimens from his 1825 publications on this species are still in the Muséum National d’Histoire Naturelle, then this may be the type of Chelus matamata and the oldest holotype for any name for the species. As best as I can determine Bruguière was one of the first to publish an illustration of the Mata mata.

At this point Ruiz de Xelva described Testudo bispinosa in 1801 and John Edward Gray described Testudo rapara and Testudo raparara in 1831 and 1844 respectively. These descriptions offered nothing new, no holotypes and are listed in the synonymy because they are available names.

The last description of note was by George Baur (1859-1898) this description is very interesting because it may be the only description of an Amazonian specimen of the Matamata. All the others appear to have been Orinoco, being from Surinam and Guyana. In a paper “An apparently new species of Chelys” published in American Naturalist he described the species Chelys boulengerii. This paper is interesting because when compared to Georges Cuvier’s descriptive anatomy paper of 1824 they are strikingly different and this is one reason that leads me to thinking they are Orinoco and Amazonian. These are all one species currently but it is important to try and find old types and try to pin down type localities when possible.

Cuvier's skull drawing (left) compared to Boulengers 1891 (right) drawing of the Chelys boulengeri skull.

Cuvier’s skull drawing (left) compared to Boulengers 1891 (right) drawing of the Chelys boulengeri skull.

After all of these attempts to name this species it was clear there were some issues and this was going to require some attention. So in 1960 Mertens and Wermuth in Case 1459 (to old to look up on the ICZN site)  apart from other housekeeping of names they also requested that Fermin’s name Testudo terrestris be overturned to conserve stability. This was responded to by Holthius (1960) that Fermin’s work was not entirely binomial and hence could be placed on the List of Rejected Works in Zoology. The ICZN handed down their decision (Opinion 660) in 1963 which on this issue agreed with Holthius and the entire work of Fermin was basically declared unavailable for nomenclature. This freed up the name Testudo terrestris (as a subspecies of Testudo graeca) for the Spur-Thighed Tortoise and maintained Testudo fimbriata for the Matamata.  Hence stability of nomenclature was maintained.

That is the complete story of the naming of the Matamata in an effort that lasted 270 years from start to finish.

The Neotype – Why, When and How

Since my last piece was rather short I thought I would write another on a totally different topic. In past posts I have mentioned Neotype’s on several occasions and defined it as more or less as a replacement, or new type for a species.

In the glossary of the Code the Neotype is defined as: “The single specimen designated as the name-bearing type of a nominal species or subspecies when there is a need to define the nominal taxon objectively and no name-bearing type is believed to be extant.”

It has the same function as the Holotype in that it is now the name bearing type of the species. My reasons for doing a post on this is that in my recent description I set one for the turtle species Elseya branderhorsti, or Branderhorst’s Snapping Turtle, pictured above is the Neotype prior to fixation. I have also seen, or at least heard about this being done the wrong way and for the wrong reasons. I would suggest for people who do not understand this to download my recent paper and look at the Elseya branderhorsti section.

First up, and I want to state this very clearly, if there is an existing Holotype (or Lectotype or Syntype) for a species you cannot set a Neotype for that species. If for some reason one is required in this situation then a Case to do so must be submitted to the ICZN for consideration and only they can set the Neotype. An example of this is Case 3628 where Ehret et al (2013) have requested a Neotype be set to replace a poor quality and essentially unusable Holotype for the fossil species Terrapene putnami. They have had to outline their reasons and provide details of a suitable specimen as the Neotype.

Under the Code there are, however, occasions where you can set a Neotype and this needs to be done in a peer reviewed journal, a high quality one that is used to publishing taxonomic or nomenclatural paper is preferred. It must be done for the right reasons and if you look at the relevant Article (75) of the Code one thing I hope is apparent is that it’s actually more difficult to set a Neotype than it is a Holotype (in the original description), and so it should be. There are good reasons for this and one such reason is one practice I have heard of which is setting a Neotype for a species essentially making it a Nomen Novum (new name) which would place it in synonymy with another species. In simple terms someone has found an old name without a type that has been found to apply to an otherwise undescribed species. They set a Neotype to destroy the old name so they can name the now un-named species.

To avoid the above scenario occurring either deliberately or accidently there are many conditions a Neotype must meet. Apart from the point that there must be no existing type you also cannot do it for no other reason than there is no type. The Mata mata (Chelus fimbriatus) has no type, never did, yet there is no justification for setting a Neotype. It is a monotypic genus with no confusion as to which species it is. Hence no justification for a Neotype. If it is demonstrated to be more than one species maybe that could change, but until then it is not justified under Article 75.2 of the Code.

Article 75.3 (1-7) are the qualifying conditions for a Neotype designation. I would suggest people look through them on the ICZN website. Basically you must demonstrate why you need to do this, that there are no other types, describe your Neotype, declare it, and ensure it is in a Museum or similar. One of our difficulties in the Elseya branderhorsti case was determining exactly where the original, lost, Holotype had been collected. We went into a detailed reconstruction of the original collectors travels through southern New Guinea and then used this to restrict the type locality (that is define it better) and then collected our Neotype from this area.

In the paper the entire section on Elseya branderhorsti was about setting up our objective of setting a Neotype for this species, the original was lost, we published photos of the Neotype, measurements, placed it in a Museum (Papua New Guinea National Museum), declared it represented the same species as the original description and importantly presented reasons for setting the Neotype. Our reasons were that Elseya branderhorsti overlapped in range with another species that was new to science that we were describing in the same paper. So it was a clarification of which taxa was which by having name bearing types for both in a region and genus that had seen some very confusing taxonomic and nomenclatural issues.

Despite the point that I have tried to show that setting a Neotype is difficult I have tried to point out why. I hope that people understand that they are, however, very important and can go a long way to clarifying nomenclatural issues. When genuinely needed they should be set and there are many reasons for this. It is generally older names that need this, ie they never had a type or its been lost but there are some newer names where the types have been lost or destroyed by accident.

Describing a species: The “Best Practices” debate.

Southern New Guinea Stream Turtle. Photo by Arthur Georges.

Southern New Guinea Stream Turtle. Photo by Arthur Georges.

I have recently described my 6th turtle species which is pictured here. It is the Southern Stream Turtle, Elseya rhodini, from Southern New Guinea. This species was described in the journal Zootaxa, and its types have been placed in the Papua New Guinea National Museum in Port Moresby. It has been a while since I made a post this is largely because I have been traveling alot and had to do significant editing to complete the paper at the same time.

In any-case in recent years there has been considerable debate about the “Best Practices” for describing new species. In a previous post I discussed taxonomic vandalism and in short the presence of taxonomic vandalism has fueled the debate over this issue. In herpetology the big issue is not how many names someone produces, but how they are done. I myself do not care at all how many species a person does or has described. What matters is that the science of this has the necessary checkpoints to ensure accuracy, integrity and that the conclusions of the examination is within accepted (at the time) scientific theory and practices. Generally it is believed in science that the best way to do this is through peer review.

Peer review and editorial review are two completely different steps in this process. The editor of an article should never be the author of that article, if for no other reason than we tend to be blind to our own mistakes. We know what we mean so that’s what we see. In a large body of text you will miss your own typos and grammar issues. Getting all this right and the formatting is the editors job. Anyone with a good command of the language of publication can in theory edit an article. Peer review though means that the article’s science is checked by people who do know that field of science. The two peer reviewers of my recent description were both scientists who have themselves published new species papers, reviews of genera etc in the past. They know the science and what would be expected and I had little say in who did that, they were chosen by the editor. Hence the editor should not be an author.

The idea in the best practices debate is that because the ICZN rules do not dictate that Peer Review is a requirement that a best practice should be adopted to ensure this happens. The problem of course; who is the judge and jury on this? who decides if an article meets the standard? these are questions that are difficult to answer. One option that has been developed for a while now is the List of Predatory Standalone Journals, this list includes journals with no standing at a scholarly level and it is highly recommended that no nomenclatural acts should be published in them. This at least provides something people can use when deciding which journal to publish in. Another option is to look to where the most taxonomic works are being published these days and that would be the journal Zootaxa that I mentioned earlier. Certainly at present it would be the journal of choice for taxonomic works.

The upside of this debate is that if people wishing to describe taxa do follow this best practice a number of highly dubious issues can be avoided. First is ethics. Science has always assumed a code of ethics among practicing scientists and for the most part all have followed it for the last 150 years or so. There have and always will be exceptions. The ICZN code was written on the assumption that this generally accepted code of ethics would be largely followed. Unfortunately this has proven to be wrong. We now have published articles that make horrific accusations against people, we have academic theft and what is genuine narcissism  overriding any common sense. Peer review should be able to get rid of this. The next is that the science is done well and in an acceptable fashion so that the work is useful. Nothing worse than nomenclatural acts that instead of clarifying an issue actually make it worse. I have discussed some of these in the past (for example Emydura). The third of course is simply the polarizing effect of such poor quality work being published. This causes issues between those that will follow the ICZN code to the letter, vs those that want a bit of decent science in it also.

The best practice debate goes beyond fringe writers trying to force their views down the majority of scientists throats, ie their on a soapbox. Another issue in this is lack of supportive data for nomenclatural acts. You cannot look at the relationships of species without examining all the known species in a group. This includes both the living and the fossil species and requires comprehensive multidisciplinary datasets. Basically what this is saying is that it is fine to present a molecular phylogeny, but without inclusion of a morphological dataset, morphometrics and the extinct taxa if there are any, nomenclatural acts should never be made. There are too many cases in recent years now where changes to the nomenclature made just on Molecular grounds have proven to be incorrect once more data is added. These are other examples of best practices, and should be done.

Rapid and unnecessary change to the nomenclature is annoying, particularly to non taxonomists. Many people who are not taxonomists want stability, unfortunately they also do not know what that actually is. They think stability includes the combination, ie the genus + species, it does not. It actually means that the species name should remain stable because of the Principal of Priority, or the Genus name.  But there is no requirement for species to be kept in the same genus as much as possible. However, too much change causes management problems. So here again the peer review process can step in as a check point. Are the changes in an article justifiable, ie is there enough data to put everyone through the annoyance of the change. With the change though it is possible to be too conservative as well as too free with changes. Ultra conservatism in nomenclature is quite frankly a cause of extinction, because if species are not recognized, they are not protected. For evidence of this go through the criteria of listing in the IUCN Redlist, one very important consideration is high endemism. Conversely ultra freedom in nomenclature wastes conservation funding. A balance between the two must be achieved. Yet another opportunity for peer review to be a checkpoint.

In the end taxonomy is a multidisciplinary science, and unlike most others its acts cannot be undone. Hence it should never be done inadequately. It is a science that needs a checkpoint process such as peer review.

Taxonomic Publication, its abuse and misuse.

I guess it was inevitable that I would have to write on this subject. After all I am discussing reptile names and herpetology is one area that has suffered a history of what is generally called “taxonomic vandalism” sometimes “taxonomic terrorism” but whatever term you use, it is an unethical means of producing names solely for naming rights and self glorification.

I recently presented at a conference on this very topic and also have one paper published (Thomson, 2014) and another in press on this issue in the Bulletin of Zoological Nomenclature. This “vandalism” is an unfortunate area of nomenclature and taxonomy and one that is degrading to the science of Taxonomy, undermining the trust other branches of science may have in it. This is not unique to herpetology with various invertebrate groups and also fish suffering from the same problems.

First off lets look at why this is even an issue. In most science we can just ignore obvious bad science, although it can still do damage. The anti-vaccination debate is a prime example of this, not only was the original paper linking autism to vaccination bad science it was also false science, so scientists can ignore it, except that in this case it had already done considerable damage by creating an anti-vaccine movement who believed this original false paper to be true. In taxonomy however we have a problem and that is the Principal of Priority. This means that if a name is available and it is the oldest name for a particular valid taxon, then that is the name which must be used. Therefore if someone creates a group of names with no real idea if they really apply to valid taxa those that are eventually proved to do so, using good scientific methods, end up being used by sheer luck.

The Code was written under the premise that scientists always acted, for the most part, ethically, and a set of ethics are included in the code but only as an appendix, and therefore they are only recommendations. It did not occur to anyone back then that people would come along who would meet the Code at a bare minimum and would ignore the ethics of good science. People who would lie, steal the work of others and self publish for the sake of “naming rights”. Unfortunately such people do exist. In hindsight this shows a lack of foresight by the original authors of the code.

One case that has been completely dealt with was that of Wells and Wellington (1985). In their self-published paper they named some 600 taxa. These names were for Australian taxa only. They also did this in a time long before the internet and hence the damage was a little limited. However their actions did cause an uproar in Australia and the Australian Society of Herpetologists submitted a Case (No. 2531) to have this work, and another from 1983 by the same authors, declared unavailable for the purposes of nomenclature. Unfortunately the ASH correspondents stated that among their reasons for objecting was the taxonomic disruption the paper was causing and this led to the inevitable failure of the case. Both the proponents and those against Wells and Wellington had inadvertently agreed that this was a taxonomic issue. As I have mentioned in my previous posts the ICZN does not deal with taxonomic issues, only nomenclatural matters, so this left the ICZN little option but to refuse to rule on Case 2531 and leave it for taxonomists to sort out, as per their Opinion published in 1991. This also effectively declared the works as available publications, which meant the usage of each name had to be determined taxonomically, which has taken some 30 years to achieve.

One factor to consider with Richard Wells and Ross Wellington is that both are highly skilled herpetologists, particularly with snakes and lizards, and hence many of their taxonomic changes have proven to be correct, hence many of their names are in use.

The subject of my recent talk however was the journal Australasian Journal of Herpetology (AJH). This particular journal has a single author and editor and is privately published. It therefore goes against the best practices for taxonomy as recommended by a number of papers (eg. Kaiser et al, 2013; TTWG, 2007, and others). What these papers recommend, and most taxonomists abide by automatically, is that all papers making nomenclatural acts (naming species, re-combinations or synonymies) must be published through the legitimate recognised scientific peer-review process. This will reduce or prevent errors, ensure there is a good scientific underpinning to the changes and ensure they are accepted by all. It will also prevent offensive rhetoric being published in papers that should not do it.

The AJH has named some 730 (approx) taxa at various levels and most are highly contentious with many in the scientific community refusing to use them at all. The problem this causes is a dual nomenclature. Dual nomenclatures are very dangerous to science as it causes communication breakdown. In this particular case the author, although an experienced herpetoculturalist and natural history herpetologist of some repute with snakes, has moved beyond his own knowledge and started naming groups for which he has no demonstrated expertise, and he is using the published phylogenies of others and basically just names their clades. It is clear this is being done because some of the names closer to his expertise are probably accurate based on some personal knowledge, i.e. Australian snakes, but as he moves further afield: e.g. American and Asian turtles, crocodiles and American pit-vipers it is clear he has never examined these species because of the clear mistakes and errors in his papers. It is also clear he has never examined the types (name bearing specimens or species depending on level) and has not actually read all the pertinent literature. This is something I went to great lengths to explain is of importance in my earlier posts.

So what should be done about this? Well many years ago on Kingsnake.com I posted a statement. It was not original, I got it from turtle expert Peter Pritchard, and this is how it goes: “Refute or accept, there is no ignore in Taxonomy”. I still stand by that statement. There are names that I have refuted, and which have since overwritten. I declared a number of names unavailable for a variety of reasons under the Code and some of the taxa involved I have subsequently given names to, while others have also renamed species. In other words I refuted the availability of the names using the Code. This was presented in a paper by John Iverson, myself and Arthur Georges (2001). But its not so easy a task with the names in AJH as many of them are available for use, yet few people want to use them, hence the options proposed by Kaiser et al. (2013).

Most recently the stakes were raised by the author of AJH. He submitted a Case (No. 3601) to the ICZN regarding one of his generic names, Spracklandus. He hopes to have the generic name validated and with it the issue of AJH that contained the description, which by default could lead to the validation of the entire journal for nomenclatural acts. This clearly requires a response and a number of comments have been published in the Bulletin of Zoological Nomeclature (BZN, the journal of the ICZN) while more forthcoming. It remains to be seen what will be done in this Case.

It is likely that no matter what happens the names in AJH will be ignored by the global herpetological community. This will lead to dual nomenclatures, and continued contention and confusion. It may in the end require the herpetologists of the world to come together to create what is known as a LAN (List of Available Names) under Article 79 of the Code. In this process a world recognised body can create a list of accepted names and submit it to the ICZN to be recognised. Under a LAN any unaccepted names can be thrown out and effectively made unavailable.

Whatever the solution as you can see, poor science is hard to ignore in Nomenclature. It is therefore imperative that you all understand the take home message of this post. Taxonomic works must go through the full peer-review in a high quality journals that specialise in taxonomy, for example Zootaxa.

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.