The Impartiality Ethic.

     Among my many current projects, including a preliminary exam, I'm writing a novel. I was convinced by a colleague to join in the National Novel Writing Month goal back in November, and have managed to put nearly 20 thousand words into an original story. Since I write what I know, the story is about grad students, imposter syndrome, taxonomy, ICZNerdery, and natural history in a world where names have power. It will probably never see the light of day, but I did want to mention one thing. In the story, the idea of Universality of Names is taken very seriously. Since names have power, and the precision of that power is derived in part from universal usage, the process of naming is heavily regulated. There's even an analog of the International Commission on Zoological Nomenclature, which is both an arbitrator of disputes and a governing body. The Commission of that world polices the usage of names, to the point where people who do their work poorly are stripped from the books.

    The Commission of this world, does not.

      This is an important distinction, and lies at the heart of the matter I want to discuss. The Commission does not police names, it is solely an arbitrator of disputes. If the taxonomy of a particular paper is bad science, yet the names are otherwise available under The Code, it is not the place of the Commissioners to act upon it. That is, as things are now.

      In the latest edition of the Bulletin of Zoological Nomenclature, Commissioners Yanega and Harvey published a Call for Comments about "Taxonomic Practice and the Code". Before I dive into that, let's look at why we're talking about it in the first place. 

      Taxonomy has a history of people with an itch, an itch to name things. And not just a need to name things, but to have one's own name be associated with those things forever. It comes from the formal practice of writing the name of the author and the date of the publication after a scientific name. The term "mihi-itch" is sometimes used to describe this affliction, as mihi is Latin for "mine; of me" (see Neal Evenhuis 2008 paper for a full history of the term). And they will often let the ends justify the means (including bad taxonomy).

     This is not new (cf. the bone wars of the 19th century for an extreme example), yet the recent explosion of journals and other easy routes of publication have enabled those with this "disorder". Furthermore, there's no requirement in The Code for science of any kind. The Code is "theory-free", it makes no comments on how to do taxonomy. In the introduction of the Fourth Edition, the late W.D.L. Ride writes, "The Code refrains from infringing upon taxonomic judgement, which must not be made subject to regulation or restraint." Nor is there a requirement in The Code that nomenclatural acts be peer reviewed, a relatively new academic invention. This hands-off attitude is important because, as arbitrators, the Commissioners must remain neutral in the cases they are hearing. The Code of Ethics in Appendix A states: '7. The observation of these principles is a matter for the proper feelings and conscience of individual zoologists, and the Commission is not empowered to investigate or rule upon alleged breaches of them.' All of this means that those with the mihi-itch do unwanted things that are outside the ability of the Commission to arbitrate upon.

      The impetus for this particular discussion is a case submitted by Ramond Hoser of Australia. Hoser is a herpetologist who has become infamous in taxonomy for what Darren Naish calls "taxonomic vandalism", and what I have heard others call "taxonomic inflation", or even hyperbolize as "taxonomic terrorism". The method is simple: Produce publications with a large number of nomina nova in the hope that some of them will pay out and actually be valid. In his recent paper "The Taxon Filter", Hinrich Kaiser writes, 

"...Hoser uses the Code as a ‘name-laundering scheme’: his mass-produced names go in and ‘clean’ names come out. The more names that are put through the system, the greater is the likelihood that some will by coincidence stand if science eventually produces supporting facts. None of these names have a rigorous scientific foundation..."

     So, the overall quality of work is poor. However, as long as the new names follow the letter of the Code, the names are still available. And if a few of the names which satisfy availability end up being new to science, they're valid. In which case occurred when he happened to raise cobra (Najas) subgenera in a scoop of other taxonomists in his own self edited journal. In particular, his genus Spracklandus was valid, and not just as a potential classification scheme, but in the exact manner these other taxonomists were working to publish as subgenera. Needless to say, Wallach, Wüster, and Broadly were not please, and published their own revision of the subgenera later that year. The three authors named the subgenus Afronaja, and claimed the Hoser publication was not available under the code because it was not properly published. They write,

"Although Hoser claims the existence of a printed version of his journal, we have found evidence of only one single copy, deposited in the Australian National Library (ANL). [...] On 9 May 2009, one of us (VW) recieved printed copies of all the issues of the Australasian Journal of Herpetology. Unlike the ANL copy of Issue 7, all these issues are printed on one side only, and give the appearance of having been printed on demand at the same time: all have a pair of longitudinal white lines along the midline of the entire page: issue 1 has the lines spaced about 2 mm apart but all the other issues have the lines spaced 5 mm apart, suggesting that they were printed at the same time. These lines are not present in the ANL copy of Issue 7. All the issues received by us are bound by a single large staple in the upper, left hand corner. We conclude that the Australasian Journal of Herpetology is an online publication that fails to fulfill the requirements of Articles 8.1.3 and 8.6, any printed copies are printed on demand and therefore do not constitute published work under the provisions of Article 9.7, and the electronic versions available from Hoser's website are not published under the provisions of Article 9.8."

     
     To make the rest of the story short, Hoser claimed the authors were frauds, saying, "the men chose not to look in the one place that the Zoological Rules said hard copies should be sent to, namely Zoological Record". (Which makes it seem like he isn't as familiar as he considers himself, since there is no provision in The Code requiring copies to be sent to the publication Zoological Record, only a recommendation.) People are now confused about which revision to use, and cobras are, as you might guess, medically important snakes. If the journal was published hardcopy, Spracklandus is available, and Afronaja is a junior objective synonym, and invalid. If the journal was not published hardcopy, "Spracklandus" is unavailable, and Afronaja is the valid name. All of this is the subject of Case 3601 Spracklandus Hoser, 2009. 


     And whatever decision comes out of that case is irrelevant to me. Before Mr. Hoser or any of his friends descend upon my blog like locusts to grain, I work on insects, not snakes, I have no stake in this. I don't care if the subgenus is named Afronaja or Spracklandus. Whatever the Commissioners decide is fine by me. I do find Hoser's journal atrocious and taxonomic methods (or lack thereof) appalling, but my opinion on that matter is powerless. Please leave me alone, I'm just a poor grad student.

      What is relevant to me is that this case has prompted a Call for Comments by Commissioners Harvey and Yanega. This is a request for opinions from the greater community of taxonomists. The Commission receives open comments on all their cases, but this is a more general call; not about the Spracklandus case in particular, but about the historic and continued neutrality towards ethics and unwillingness to police the taxonomic community. They write,

"The question has been put before us, however, as to whether the desires of the community can compel a re-evaluation of the policy of neutrality; specifically, whether taxonomic freedom requires us to remain blind to ethical considerations, including a failure to adhere to proper standards of scientific conduct. Therefore, we seek guidance from the taxonomic community as to whether there is a perceived need for change, and we wish to solicit comments in order to ascertain a clearer picture of public opinion. We are, ultimately, at the service of the community, and if there is a consensus indicating that the community feels neutrality does not serve their needs, then we wish to be clear about it. 

[...] Basically, what we seek to know is whether the taxonomic community wants to continue dealing with these issues at their own discretion, or whether they want the Commission to be empowered to do so (or something in between); we will not do so on our own initiative."

     I love that, a perfect exposition of neutrality, and the unwillingness to wield power unless asked. The antithesis of politicians. They're asking us how they may best serve all of us. Go over and read all of it, it's short and sweet.

     So. As stated above in the bold text, I'm just a lowly grad student. They're asking for comments, but I'm not confident enough to submit my opinion to the Commission on this matter. But if I were to submit a comment, maybe it would go something like this.


     The long standing neutrality of the Commission is an important part of remaining above conflicts within the taxonomic community. A reduction in the sort of neutrality described in the Code of Ethics will mean the Commission has the possibility of becoming a 'political tool' rather than a body for impartial arbitration of conflicts. It will set a precedent in a system which is supposed to avoid making precedents. The Commissioners should continue to arbitrate only on cases brought to them, and only on conflicts covered under the Code, and should not seek out problems for which to "apply justice". Instead, taxonomists should band together in rejection of those who fail to uphold scientific ethics and good taxonomy. 

     I am a student, and I have little power. But, if I am worthy, I would hope someday to be selected to serve this community. If I am honored with that task, I would like be the sort of arbitrator described illustrated in the Call for Comments: impartial, restrained, and dedicated.

"By people who don't need them for people who can't use them."

Recently, I discovered the long awaited revision of the North American black winged fungus gnats (Sciaridae) has finally been published (Note: link is only the first page). Studia Dipterologica is a relatively obscure publications for fly nuts, so it took some digging to get a copy. In my excitement upon arrival, I scanned through the entire text, looking for the thing I was really excited about. And it's not there, there's no genus key.

A bit of background: The Manual of Nearctic Diptera remains today a masterpiece, 30 years after publication. It includes generic keys to every family of Diptera in North America, for adults and sometimes for larvae as well. And it's freely available online, too, so all the better! But even in this continuing piece d'resistance of the Canadian National Collection of Insects, there are problems. Things have changed since 1983, there are new genera, synonyms of old genera, and elevated subgenera. And some keys simply don't work very well, or are not trustworthy. This is not true for all the keys, of course. Most of them still work perfectly fine. And even for some of the ones that don't work perfectly, that's just the nature of the game for those groups. I'm looking at you, Tachinidae. It doesn't matter how well a tachinid key is designed, they're the most difficult group of flies and they are going to be difficult until the end of time.

In other cases, however, it's more a matter of updating. Black winged fungus gnats are not the easiest group of flies to identify, but there have been changes since Volume 1 of the Manual was published. What's frustrating is, the Mohrig et al revision is a very nice catalog of all the described North American Sciaridae, with updated names, descriptions, and genitalic illustrations in many cases, but there is no revised genus key. Why? Not THAT much has changed since 1983, it wouldn't be that difficult. Why didn't they include an updated key to the genera in their revision?

This reminds me of another situation.

For about two years now, I have been sitting on this key. It's an updated genus key to the keroplatid fungus gnats of North America, meant to replace a section of the Mycetophilidae in the Manual of Nearctic Diptera. It's even available online, though not exactly pretty. Last week, my adviser said, you know, you should really publish that. Emphatically, he said it. And he's right, I should publish it. But I'm not going to, not now, anyway.

Why? Three reasons:

1. I can't verify it without more research. I've used a combination of several publications, the world checklist, and intuition to build it. But I've looked at very few specimens, and I have no collection to back it up. This was the preliminary work for what was going to be my dissertation, and when I ended up working on tachinid flies instead, well... The Orfeliini is the real problem, with the previous genus Orfelia split up into a large number of what used to be subgenera. Since I don't have a good collection, I don't know if species in the World Catalog are correctly placed. There may even be genera in North America not currently in my key. And I haven't had time to follow up.

2. It needs illustrations. I could quickly and easily format the thing for ZooKeys or the CJAI, but without illustrations it's not going to be easy to use. Especially for all the 'new' Orfeliini genera. I don't have illustrations because I need specimens from all the genera to make them. See item 1.

3. I feel like I'm going to be stepping on someone's toes. I don't think anyone is working on this right now, but I can't be sure. And the key is derived, it's a synthesis; there isn't really any new stuff there, it's a combination of the MND key PLUS Lane 1951 PLUS Vockeroth 1981 PLUS the Manual of Paelearctic Diptera and others. I'm afraid someone is going to accuse me of plagiarism, or of trying to inflate my publication number, or tell me the Manual is good enough as it is, just leave it.

The title alludes to a common saying about identification keys, that they're written by people who don't need them (experts), for people who can't use them (non-experts). Yet they are incredibly useful, even in this day and age when digital HD photographs are a click of a button. Keys are the technology side of our work, they're the tools we create to make our lives easier. Not every specimen is perfect, and not every taxonomic group is nicely defined by a single, specially shared character that no other group has (cf. Tachinidae, again), it's true. Digital identification keys such as Lucid Keys allow much greater flexibility, with multiple starting points, the ability to account for character variability (e.g. lengths), and overall more characters to work with. However, in most cases, a good dichotomous key is much faster to use, in spite of the learning period.

But there seems to be some barriers to publishing keys, especially updates of older works. There's only so many ways I can split up Keroplatidae. Since the parsimonious way is the best way, and since THAT way is the way the Manual is set up, why NOT use the Manual's key as the basis? Maybe my reasons are the same reasons for no updated Sciaridae key in Mohrig et al.

So, some general questions for ya'all:

Is the reworking and synthesizing of old keys into a single, updated key for publication plagiarism?

Is the publication of revisions without dicotomous keys a trend, or is this an isolated case?

How much extra work needs to be put into an update before it becomes worthwhile to publish? Half? One-fourth? The whole shebang?

Do any of you have any keys you're sitting on, not publishing, for the above reasons or others?

Beating the dead horse Paraphyly.

I know I said I was going to cut back on the ICZNerdery. But this letter by Jaroslav Flegr to Zootaxa this week was too weird to pass up. Morgan Jackson summed it up nicely:

Sometimes I wonder if I could submit some of my blog posts to journals. Then I read stuff like this http://t.co/Ezy6niv5pn & realize I could
— Morgan Jackson (@BioInFocus) November 26, 2013

Summary (tl;dr): There is not one shred of anything new here. There's not even anything nomeclature related. The author is using Zootaxa to opine about paraphyletic inclusive classification, that is it, there's nothing else to this "paper" if it could even be called that. (Though, note: the link above only contains the first page and references if you don't have a subscription.)


The title, "Why Drosophila is not Drosophila anymore, why it will be worse and what can be done about it?", suggests this is going to be about the Drosophila melanogaster ICZN case last year. I never wrote a proper post about it, and given the complicated nature of the case I'd prefer not to repeat it here. So check out Kim Van Der Lin's summary in the link if you need a reminder. 

But the title is deceptive. Flegr starts off discussing the case, and he gets one thing wrong immediately. Molecular taxonomic studies have not shown that "the correct name of this species should be Sophophora melanogaster". What they have shown is that Drosophila as it stands now is a paraphyletic taxon. The actual raising of the subgenera to genus level is something that has yet to happen. And when, inevitably, someone revises the genus and raises them, the rest of us can dispute that action. That's right, you heard me correctly. Changing a taxon's rank, changing it's genus, etcetera, are subjective decisions, and unlike the fixation of types are not regulated under the Code. Someone else can come along later and challenge it without getting the Commission involved. D. melanogaster is also not "the fly that eats their fruit". Though they are often called "fruit flies", the common name is "vinegar flies" because they feed on fermenting fluids.

The rest of the "paper" is devoted to supporting a paraphyly friendly classification system, something that seems quite strange to the Cladist majority of taxonomists. Now, mind you, there's nothing in the Code prohibiting paraphyly, but the majority reject it because we've become devoted to a classification system that is descriptive, predictive, and explanatory. We've discovered that when our biological classification is based upon evolutionary descent, and in particular on monophyletic groups (groups that contain a common ancestor and all of it's descendants), it is a powerful general reference system. And when that system includes paraphyletic groups (which contain a common ancestor and only some of it's descendants), it looses predictive and explanatory power.

Flegr moves to his point in a roundabout manner, first starting with an utterly confusing explanation of paraphyly. (Note: Taxonomists are overwhelmingly visual. Reading a long list of possible relationships between Taxon A and Taxon B is about like trying to decipher one of my grandfather's differential equations.) Fer Linneaus sake, use a real life example!  He blames molecular systematics for the multiplication of paraphyletic taxa in recent years, which is a common enough theme in the literature that I don't pay it much attention. All it tells us is that the author is a traditional taxonomist who probably uses physical structures of the organism exclusively.

His statements about "inner and outer similarity" reflect a real problem in systematics, sometimes called the phenotype/genotype conflict. When we infer evolutionary relationships, often times the physical and DNA characters deliver us a differently shaped tree, and we're unable to tell whether one or either of these reflects reality better. But calling it a "conflict" is a misnomer. As one of my committee members recently told me, there is no real conflict between between the morphological and molecular characters. The conflict is in the methodology, and how we analyze the data. Flegr writes "nothing might be possible to guess from a system that would not reflect the inner similarity of the species", as if morphology is doomed to forever represent convergence and DNA is innately neutral to selection. Neither of these are right. 

The deep and real problem that he is reaching for but missing, is that many traditional classifications are based upon obvious physical characters rather than evolutionarily meaningful ones. There are, for example, many characters that place birds as a therapod lineage. But since these are not as obvious as "has feathers" and "is warm blooded", and since this uniqueness is part of a traditional classification, people continue to place them in a separate lineage from other archaeosaurs. Why? Because tradition, because, as Flegr puts it, "secondary school biology teachers are far much more numerous than theoretical taxonomists."

I'll refrain from commenting upon this except to say that allowing high school biology teachers to dictate how we should classify organisms is ridiculous.

Flegr's solution is to allow paraphyletic groups to stand. Of course. What better way to solve a problem than to ignore that it exists? Then you don't have to go through the messy route of educating people. And while we're at it, why don't we just throw out this whole evolution thing? It's so much easier to classify organisms based on obvious characters like, for example, lacking wings. The insect order "Aptera" worked out so well.

There are also some fairly ugly diagrams which are not at all convincing. 

Throughout, Flegr tries to make his case using the prevalence of punctuated equilibrium in major radiations rather than gradual change. Somehow this is evidence for rejecting reciprocal monophyly. I don't see it. There's also the opinion that these phylogenies will make our classification system inherently unstable. To which I reply: They are unstable now. Classifications that are based upon obvious similarities rather than evolutionarily relevant characters will forever be subject to the whims of authority opinions. What Flegr wants is to go back to the days of evolutionary taxonomy, where if Dr. Smith was the expert on so and so group, then whatever he said goes. NOPE NOPE NOPE. 

This is all very much a Dubois-ism, in the spirit of the last paper I wrote about. He concludes,

It is, of course, probable that most of the current theoretical taxonomists, who spent a large part of their active professional life fighting the fuzzy eclectic phylogenetics and taxonomy, would not be very enthusiastic about the recurrent more and more urgent suggestions of rehabilitating the paraphyletic taxa (Hörandl, 2006; Hörandl & Stuessy, 2010; Podani, 2010a; Zander, 2010). The change, fuelled by practical taxonomists who mostly use a ‘wrong’ eclectic taxonomy in their everyday practice anyway, will be probably slow and painful. It is, however, necessary to start the change as soon as possible. Otherwise, we might soon have to say farewell not only to drosophilas but to the whole taxonomic system.

I suspect these authors he cites are all in the same boat, a bunch of "taxonomic reactionaries" who can't cope with their authority being overturned and their traditional taxa being reshaped by evolutionary understanding. They call it "practical taxonomy"; I call it the easy way out. Flegr also shows himself to be a doomsayer by the last line. It's the end of the world as we know it, apparently.

In closing, no, wait. I don't think this mess merits a wrap up. Flegr leaves us one last gift, a tagline. 

"Australopithecus sapiens, possibly Reptilia, Pisces"

1. Australopithecus does not have priority over Homo. 
2. Reptilia is a paraphyletic group.
3. So is Pisces.

Important kernels lost in the chaff.

There are clear, concise collections of criticism. And then there's this paper. At 94 pages, it's not a short read, so I don't blame you for skimming. It's already received a lot of flack. In short summary, Alain Dubois and 18 other authors published an almost op-ed style article on problems existing in zoological nomenclature, particularly in reference to electronic publication of names and nomenclatural acts. The above links already have eviscerated it.  By that standard, I shouldn't even bother. But wait, what's this?

Given the demands on their time, the ICZN members could probably do without a reprisal of the online versus print naming debate — a debate, remember, that saw the farcical printing to paper of hard copies of online-only papers, which were then handed to libraries to fulfil the exact wording of the code. The Zootaxa authors seem unwilling, or unable, to move on. They have a semantic bee in their bonnet over the code’s requirement that species descriptions must be always “available”. When the online publishers they contacted explained that, no, they did not routinely supply paper versions of the files on the journal’s websites, the authors, rather uncharitably, deemed the information unavailable to them. ---the Nature editorial

Uhhhh.....cue Indigo Montoya. "Availability" does not mean "I can pick it up at the library" under the Code. To be available is to satisfy all criteria within the Code necessary to be considered for validity, priority, and other things. It is a whole lot more than the location of the published work. For example, a nomina novum, or 'new name', is not available unless the type specimen(s) are referenced explicitly, as well as the location where the types are to be deposited. You forgot to do this? Sorry! Your new name might as well have never been put in the literature for all it means to the Code. Refining the articles on availability means that species descriptions have higher standards, which is considered good by anyone who's tried to wade through the old literature.
 
Given that Nature failed to understand that, a basic and important concept in the Code, I wondered how much more they were flubbing about the article. So I read it. All 94 pages.

What I discovered was, well, a mess. Oodles of footnotes, most of them irrelevant to the paper. CamelCase, really? Symbols in journal names? Philosophizing about supplementary materials? It doesn't matter if I agree with them or not, this is supposed to be a paper about problems with electronic publication of new names. Then there's the intentional emotive, non-academic language. See the footnote on page 29 for an example. And in all things there's this sort of ivory tower dictatorial outlook, as if their opinions are final. Maybe from the authors' point of view they are. The majority of the authors hail from old European natural history institutions. And there's the fact that Dubois cited himself 38 times in the references. 

It's unfortunate that within all this there are some actual relevant criticisms, some of which were not covered in electronic vs. paper debates before the 2012 amendment. For example, some journals mistook the allowance for optical disk deposition (sometimes called the "5-copy rule") to extend to all electronic publications, including PDFs. Which means there are a whole bunch of names between 1999 and 2012 which are not available due to poor reading of the Code. This does not include mixed-model journals like Zootaxa, which publish both an electronic and a printed version with separate identification numbers. In those cases, the printed versions satisfy the Code. The rest, not so much. 

There's also criticisms of pre-publication editions (which make establishing date of publication more difficult), publishing of new names in electronic supporting information (which does not fulfill the criteria of availability, even under the 2012 amendment), and the treatment of online checklists as authoritative. All of these are useful criticisms, as is the main (lost) point of the appendixes, namely, that authors and journals don't understand the changes in the 2012 amendment very well. BioMed Central has responded to the authors' complaints, which is understandable as they took the brunt of the criticism. They reference their editorial policies on describing new taxa, which is available for all to see. They also reference the "5-copy rule", saying they followed the Code. (Note: there is no 5-copy rule in the code anymore. Even if this prior rule could have been interpreted to include deposition not in the form of optical disks, all electronic-only publications before 2012 are considered unavailable.) All of this is irrelevant, as they are still publishing unavailable names even now, after the 2012 amendment. Again, I don't blame them for being upset. The Dubois et al. paper was purposefully inflammatory and should be derided as such.

In summary, there are still problems with electronic publishing of names. But this paper will not be remembered for valid criticisms. Instead, it will be another sign that taxonomy has lost sight of the times. As the Nature editorial pointed out, all the recent ICZN news seems to be bad press. Taxonomists look as if we are a bunch of doryphores, interested more in trivial piddly lawyerisms than solving actual problems. Spend some time on the listservs, for example, or read this paper, it's the same. Without change we'll be irrelevant.

The story behind "Range and Variation of Oecetis parva".

Disclaimer: The views, opinions, and judgements expressed in this blog post are solely those of the author. They are not intended to represent the views or opinions of Clemson University, the Department of Energy, or Savannah River Ecology Lab. Nor are they meant to represent the opinions of the other authors of the "Oecetis parva" article. Just to  cover all bases and my rear.

An Island of Green from Space: Savannah River Nat'l Laboratory is just right of center, a circle of green forest surrounded by agriculture and suburban development. (from Google Maps)

During my last two years at Clemson University, I was employed as a research assistant in conjunction with the Savannah River Ecology Lab (SREL) at Savannah River National Laboratory (SRS) in Aiken, South Carolina. The SREL had received a grant from the parent organization, the Department of Energy, to repeat a thirty year old aquatic insect survey of Upper Three Runs Creek and it's tributaries.

Upper Three Runs Creek and Tributaries. The four sampling sites marked are the same as the previous study, all of them located downstream from a bridge crossing. (from Google Maps)

These stream systems, located in the northern part of SRS, have among the richest levels of aquatic insect diversity in the world, with at least 575 species recorded, including some species endemic only to this location. In comparison, tropical streams surveyed thus far have an average of 400 species. You could chalk this up to sampling completeness, but Upper Three Runs is still a gem of aquatic insect diversity in North America. These numbers come from a year long study conducted from September 1976 to August 1977 (Morse et al. 1980), where a team of aquatic insect taxonomists, including my master's adviser Dr. John Morse, collected black light samples at 4 locations along the stream corridors. These collections were repeated every two weeks for the entire survey year, ending up with 51 total light trap samples and a massive amount of material to sort and identify. Since the majority of aquatic insects are nocturnal, including caddisflies, mayflies, and stoneflies, a year long black light survey will pull in most of the aquatic insect diversity in an area. And if that wasn't enough, the researchers also took two benthic net samples at each of the four locations every two weeks. (You might notice the 51 samples don't add up to a complete sampling regime. Not every location was surveyed every two weeks, either due to failures of traps to work, not enough traps, or other issues. But at least one site was sampled for that entire year, and the rest for at least half all the collection dates.)

Site A, Upper Three Runs Creek, looking downstream. No rocks, but plenty of woody debris and aquatic plants.

The really interesting thing about Upper Three Runs Creek and it's tributaries, Tinker and Mill Creeks, is they don't really look like biodiversity hotspots. Most aquatic entomologists associate high diversity with mountain streams, or at least with rocky riffle areas. Upper Three Runs Creek is located in the sandhills and coastal plain region of South Carolina, a black water stream with high tannic acids. It flows through southern pine forest and swamp. It has no rocks. So, when entomologists first look at the creek, it's kind of disappointing. No rocks, just shifting sand and silt substrate.

Upstream, at Site B. Those rocks are part of the bridge stabilization structure and are not naturally occurring.

What they soon find out is that all the tremendous diversity is tied up to these little pockets of heavy woody debris and submerged aquatic plants. These microzones of the stream are absolutely coated with aquatic insects. And so, Upper Three Runs Creek is sort of obscure in it's diversity, unless you happen to stick your D-net in the right place. Or, if you set up a black light and sit back as the sun goes down.

In Fall of 2008, I had the opportunity to see for myself. My adviser, Dr. Morse, was contacted by Dr. J Vaun McArthur of Savannah River Ecology lab about a repeat of the 1978 survey. In particular, they were interested in adult caddisfly diversity. I had plenty of prior experience identifying the larvae, but almost none identifying the adults, so I knew this would be a particularly challenging project. In the previous survey and subsequent work, nearly ~160 species were found at these locations, some of which were new to science. We were also hoping to have a more complete sampling regime, with traps running at all four locations for the entire year. Since SRS is a high security government facility with high safety standards, we had to plan ahead for each of the collecting trips and could not stay with the traps overnight.

Rube Goldberg Setup at Site A. This was taken in March, thus the early spring plant growth. By May they were as tall as the umbrella.

As for the traps themselves, they were a makeshift contraption. A pvc pipe tripod suspends a black light over a plastic pan filled with ethyl alcohol. The light is hooked up to a deep cycle battery, and the whole unit is placed under a tied and staked down umbrella in case of rain. But despite looking like a Rube Goldberg machine, they worked quite well for our purposes.

Less Rube Goldberg: This trap was under a bridge so it didn't need an umbrella.

When I returned from a collecting trip, I would sort the caddisflies out the samples.

Insect Cometary: This was an average night of sampling. I don't like killing so many insects at once, but when doing faunistics this is often necessary. We sort out what we need and save the rest for future research. The only thing that gets tossed are the moths, which we can't do much about.

I also picked out a goodly portion of the other orders of aquatic insects for identification at some point down the line.

A Really Good Day: This was the best (worst?) sample I ever sorted, and this is only the caddisflies, some of which had already been removed.

 The caddisflies were often very dense in the samples. Some of the spring collections had thousands of individuals.

Oodles of Caddis: There are at least 7 genera in this shot, probably twice that number. Everything in view is less than 15 mm in length, most around 10.

Identification was slow at first. Like I said, I had no experience with adult Trichoptera before this assistantship, and I was doing species level identifications of both males and females. For the males, we had an atlas of genitalia, but for the females I was working from primary literature and guesswork.

Largest and Smallest: Hydatophylax argus, the largest caddisfly in North America, and Neotrichia falca, one of the smallest. Note: H. argus is not found in Upper Three Runs Creek.

Some caddisflies are tiny, as shown in this picture of Neotrichia falca (Family Hydroptilidae) next to the massive Hydtatophylax argus (from the Clemson Arthropod collection). I was careful to pick out the hydroptilids along with the much larger species of other families.

Despite the previous work, I was finding species not previously known from Upper Three Runs. But it wasn't until I saw these guys that I was stumped.

Males of the mystery caddis, now known to be Oecetis parva Banks. Individuals are ~5 mm.

These are tiny caddisflies, only 5-6 mm in length, but they aren't hydroptilids. When I keyed them out, I found they were in the family Leptoceridae, the long horned caddisflies. Called such because usually they have long antennae. As you can see, these didn't. My identification placed them in the genus Oecetis, but they weren't in genitalia atlas. Eventually I checked the literature for every species of Oecetis in North America. Through a roundabout way I finally found illustrations of the last species, Oecetis parva. Nathan Banks, who originally described O. parva in 1907, didn't include an illustration in his publication. It took a trip to the British Museum by the late Herbert Ross to remedy this situation. And in 1938, Ross published an illustration of the lectotype. The illustration matched my specimens.

Or...they sort of matched.

The first law of Biology is "variation exists". This is something every taxonomist must keep in mind during his or her work, or enter the folly of unnecessary junior synonyms. My specimens had the same general look, the same clasper shape, the same size and color, but there was something off about the tenth tergite. This part of male caddisfly genitalia is the last dorsal plate of the abdomen, often modified into various shapes. The shape of the male genitalia fits that of the female like a key in a lock, and it's thought this is one of the reasons there are so many species of insects.

Left lateral view of O. parva male genitalia. Between the pad with hairs near the top is a long finger projection, and under that a pair of mebraneous hooks. Insect reproductive parts are complicated.

The tenth tergite was different. It had a long, fingerlike extension between the cerci, visible both from lateral and dorsal view. And just below the finger, there were a pair of membranous hooks, visible from lateral view. Ross's illustration didn't show these distinctive structures. So I became excited. I thought I had a new species. For two months I waffled back and forth: it was a new species, it wasn't a new species, it was a new species, it wasn't a new species. As if I was picking petals off a flower.

There was also another issue with Oecetis parva. The only places this species was known from were 14 sites in Florida and the southern tip of Alabama. It was thought to be a far southeastern endemic, found only in forest pools. Aiken SC was two hundred miles outside its known range.

But as I sent for specimens from the Florida State Arthropod Collection, I soon found out my excitement was hubris. Variation exists, and there was variation in the Florida and Alabama specimens as well. Nothing quite as extreme, but intermediates between the reduced and elongate finger of the tenth tergite. Needless to say, I was a little crushed. This would have been my first species discovery.

There were still some interesting issues. Namely, why was Oecetis parva found so far outside of it's known range? And why was it found now, and not in the previous survey?  Talking to other southeastern Trichopterists, I learned that O. parva had been collected recently at two other new sites, one in Georgia, and another near Columbia, South Carolina. So Dr Morse, Dr. McArthur, and I decided to publish this new information. This included new illustrations, of the variation seen in males from South Carolina, and of the female genitalia, which had not been previously illustrated.

More genitalia. These are, however, much prettier, as this was after I learned how to use a vector image program. (Burington et al 2011)

 Around the same time we were finding Oecetis parva in our traps, the Center for Biological Diversity presented a petition to the US Fish and Wildlife Service, with 404 southeastern aquatic species they felt warranted listing under the Endangered Species Act. Several months later, USFWS released a slightly shorter list of 374 species which were slated for a 90 day finding, and Oecetis parva was on this list. Yes, this is the caddisfly I mentioned rather cryptically in a post way back in 2011. However, my publication may have had an effect on the listing process, because I don't believe O. parva is any longer being considered. Which would mean that I as a taxonomist publishing basic natural history research has somehow influence government policy. Regardless of your opinion about whether it should have been or should not have been listed, that is kind of cool.

Recently, I gave a presentation on my master's research, including a segment on Upper Three Runs Creek and it's diversity.  I was looking at my range map for Oecetis parva, and a little hypothesis started to form, and over a few days it got bigger and bigger, until I felt like I had to share it. So, please allow me a little speculation.

Range map of Oecetis parva. Gray dots are those localities known previously. Black dots are new records. Red dot indicates unpublished previously unknown locality. Modified from Burington et al 2011

On the map, the grey dots represent all the prior localities for O. parva. The black dots are new localities in our paper. The red dot indicates a new location I recently heard about, in northeast South Carolina. And the first thing to notice is, it really does seem O. parva is limited to the sandhils and coastal plains of the Southeast United States, and particularly to well protected pine forest habitat. I also have word that Cheumatopsyche richardsoni has been collected at that red dot location, a species that we thought was endemic to Upper Three Runs Creek.

So, back to the big question: Why Savannah River Site? Why the massive diversity at Upper Three Runs Creek? Savannah River Site is known locally as the "bomb shop", because it was used for weapons grade plutonium manufacture during World War II and the Cold War. During presentations about the original 1976 survey, some wise-cracker would get up and ask "Maybe it's the radiation?" And we laugh at that joke, except, we didn't really know why there was this high diversity just here, not in the surrounding stream systems.

But it now seems that there are few if any true site endemics. Nearly all the species of Upper Three Runs Creek have been found elsewhere, and some of them widely separated, like Cheumatopsyche richardsoni. This suggests an answer, and that is: Yes, Upper Three Runs Creek is a beautiful diverse gem, but it is not unique. The southern pine forests and their stream systems used to stretch in an unbroken chain across the entire sandhills and coastal plain region of the southeast US. This diversity was probably all over the place. When industrial agriculture arrived in the early 20th century, almost all these original forests were plowed into farm fields. And now, this original diversity only remains in a few well managed pockets with protected headwater streams. We could test whether this is isolation or recent dispersal by the methods of population genetics. Unfortunately, I don't have the resources to do this currently.

This also suggests a second idea. When aquatic entomologists and aquatic ecologists just look at blackwater streams like Upper Three Runs Creek, we expect them to be of low diversity. But the natural state of these streams is HIGH diversity, and it's only because of widespread agricultural impacts that we are inclined to think differently. We need to turn the idea of blackwater streams as species poor on it's head. There are species new to science still being found in these pockets, indicative of what was lost and what treasures still are left.

Afterword: This project is in no way finished. Identifications are ongoing, and the material left is huge. I am no longer directly associated with this project and I hope it will be completed. During a recent conversation with Dr. Morse, he told me he was working through a sample from May of our collecting year. So far, that single black light trap sample has yielded over 5000 individuals and 57 different species of caddisflies. I remember that night. That was a good night.

Burington, Z. L., Morse, J. C., & McArthur, J. V. (2011). Distribution and variation of Oecetis parva (Trichoptera: Leptoceridae). Entomological News, 122(1), 100–106. [ed.: unfortunately, this is not open access. Entomological News does not yet have this option, despite being one of the few publications which will publish these sorts of articles.]

Morse, J. C., Chapin, J. W., Herlong, D. D., & Harvey, R. S. (1980). Aquatic insects of upper Three Runs Creek, Savannah River plant, South Carolina. I. Orders other than Diptera. Journal of the Georgia Entomological Society, 15(1), 73-101. 

The story behind "Azana sinusa: remarks on range and records."

I previously promised to blog every one of my future publications. And finally, I am able to follow through on the first one. I'll be using Eisen's brilliant blog post about the "Stalking the 4th Domain" paper as a format guideline, but since this is very much a small scale natural history story rather than a large scale molecular biology story, I'm mostly making this up as I go. As a natural history story, it may not seem like science to all people. Taxonomist FPD Cotterill calls natural history an ideographic science, a science of details that provides the primary support for the wide scale theorems of law-like or nomothetic science. And as such, denigration of natural history does not fair well for biology in general. So I will pass by the naysayers and move forward.


Burington, ZL. 2011. Azana sinusa Coher, 1995 (Diptera: Mycetophilidae: Sciophilinae): remarks on range extension and collection records. Check List 7(6):815-816. PDF


The Backstory

In late 2010 I was attempting to organize the wet-stored specimens of Sciaroidea (fungus gnats) in the Clemson University Arthropod Collection. The CUAC does not have a very large collection of the group, only 100 to 200 specimens, most of them collected before 1990 by former students or in flight intercept traps. Fungus gnats are of great interest to me, since they are greatly understudied in North America, with perhaps less than 50% of all species described. In particular, I'm interested in the Family Keroplatidae, the predacious or web-spinning fungus gnats, the larvae of which spin a web of sticky silk to capture small arthropods or fungal spores. You may have heard of the cave glowworms of New Zealand, a popular ecotourist destination; these bioluminecent fungus gnat larvae are keroplatids.

I was using the genus key in the Manual of Nearctic Diptera (MND) (now available for free online) to identify the adults. Despite being thirty years old and somewhat out of date, the MND worked well enough for my purposes. When I identified specimens from two different vials as the genus Azana, Family Mycetophilidae, I was intrigued. The specimens were less than 10 cm in length, with a distinctive reduction or loss of the medial and cubital wing veins (see figure at end).

At the time of the Nearctic Manual's publication, no North American species of Azana had been described, although Vockeroth believed there was at least one species on the continent. Both Jean Laffoon and Elizabeth Fisher had previously noted collections of the genus which remain unconfirmed, from Minnesota and Cape Breton Island (Nova Scotia), respectively. It wasn't until 1995 that Edward Coher finally described this species from Maine, New Hampshire and Massachusetts as Azana sinusa, which tells you just how rarely collected this organism is. From an additional male specimen in the pinned collection, I was able to confirm from the genetalia that these were probably all A. sinusa Coher. Although Peter Kerr of California Department of Food and Agriculture recently described two new western species, A. malinamoena and A. frizzelli, A. sinusa remains the only Eastern species.

All these facts were not so intriguing as was the /location/ of the collections: the coastal plain and sandhills of South Carolina. The type specimens from Coher's paper were collected in the mountains and coastal areas of New England, approximately 1200 km to the North, with no specimens ever collected below 40 degrees latitude. Since this continues to be a poorly known, seldom collected species, and since the specimens I had found in the CUAC were so far outside the known range, I decided to publish this information.


The Journal

I wanted to put a note here about the journal I chose for publication, since most readers are probably not familiar with it. Check List is a peer reviewed, open access online journal specializing in regional species lists and notes on range and distribution. Traditionally, a short note such as this would have been published in Entomological News, but that particular journal has had a large backlog over the last year; as I already had one article waiting for publication in that journal, I thought it wise to try Check List. Though the website and editors are Brazilian, the journal is published in American English, and the editors were timely about corresponding with me. The best thing about this journal is that it's completely open access and free for authors. Since they do not publish anything that might be considered a nomenclatural act or new species descriptions, a print version is not necessary. It also means that there is no limit on publication size, and that what limits the publication speed is the peer review process, correspondence time, and copy editing. I will say that the journal guidelines are very picky about formatting, and I was asked to remake the distribution map I originally provided; this is perhaps for the best. I will definitely be coming back to this journal with future manuscripts. They fill a publication niche that used to be a large portion of the entomological literature, but fallen into disrespect because publishing short notes is nowadays seen as cheating, as padding one's CV.


The Denouement

Some readers may be wondering why I would take the time and effort to publish such a short note on the range of a rare and seemingly insignificant species. And I admit, the reviewers taxed me with this same question: is this really /worthy/ of publication? Well, certainly the editor would have rejected it outright if he didn't see something worthy in it. And of course, it would have never been published if the reviewers hadn't eventually felt it worthy. The photo I published with it is the first photo (to my knowledge) ever taken of this species, and the distributional data and map the most complete. It continues that we know essentially nothing of the biology of this species. Little information was contained on the specimen labels, and it's so rarely collected that trends are hard to draw. Coher, in his 1995 publication, said that the morphology of the mouthparts suggests the adults are nectar feeders, but we have no observations of this. Kerr collected his Azana species from flight intercept traps suspended from redwood in California. Might Azana sinusa as well dwell in the tree tops? There's no way of knowing from the scant information we have, though this behavior would suggest why it is rarely collected; combining the data from all publications, less than 50 specimens have ever been reported.

Overall, working on this manuscript has given me more puzzles than answers. But, I think it was overall good; it synthesizes the known information, and shows us a wider picture of the species than we realized. I never undertook the project as an attempt to pad my CV or make a name for myself. Goodness knows there are easier ways to accomplish this. The synthesizing and editing was far more work than I had anticipated, and the process far longer than I had hoped, but I think it turned out alright. Despite my past criticisms of Encyclopedia of Life, I plan to create a full entry using the information in this and previous publications.

The species Azana sinusa, and little forgotten or seldom noticed species everywhere, remind me of my favorite vignette from Aldo Leopold's A Sand County Almanac:

Within a few weeks now Draba, the smallest flower that blows, will sprinkle every sandy place with small blooms.

He who hopes for spring with upturned eye never sees so small a thing as Draba. He who despairs of spring with downcast eye steps on it, unknowing. He who searches for spring with his knees in the mud finds it, in abundance.

Draba asks, and gets, but scant allowance of warmth and comfort; it subsists on the leavings of unwanted time and space. Botany books give it two or three lines, but never a plate or portrait. Sand too poor and sun too weak for bigger, better blooms are good enough for Draba. After all it is no spring flower, but only a postscript to a hope.

Draba plucks no heartstrings. Its perfume, if there is any, is lost in the gusty winds. Its color is plain white. Its leaves wear a sensible woolly coat. Nothing eats it; it is too small. No poets sing of it. Some botanist once gave it a Latin name, and then forgot it. Altogether it is of no importance--just a small creature that does a small job quickly and well.

Leopold was king of qualitative natural history, he wrote in a way that even the smallest and seemingly insignificant of organisms glowed with individuality and purpose. While I don't claim to equal him by any means, I hope to shed some light on the matter of species like Azana sinusa, which now at least has a face to put on the name.

Azana sinusa male, left habitus