Thursday, November 28, 2013

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:

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.

Friday, November 22, 2013

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.

Tuesday, November 19, 2013

ICZN funded...for now.

Earlier this year, we received word that the International Commission of Zoological Nomenclature was broke. As you might imagine, I was and still am concerned.

But there is a temporary reprieve. The National University of Singapore will fund the ICZN secretariat for the next three years. In other words, they will pay for the ~$80,000 in costs it takes to run the basic "government" body of the commission. This includes Zoobank, the zoological name registry, which takes the majority of those funds to upkeep.

But this is all temporary. When the funding runs out in three years, will another organization step forward to help out? The ICZN isn't the Olympics here, nations aren't lining up to back the Commission. About the only thing any individual institution gets out of funding the ICZN is the associated prestige, which doesn't go far in this modernist world where value equals direct monetary gain or less cost.

So now there will be the inevitable talk about "business models", which works fine for a natural history museum but horribly for a multinational consortium. There's no ICZN giftshop where we can buy nomenclature themed t-shirts saying things like "Deus creavit, Linnaeus disposuit" and "Save the ICZN!" with a picture of Hugh Strickland. (Though, that's not a bad idea. Hipsters might be good for something after all. Hmm....)

Usually in these situations you have member states or institutions contributing to the total cost, e.g. UNESCO. Or, like the International Union of Biological Sciences (IUBS), there are membership fees. Or, like the International Botanical Congress (IBC), there is a meeting that coincides with the arbitration.

But the Commission is a small body of 26 people, and their respective institutions do not provide funding. Nor are there membership fees, or a large meeting associated with arbitration.

One way to fund it may be to enlarge the membership, make it the entirety of the International Congress of Zoology, and increase the membership fees to coincide with voting rights. Then amending the Code is something everyone at the ICZ can take part in, just as it is at the IBC. But the Code itself is written to be arbitrated by a limited commission, not a large governing body, so the change in itself would require an amendment. With 15,000 new names a year, a number which grows yearly, maybe it's time for a change. There were 36 cases (or at least that many decisions) this year. Can the Commission keep up?

In any case, this problem isn't going away. And where is IUBS in all this? They're the mandating body, they're the organization from which new commissioners are chosen. Three years will speed past. Now is the time to find a solution.

Monday, November 18, 2013

Smart Phone Etiquette

We now have tricorders.

Back in the day (or more recently), did you watch the original Star Trek series? Remember those communicators everyone carried around, the ones that could record and transfer data? They were called tricorders, and we have those. People have in their pockets, a camera, video camera, global positioning system, Internet interface, data recorder, communication device, music player, and a whole lot more in a package no bigger than a deck of cards. Not just a few people, but a whole LOT of people. Yes, true, there are a few things smartphones can't do, like take lifeform readings, but apparently there are people working on that.

I'm what you might call a "late adopter" or "laggard" when it comes to new technology. Some might even say "neophobe", since I tend to be dragged into the New kicking and screaming. 30 years from now when everyone has moved on to the next interface I'll be still using the old laptops. I'll complain that the new tech feels insubstantial (because it practically is), and that a good computer is weighty and takes up more space than a sheet of paper. How can I even type anything worth reading without the physical clicky-clack of a keyboard?

But, staring down at my 2007 Nokia Tracfone, so old that I have to go to tech support every time I want to add minutes, and looking at the new technology and all it can do, I wonder if it's time. How incredibly useful would it be to have a combination camera/GPS/phone with me every time I go in the field? Or, at professional meetings, I could join in all the community building on Twitter and tweet about talks. Some of my colleagues have designed apps which allow the recording of behavioral observations in the click of a button, and then upload the data to the cloud. No need for a clipboard checklist and stopwatch.

At the same time there's so much that disgusts me about smart phone use, and cell phone use in general. This video pretty much sums it up. It's become a huge distraction that keeps us from interacting with one another. This is because there's no standard etiquette for smart phone use. We've finally gotten to the point as a society when cell phone use in each other's company is shamed. The same does not apply to smart phones, since they aren't so much a phone as they are a tiny computer interface. The standard rules of "turn your phone off in a meeting" do not apply anymore, because most of the use isn't making phone calls.

I'm afraid that when I take the leap, I'll be tempted to use this wondrous tech to distraction. Which is why I'm proposing in advance some basic etiquette rules for smart phone use. And I'd like to hold everyone else to the same standard because that's just the world I want to live in.

The first and foremost rule in smartphone use is the Rule of Engagement, which is:

Your present company is who you should be engaged with.

By company, I mean "anyone who is either with you or currently holds your attention." And it really cuts to the heart of when and why smart phone and indeed, all cell phone use is rude. It's taking us away from engagement with whatever is happening around us. Including, but not limited to, the people we are presently with.

Why I'm using the Rule of Engagement as prime is because there are many instances where using a smartphone while with company can add to engagement. You may, for example, be viewing a talk at a professional meeting and wish to right then and there share what you are learning on Twitter. This is not only engagement, this is hyper-engagement. What the speaker is telling you excites you so much that you feel impelled to share their conversation with everyone else by using the hashtag for the meeting. There is absolutely no shame to this, in fact, it should be encouraged. Last week, tweeting at the 2013 Entomological Society of America meeting (#EntSoc13) allowed me and other people who were not able to attend to actually feel involved and learn and build community. Tweeting the talks as they were actually proceeding was outreach! Other cases where smartphone use doesn't limit engagement is when you can provide a piece of information to move a discussion forward (e.g. by a simple Google search).

In these cases there are still limits. In addition to the Rule of Engagement I have a few more.

1. All the old cell phone rules still apply. If you're in public and with company, using your smart phone for calling is still discouraged. And this is equally true with company in private. In other words, talking on the phone or texting in the company of others is rude. You are telling that other person or people that you don't value their time or presence, that they are boring or at least less interesting than the person you are talking to or texting on your phone. Since these classic examples violate the Rule of Engagement, they are still rude and should be avoided.

2. Other smart phone applications should be used sparingly in company. By which I mean, don't use your phone without a legimate reason. This is not the time to go link jumping on TV tropes, or check your email, or Facebook, or do /anything/ that takes more than a few seconds. Whatever you /do/ use it for should be relevant to the circumstances, like the examples I gave above. It's a tool, not a distraction device.

3. Approved smart phone use in company should be discrete and efficient. In and out, and as little of a distraction for everyone around you as possible. In a dark room, this might include dimming the screen so it isn't as bright. The point is not to be bothersome, and to cut away from it as quickly as possible so as not to disengage your company.

4. If use is extended, you should excuse yourself from present company.
This was true for phone calls, and it's true for apps. You may find it inconvenient, but frankly is so freaking rude to sit with me and stare at your smartphone for five minutes as I try to have a conversation with you. If you have to do that, I'd rather you go elsewhere and indicate you need that privacy.

Now, I've made some of these mistakes in the past. Not with a smartphone, but with my laptop. Even with a 10 inch screen and keyboard on my lap it's so easy to disengage from physical reality and forget my surroundings. We need to treat these tools as what they are, tools, not as entertainment units to distract ourselves from being truly present with others. And when used legitimately we still need to be considerate of others.

The ultimate goal is more engagement. Smartphones can help with that, but they can also harm. We should be aware of their consequences and use them wisely.

Thursday, November 14, 2013

Caddisfly weirdos.

Previously on Trichopterology...about 5 years previously, I talked about some very cool caddisflies that live in tide pools. These marine caddisflies feed on soft corals, and also use it to construct their cases. And the females of at least one species, Philanisus plebeius, oviposit into the body cavity of sea stars. Now, I'm not quite sure you'd call this relationship parasitic, because I don't know if the sea stars are harmed at all by the oviposition or the eggs. As soon as the larvae hatch, they leave the sea star through its stomach and out its mouth, and start munching on coral. They seem to be more of a commensalist incubation chamber than a host in a parasitic relationship. It's unfortunate that there hasn't been any more recent research in the literature, nor photographs because I would really love to show you all one of their cases.

Out of the three main indicator aquatic insect groups (caddisflies, mayflies, and stoneflies or EPTs), Trichoptera seem to have the widest range of niche. They range from free moving predators to plant shredders, to filter feeders, to scrapers and grazers. You can find them in tiny spring seeps and large rivers, in temporary pools and the wind swept shores of the Great lakes, and in aquatic habitats ranging from fully freshwater to marine. This diversity of habitats and feeding guilds is a testament to their wondrous use of silk, building cases out of practically every kind of material that can be found in aquatic habitats, or spinning silk into webs and nets.

Marine caddisflies are pretty weird, they have a semi-parasitic lifestyle and they live in habitats that are avoided by all other insects. But, there are other weirdos.

I've talked previously about the tethered casemakers, Limnocentropodidae, which connect their cases to the substrate with a sturdy silk stalk, sometimes tethering to other cases in long aggregations during pupation.

Then there's the Atriplectidae, which really deserve a blog post of their own. They're sometimes called the 'vulture caddis' due to their specialized telescoping head. Much like a vulture, they feed on carrion, but in this case it's other arthropods. The long 'neck' allows them to stay outside the corpse and insert only their head for feeding.

There are several species of caddisflies which spend most of their lives out of the water, in moist habitats. This includes the Platte River caddisfly, Ironoquia plattensis, which undergoes a terrestrial estivation period as larvae during the summer. There's also a British species, Enoicyla pusilla the land caddis, which feeds on dead oak leaves in humid forests and spends most of it's lifecycle out of water. A stranger habit is that of the retreat maker Xiphocentron sturmi. Typical of it's family, it makes a network of tubes appressed to a substrate, in this case rotting wood. What's not so typical is the tunnels are out of water, and weirder yet is it's "chrysalis". When X. sturmi finish larval development, they build a hanging structure that looks sort of like a tiny lemon on a rope, and pupate inside of it.

But really, these are all sideshows compared to the main attractions, a caddisfly-sponge mutualism and an honest-to-god caddisfly parasitoid.

Ceraclea is a genus of caddisflies in the family Leptoceridae, the long horned caddisflies. As the name implies, most leptocerids have long antennae in both adults and larvae. Ceraclea is unusually for a number of reasons, first of which is that their antennae are much shorter than other leptocerids. Another reason is that several species feed on freshwater sponges. I wouldn't suggest trying sponge for yourself, though. It would be like eating fiberglass, since the sponge skeleton is made of tiny glass bars called spicules. These sponge feeding caddisflies are able to ingest both the soft tissues and the spicules without damaging their guts because they have a super tough midgut. They're really feeding on the zooanthellae, endosymbiotic algae that live within the sponge tissue.

The sponge outwardly seems to be the host in a parasitic relationship, since the caddis feeds on and damages host tissue but doesn't consume the whole colony. But according to research from 2003, the sponge benefits as well. Electron micrographs of Ceraclea fulva cases showed that they are composed of a tightly bound series of silk bridges attached to sponge spicules. Furthermore, pieces of living sponge attach to the cases, especially in the late larval instars. Since sponges often spread by fragmentation, the combination of larval integration of living sponge fragments into its case as well as fragmentation during feeding means that the sponge can spread to new habitats with help from the caddisfly larva. Mutualisms are rare enough in aquatic insects that this is the only example I know where both species benefit. There are other aquatic insects that feed on sponges, the spongillaflies for example. But these are parasites, and are not dispersal agents for the sponge like Ceraclea cases.

Case of C. fulva; 'S' indicates living sponge tissue (Corallini & Gaino 2003)

At the other end of the spectrum from mutualism, you have parasitoids. This life history includes many groups of terrestrial insects, like the tachinid flies on which I am currently working. Most aquatic parasitoids are not truly aquatic, since they have no special adaptations for the aquatic environment. There is at least one species of truly aquatic chironomid midge which is an ectoparasitoid of caddisfly pupae. And, there are at least a few species of microcaddisflies that do the same.

Orthotrichia species, like all members of the family Hydroptilidae (microcaddisflies), spend 4 out of five of their larval molts as free living. In the final instar, hydroptilid larvae undergo hypermetamorphosis, greatly inflating their abdomens and building a portable case. This is believed to be an evolutionary link between the free living habit and the true casemaking habit, not quite a casemaker but not completely free living either. Orthotrichia in particular builds a tiny purse shaped case out of sand grains. The case is open at both ends and unlike true casemakers can be used bidirectionally.

Orthotrichia spp. larvae; 1. in pillbox case; 2 & 3. with host pupae; note distended abdomen (Wells 2005)

In a few unusual Australian Orthotrichia, the initial case is much smaller and pillbox like. The larvae are swept by the current into the nets of filter feeding caddisflies, which they somehow escape and get enclosed within the pupal case of their host. From there, these Orthotrichia construct their normal case, and begin feeding on the caddisfly pupa. This continues until the Orthotrichia abdomen is big and swollen, and the host is no more than a pupal husk. Having taken over it's host's pupal case, the Orthotrichia larva spins it's own cocoon and pupates. The adults are apparently larger than non-parasitic Orthotrichia, which could be in part due to the easy and massive food supply provided by a net spinning caddisfly pupa.

Even the sea star ovipositing marine caddisflies don't seem too bizarre when I consider all the other Trichoptera oddities. Parasitoids bring to mind tachinid flies and brachonid wasps, not aquatic insects. But I guess that caddisflies prove once again that if there's an aquatic habit, they'll find some way of making it work.

Wait...who am I kidding? Marine insects, feeding on soft corals, ovipositing into sea star incubation chambers? Nothing can beat that level of weird.

Monday, March 4, 2013

Trichoptera to Tachinidae

Well, it has been a while, hasn't it? I just recently got back into the swing of posting regularly. Before that there was a long silence, a diapause (as Bug Girl recently characterized her absence from blogging). And to be honest, the things I was posting about weren't terribly interesting. Minutia of The Code is a technical activity at best, a lawyerly pursuit at worst (reading the backlog for the ICZN-listserv shows this), and not something for general audiences.

I started this blog in 2008 during the first semester of my Master's degree, in part inspired from Bug Girl's Blog and the few other insect blogs around at the time. I wanted to improve my writing, and I wanted to relate my interest in caddisflies, a group I had just begun to investigate. Caddisflies will forever be my first love, no doubt, but in the denouement of my master's thesis I became interested in other groups. It was both temporary burn out and lack of funding in that direction; I was without a "real" job, working in a restaurant, trying to pay back some of my student loans. I had a brief, unpaid internship at Chicago Field Museum (which has had it's own recent financial difficulties), still operating under the assumption that if I just got enough practical experiences in museums one would actually hire me.

It was half way through that valley year that I discovered I was really missing research, and I was missing universities and academia. The long term revision of the North American Keroplatidae that I had been planning seemed like the perfect project for a PhD thesis. Unfortunately, the programs I applied to didn't agree with me, or more likely they didn't have the space or money for that sort of research.

Cutting to the point: I finally found a PhD assistantship! But the work was in neither caddisflies nor fungus gnats. This was an entirely new to me group of insects, an important and diverse group of flies called tachinids. 

A Plethora of Tachinids: Most look like the gray and silver ones at the right side of the third row.

Tachinid flies (Family Tachinidae) are a worldwide distributed, ultra-diverse family of true flies with around 8,000 described species, and many more yet to be described. And we think that all this diversity is relatively recent, with the stem group branching out around 30 to 40 million years ago. The really special thing about tachinids is that they are all endoparasitoids of other arthropods. By which I mean, they all do the 'Aliens' thing. Yeah, that thing. The young get into their hosts by some means, and there the larvae grow and slowly eat the host out from the inside. When they pupate, they burst out and metamorphose inside their last larval skin (called a puparium), leaving behind the empty husk of their host. Endoparasitoids (or the techinical term, koinobionts) do not make a good bedtime children's story (The Very Hungry Caterpillar this is not), but they are a great platform for studying evolution and evolutionary interactions. Parasitoids can be ultra specialist, like many tiny braconid wasps that have only one host species, or super generalist like the tachinid Compsilura concinnata, which feeds on over 120 species and across several insect orders. Most tachinids are in the middle range, with a few to 10s of host species. Why they aren't particularly host limited like other groups will be the subject of a future post.

The majority of tachinids attack plant feeding insects, especially moth caterpillars, sawfly larvae, and beetle larvae, and are probably a significant factor in controlling agricultural pests. A few species have even been mass released as active biological controls. And there are some tachinids which are pests in their own right, including the Uzifly which attacks silkworms and causes millions in damages to sericulture every year. Some of the more unique tachinid groups have unusual hosts, like crickets or stick insects, or ant queens, or stink bugs. There is even a tachinid that attacks trapdoor spiders (Antrodiaetidae).

It's a little funny to me that as important and ubiquitous as tachinids are, they don't really have a common name. The family name, Tachinidae, comes from the Greek word tachys meaning 'swift', so I guess we could call them swift flies. Other names people have used include: parasitic flies, hairy parasitoid flies, hedgehog flies, and bristle flies. None of those names have really stuck, despite being wonderfully descriptive, so people continue to use the abreviated form of the family name. In general, tachinids are small to large sized dark colored, hairy house fly like insects, often with patches of silvery wax, and sometimes with bright orange, yellow or metallic coloration. The hairyness is probably the thing that stands out the most about tachinids, and many of the individual bristles are used in identifying and classifying these flies. A good number of tachinid adults are flower feeders, and some are striking bee and wasp mimics.

If you want to learn more about tachinids, the best place to start is the Homepage for Tachinid Resources. There's also the Tachinid Times, an annual newsletter for tachinid research. This year's issue just came out yesterday, and it's a particularly nice one. Dr. O'Hara (the editor) was kind enough to allow me a full page to describe my intended PhD research, which I will be outlining more in detail next week. There are also lots of pretty pictures, so go check it out!

Monday, February 25, 2013

The ICZN is Broke; Anyone have a hat?

This unfortunate news came to my attention over the past week:

Since 1895, the International Commission on Zoological Nomenclature (ICZN) has helped ensure animal names are unique and long-lasting, with a panel of volunteer commissioners who maintain naming rules and resolve conflicts when they arise. But the U.K.-based charitable trust that supports all this is slated to run out of money before the year's end—and that could spell trouble.

This isn't just a problem for the arbitration process. Six months ago, the Commission passed an amendment allowing electronic only publication of names and other nomenclatural acts. Part of this amendment was provisions for an official registry of nomenclatural act publications, with a mandate that all electronic only articles must be registered with Zoobank prior to publishing. Otherwise, these names and acts are not considered available. A large portion of the ICZN's trust funds have gone to building and supporting the registry, so that may explain why the Commission is suddenly out of money after 66 years with "the Trust".

When the electronic publication amendment was decided on last year, I was worried. Then the worry went away as the Taxonomic End of Names did not arrive and tear asunder the work of centuries. (Note: taxonomists do not actually believe in an End of Names.) And now, the worry is creeping back.

If the ICZN cannot find funds in time, and Zoobank can no longer be supported, the rules of electronic only publication will fall apart, at least under the amendment. I won't even go into arbitration; you can imagine how bad it would be if the ICZN became a static document with no governing body. 

Not that there hasn't already been trouble with people not following the amendment rules. The best example is of a number of fossil species described recently in PNAS, including a lizard named 'Obamadon', after President Obama. Not only did the authors fail to register the publication with Zoobank, they published these descriptions in supplementary information, which is explicitly not a valid way of publishing species. (Catalogue of Organisms has a complete summary.) And the Philadelphia Academy of Sciences isn't exactly a low impact journal, so you can expect this sort of thing is happening more often than once.

But back to the point, which is that the stability of animal names is in trouble. Dr. Roderic Page pointed out on his blog that the funds aren't impossibly high; only 78 thousand is needed to get through the year. While Dr. Page suggests hitting up Kickstarter, and the chair of the trust's board says he will be begging for money at natural history museums (which are woefully funded as it is), a better idea may be to go to online bioinformatics organizations for help. Websites like Encyclopedia of Life, Integrated Taxonomic Information System, Discover Life, and BOLDS require accurate taxonomic information for their databases, and so have the greatest benefit from seeing Zoobank succeed. It would make sense for these large scale databases to collaborate funds and help out the Commission, because that rides well with their individual missions.

Another idea may be to go the way of the Other Code. The International Botanical Congress is a completely volunteer organization that meets every six years and updates their Code of Botanical Nomenclature, as well as arbitrates disputes. The argument against this is that there is no equivalent meeting for zoology that is well attended. Although, if things continue to worsen for zoological nomenclature people may find it more reasonable. I'm hoping it won't reach that point.

Monday, February 18, 2013

Waterfalls and Wandering Gliders

During August of last year, I was doing some consulting work in southwestern Pennsylvania. In the time off I would visit state parks and forests. I was staying just West of the Central Appalacian Ecoregion, and Laurel Mountain was only 10 minutes away. This is a beautiful area of the state. The abundant mountain laurel reminded me so much of the Blue Ridge in South Carolina, where I did my Master's degree. 

One day I had the opportunity to visit Ohiopyle State Park.

The eponymous Ohiopyle Falls.
The town of Ohiopyle is situated on a large bend in the Youghiogheny River as it makes it's way Northwest to Pittsburgh, and gives it's name to both the surrounding state park and the 20 ft falls in the above photograph.

Ohiopyle Falls, looking from the West bank.
The Yough (say it like yawk) is calm enough upstream of the falls for swimming, but then there is a point of no return where the water tumbles over a sandstone cliff stretching the width of the river.

Looking downriver from the East bank of the Falls.
Downstream there are daily whitewater rafting tours. Brave kayakers are allowed to go over the falls on certain summer weekends, and there is an annual Over the Falls Race where many kayakers compete for best times.

Crayfish washed up at the edge
On the West side of the Falls is Ferncliff Natural Area, which includes a rocky, cycad fossil covered trail along the river. When the water is low enough, you can skip the trail for the exposed bedrock of the riverbank. I was able to rock jump out to the edge of the flow, where there were plenty of washed up signs of invertebrates, including crayfish and stonefly skins.

Ephemeral pool, ~3-4 feet across, ~1-2 inches deep
Here and there the rock formed shallow cavities which had filled with rainwater. Some of these had abundant mosquito larvae wiggling around, and some of them were strangely quiet. When I looked closer at these still pools I found the answer lurking in the sediment.

You can't see him, but he's there. The floating shed skin at the left end of the pool is a clue.
There are a couple dragonflies known for laying eggs in ephemeral pools, and after examining a larva under the microscope later, I was pretty sure which one. The mosquito larvae had all been eaten by a Pantala, a rainpool glider larva. Probably Pantala flavescens, also known as the wandering glider or globe skimmer. Wandering gliders are well known for their annual migrations accross continents and oceans worldwide, and equally well known for laying their eggs in any small pool, including artificial containers. I unfortunately didn't see any of the adults about; they have cheesy yellow colored abdomens, and paired with their effortless flight pattern they are pretty difficult to miss.

Dusky dancer (Argia translata) male, at the edge of Ohiopyle Falls.
I also spotted a damselfly perched on the edge of the falls. With the above photo I was able to confirm later that it was a male dusky dancer (Argia translata), a new one for my life list. What threw me off at first is the strange band of white near the tip of the abdomen. If you look close you can see it's pinching the abdomen like a damselfly elastrator (and if you don't know what that word means, don't look it up; this is your only warning). This ring of skin is probably left over from the last larval molt, which sometimes is incompletely shed. When the adult skin expanded and hardened, the leftover ring started pinching. This male is probably still reproduction ready, but it definitely doesn't look comfortable.

Cucumber Falls from above.
The big Falls isn't the only waterfall in the park. Off of the main channel, in a small tributary valley, is the smaller, more private, yet more spectacular Cucumber Falls.

Cucumber Falls from downchannel.

Walking up to Cucumber Falls puts me back in the rainforests of O'ahu. Albeit, the rocks are sandstone and shale, not basalt, but the feeling of overgrown lushness is the same. The ice cold stream drops off a natural overhang into a crystal clear pool with a school of black lined dace. And from there it disappears underground to reappear several hundred feet away, nearly at the Yough, seen through the trees at a distance. How many years have these dace been locked in, diverging under the selection of this small pool from their parents, either upstream or down?

Blacknosed dace (Rhinichthys obtusus?) in the splash pool at the base of Cucumber Falls.
And of course, any trip to a forest stream wouldn't be complete without the appearance of my spirit animal. 

An ebony jewelwing male, doing what it does best: glistening in the sunlight.
It seems I see Calopteryx maculata, the ebony jewelwing, no matter where I go in Eastern North America. They're common as can be, but still remain my favorite insect.

Acknowledgement: Much thanks to Stephanie Sanner-Fallon of Powdermill Nature Reserve for being my "tour guide" to the beauties of southwest Pennsylvania, especially Ohiopyle State Park.

Monday, February 11, 2013

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.