The ICZN and Electronic Publication: Where Did It Go Wrong?

Reconstruction of the dinosaur Aerosteon riocoloradensis, from here. This species was published in electronic-only format in September 2008; it was nearly six months before anyone noticed that this was a problem.

Since the ICZN approved electronic publication, we've had a few weeks to get over the initial heady rush of excitement and further assess the situation. Which means that we have to ask the question: what is wrong with the new rules?

There is no question that some of the new rules on electronic publication will need to be adjusted. This, I hasten to point out, is not an indictment. The International Code of Zoological Nomenclature for dealing with paper publications first appeared over fifty years ago, in 1961, and the earliest attempt at a formal code of nomenclature had been proposed by Hugh Edwin Strickland another 120 years before that. Despite all this time, the Code as it pertains to paper publications has still not been perfected, and revisions continue to be proposed and published. Indeed, some of the issues the code grapples with (such as what does or does not constitute 'publication') are, in the end, probably not universally soluble, because they deal with factors such as judging ethical behaviour that cannot be expressed in simple formulae applicable to every situation. So it should hardly be expected that rules for electronic publication should have immediately attained perfection when not even those for paper publication, with 170 years or more of a head start, have not yet done so. What is more, some of the failings in the current rules will not become apparent until they are able to be tested. Loopholes will have to be closed, terms will have to be clarified. And as I airily critique issues with the current rules in this post, I am well aware that the rules' composers will have probably already discussed them to death, and any suggestions I make may have their own problems that I have overlooked.

What, exactly, is an electronic publication?

As I noted in the earlier post linked to above, the ICZN effectively requires that any electronic publication has an associated ISBN or ISSN (this does not have to appear in the publication itself, but it is required for the registration of the publication on ZooBank). To a certain extent, this makes sense: it means, for instance, that taxonomists do not have to worry about taxa being 'accidentally' published in mailing groups, blogs, etc. that may not be reliably archived. But it does raise the question: in the electronic age, why should a publication necessarily be a 'book' or a 'serial'?

The ICN (International Code for Nomenclature of plants, algae and fungi; what we used to call the ICBN) apparently requires that electronic publications be in pdf format. The ICZN does not make this an actual requirement, though pdf is cited as an example of a format that meets the requirement of 'widely accessible electronic copies with fixed content and layout'. I think that the ICZN is in the right here; while it is difficult to see pdf being superseded at the present point in time, it is perhaps hazardous to assume that this will never happen. I suggest that the requirements of an electronic publication should be that, (A) at least the content (if not the format) should be intended to be immutable*, and (B) it should be somehow 'stand-alone', not requiring a larger context other than the standard requirements for reading electronic files (so, for instance, a database entry that can only be accessed as part of that database may not be acceptable).

*It is worth noting at this point that even a paper publication is, in a sense, not 'immutable' if its publishers do not behave ethically. If a publisher produces a second, altered print run without explicitly marking it as a revised edition or changing the reported publication date, there may be no indication that it represents a distinct publication from the original run. Most people will not read through two separate copies of a publication just on the off-chance that they may differ.

Do pre-releases count?

There is one clause in the new rules that I expect will be guaranteed to cause immediate problems. This is the new Article 21.8.3: "Some works are accessible online in preliminary versions before the publication date of the final version. Such advance electronic access does not advance the date of publication of a work, as preliminary versions are not published (Article 9.9)."

Remember old Scansoriepidendrosauropteryx? This was an animal that first debuted in an electronic online-early form in a well-known journal, but before the print edition of that paper was finally published the animal was described under a different name in a paper-only publication. The resulting confusion, when the earliest name publicised was not the one with technical priority, was one reason why at least some people were calling for electronic publication to be recognised. Well, guess what? Under the current rules, this case would have played out no differently. Some would look askance at accepting pre-releases as validly published because of the possibility of alteration between the pre-release and the final edition, but as I said above, perhaps this is something that requires us to discuss what exactly we regard as a 'publication'.

There is also the new Article 21.9 to consider: 'A name or nomenclatural act published in a work issued in both print and electronic editions takes its date of publication from the edition that first fulfilled the criteria of publication of Article 8 and is not excluded by Article 9.' Some may read this as saying that an electronic pre-release counts as a valid publication if, in itself, it meets the requirements of electronic publication. Some may read this as being trumped by 21.8.3.

And what about electronic versions of paper publications?

To be validly published, an electronic publication has to be registered with ZooBank and include evidence of its registration. Paper publications, on the other hand, do not yet have to be registered. The problem is, many researchers are now more likely to access electronic copies of paper publications than the original paper edition itself. And if I do so, how can I be sure that the paper edition actually exists? Even for some of my own publications in recent years, I've never actually laid eyes on the original journals. I've only seen the pdfs, and I've trusted in the publisher that the paper edition exists and that taxa I've erected are indeed validly published. Similarly, if I come across a publication from an unfamiliar journal (and with hundreds if not thousands of journals publishing in biology worldwide, I will not be familiar with them all) when searching online, would I necessarily know whether that represents an electronic-only publication or an electronic copy of a paper one?

When the question of electronic publication was still being debated, I stated more than once that the biggest problem with not accepting it was that, for many readers, it was all too difficult to distinguish valid publications from invalid. I have my doubts whether this problem has yet been solved.

Asperdaphne, I Don't Know Who You Are Any More

A true Asperdaphne: the type species A. versivestita, photographed by Des Beechey.

The subject of today's post has been going through something of an identity crisis recently. Asperdaphne was listed by Powell (1966) as a genus of small conoid gastropods found in Australia, New Zealand and the Pacific coast of Asia, with a fusiform shell and coarse clathrate (lattice-like) ornamentation. This remains the sense in which it has been most commonly recognised. However, in a paper published just last year, Beu (2011) revealed that this picture of Asperdaphne was a fraud. The majority of species assigned to Asperdaphne by Powell (1966) were not members of the same genus as the type, A. versivestita. Instead, they belonged to another genus, Pleurotomella, the type species of which Powell had not been familiar with. Meanwhile, A. versivestita was more appropriately placed with what Powell had called Tritonoturris, an Indo-Pacific genus of larger conoids with a more ovate shell shape. As Asperdaphne was an older genus name than Tritonoturris, this meant that what had been Tritonoturris was now Asperdaphne, while what had been Asperdaphne was now Pleurotomella. The identity of the two east Asian species assigned to Asperdaphne by Powell (1966) was not discussed by Beu (2011).

Not an Asperdaphne: Pleurotomella hayesiana, also photographed by Des Beechey.

We have encountered this paper of Beu's before, when I cited it in the post on another conoid genus, Kuroshioturris. As with that genus, the recognition of Asperdaphne had been confused by differences in protoconch morphology related to larval nutrition. Species assigned to 'Tritonoturris' had a tall conical protoconch, indicating a planktotrophic (feeding on plankton) lifestyle as a larva, while Asperdaphne versivestita has a blunt-tipped paucispiral protoconch, indicating that its larvae are lecithotrophic ('fed' by energy reserves in the yolk).

Diagram of the foregut of 'Tritonoturris' subrissoides, from Fedosov (2008).

Slightly more mysterious are Asperdaphne's feeding habits as adults. Foregut structure has been investigated for one presumed Asperdaphne species, under the name Tritonoturris subrissoides (Fedosov 2008). T. subrissoides is one of a number of members of the family Raphitomidae to show a reduction in foregut structures, and has lost the radula and venom gland of most conoids. Instead, it has a large introvert (extendable proboscis) that probably functions in prey capture. However, the roof of the introvert has a large and elongate outgrowth, unlike any found to date in any other conoid, with a well differentiated muscle system indicating that it is capable of complex movement. Presumably, this outgrowth functions somehow in prey capture (perhaps as a grasping 'finger'?) but its exact purpose remains unknown.

REFERENCES

Beu, A. G. 2011. Marine Mollusca of isotope stages of the last 2 million years in New Zealand. Part 4. Gastropoda (Ptenoglossa, Neogastropoda, Heterobranchia). Journal of the Royal Society of New Zealand 41 (1): 1-153.

Fedosov, A. E. 2008. Reduction of the alimentary system structures in predatory gastropods of the superfamily Conoidea (Gastropoda: Neogastropoda). Doklady Biological Sciences 419: 136-138.

Powell, A. W. B. 1966. The molluscan families Speightiidae and Turridae: an evaluation of the valid taxa, both Recent and fossil, with lists of characteristic species. Bulletin of the Auckland Institute and Museum 5: 1-184, pls 1-23.

Deceptive and Poisonous Sisters

Iphicleola sister Adelpha iphicleola, photographed by Arthur Chapman.

The butterfly genus Adelpha includes 85 species, many with multiple subspecies, found widely in North and South America (Willmott 2003a). Some of you may recognise 'adelpha' as the Greek word for 'sister', which is also the vernacular name for these butterflies. Supposedly, the white stripes on the wings of many species resemble the edges of a nun's habit (or, at least, so sayeth Wikipedia). The sisters belong to a group of butterflies called the Limenitidini, members of which tend to sit with their wings open when resting, and have a distinctive gliding flight pattern in which the wing tips are pointed downwards (Willmott 2003b). Adelpha is the only genus of Limenitidini found in South America. In North America, Adelpha bredowii is found as far north as Oregon, while in South America species are found down to Uruguay. Not surprisingly, the highest diversity is found in the tropics, though some species are relatively uncommon throughout their ranges (Willmott 2003a).

As caterpillars, Adelpha species feed on a wide variety of food plants, with individual species varying from very host-specific species to broadly catholic species. As befits Neotropical caterpillars, some species possess a ludicrous array of protrusions and outgrowths:

Caterpillar of Adelpha serpa selerio, photographed by Artour A.
When feeding on a leaf, the caterpillars leave the midrib intact, and use it as a support when resting. Over time, they extend the midrib using a combination of faecal pellets and silk to extend their support, and they also sit on this support when moulting. After moulting to the final larval instar, they leave the support and rest on the upper leaf surface. They also attach masses of mixed silk and faecal pellets to the base of their support or hanging off it. One species, Adelpha basiloides, builds small, curved, larva-shaped faecal masses that it places on the leaf surface several millimetres away from its support: Aiello (1984) speculated that these might functions as decoys to distract potential predators from the real caterpillar.

Arizona sister Adelpha eulalia, photographed by Tom Bentley.

The adults of Adelpha have a reputation for being tricky to identify; DeVries described them as "the most difficult and trying taxonomically of all the nymphalids". For a long time, Adelpha species were divided into groups on the basis of their wing patterning, but comparisons with other features such as caterpillar morphology have revealed that species with similar wing patterns are often not closely related (Aiello 1984; Willmott 2003b). Instead, it has been suggested that mimicry has been a significant factor in the genus' evolution: certain species feeding as caterpillars on toxic plants such as members of the Rubiaceae (and hence sequestering the plant toxins to render themselves distasteful) are imitated by species with more innocuous diets. Because the appropriate model for such mimicry may vary with distribution, some mimetic species are quite variable in appearance; prior to the genus' revision by Willmott (2003a), some members of a single species were classified in entirely separate species groups!

REFERENCES

Aiello, A. 1984. Adelpha (Nymphalidae): deception on the wing. Psyche 91 :1-46.

Willmott, K. R. 2003a. The Genus Adelpha: Its systematics, biology and biogeography (Lepidoptera: Nymphalidae: Limenitidini). Scientific Publishers.

Wilmott, K. R. 2003b. Cladistic analysis of the Neotropical butterfly genus Adelpha (Lepidoptera: Nymphalidae), with comments on the subtribal classification of Limenitidini. Systematic Entomology 28: 279-322.

Brine Fairies

The once-ubiquitous 'sea monkey' advertisement. Take a very good look at the words in the lower margin.

Readers of a certain age (or readers who have perused the comic books once belonging to readers of a certain age) will instantly recognise the image above. It appeared on almost every comic book published between 1962 and 1975, and offered a something truly mind-blowing. For a couple of bucks, you could receive a small packet in the post that, when its contents were added to water, grew into minute fish-tailed humanoids that would create their own minute society, all in one goldfish bowl sitting in your bedroom!

As Robin Ince summed up the sea monkey experience in his Bad Book Club: 'This was a lie'. You did receive a small packet in the post, the contents of the packet did hatch out in water, but you did not get the pictured anthropomorphs. What you actually got were these:

The North American brine shrimp Artemia franciscana, photographed by Jean-François Cart.

The 'sea monkeys' became labelled one of childhood's great disappointments, which I call an utter shame. Because I personally would describe them as some of the most elegant crustaceans that I've ever seen.

Brine shrimp and their relatives belong to a group called the Anostraca. The Anostraca, sometimes referred to as fairy shrimps, are a group of a little under three hundred described species. They are generally less than an inch long, though the larger species can grow to several inches. The taxon name basically means 'without a carapace', and this is one of the distinctive features of the group. The body is elongate and, behind the head, is divided into a thorax bearing feathery swimming legs and an abdomen lacking appendages except a terminal pair of uropods. Most species of Anostraca have eleven pairs of swimming legs, though the species Polyartemiella hazeni and Polyartemia forcipata have, respectively, seventeen and nineteen pairs (Weekers et al. 2002). Anostracans have a distinctive slow swimming style, lying on their back. They are found living in ephemeral or hypersaline waters where predatory fish are few or absent; in order to persist in such environments, they produce resistant eggs that are able to survive drying out, hatching when the temporary pool is refilled by the rain.

Conservancy fairy shrimp Branchinecta conservatio, from here.

The phylogeny of Anostraca was investigated by Weekers et al. (2002), who found that they could be divided between two lineages: one including the genera Artemia and Parartemia, which are found in hypersaline waters, and the other containing the remaining freshwater genera. Most members of both lineages are filter-feeders, but some larger members of the freshwater lineage in the genus Branchinecta have become predators. The most favoured prey of these large Branchinecta? Why, smaller Branchinecta! Studied specimens of the predatory Branchinecta raptor would only deign to take other invertebrate prey if their preferred B. mackini was unavailable (Rogers et al. 2006). These predatory Branchinecta are found living in turbid, sediment-filled waters with low visibility, and mostly found their prey by coming into contact with it whilst swimming in the water column. Squeezing water out of a pipette near one would incite it to try and attack the pipette. If unable to find swimming prey, B. raptor would swim down to the sediment bed and stir it up, then attempt to find invertebrates flushed out of hiding.

Streptocephalus torvicornis, photographed by J.R. Casaña & Manolo Ambou Terradez.

The two hypersaline genera have complementary distributions: Parartemia is endemic to Australia while Artemia is found on the remaining continents (though Artemia is now present in some localities in Australia as an introduced taxon). In the past, all Artemia around the world were often treated as a single species, A. salina. However, the existence of a number of geographically distinct lineages has now been established, with these treated as separate species (A. salina proper is found in Europe). Both sexually and parthogenetically reproducing forms of Artemia exist. The parthenogenetic forms are treated as a single species, A. parthenogenetica, and derive from a single Eurasian origin, but are themselves genetically diverse, including diploid, triploid, tetraploid and pentaploid individuals (Triantaphyllidis et al. 1998). Sadly, this new-found taxonomic complexity of Artemia is in some danger of re-simplifying: the international trade in brine shrimp, used mostly as food for fish, is almost entirely based on eggs derived from the Great Salt Lake in Utah. As a result of this trade, the North American species A. franciscana has become introduced, both accidentally and deliberately, to saline waters around the world, and has been found in many localities to be replacing the native brine shrimp.

REFERENCES

Rogers, D. C., D. L. Quinney, J. Weaver & J. Olesen. 2006. A new giant species of predatory fairy shrimp from Idaho, USA (Branchiopoda: Anostraca). Journal of Crustacean Biology 26 (1): 1-12.

Triantaphyllidis, G. V., T. J. Abatzopoulos & P. Sorgeloos. 1998. Review of the biogeography of the genus Artemia (Crustacea, Anostraca). Journal of Biogeography 25: 213-226.

Weekers, P. H. H., G. Murugan,J. R. Vanfleteren, D. Belk, & H. J. Dumont. 2002. Phylogenetic analysis of anostracans (Branchiopoda: Anostraca) inferred from nuclear 18S ribosomal DNA (18S rDNA) sequences. Molecular Phylogenetics and Evolution 25: 535-544.

It's the End of the World as We Know It...

...maybe.

For lo, it did come upon this day that the ICZN did look upon electronic-only publication, and say that it was good. Provided that it met the following requirements:

(1) the published work must be registered with ZooBank prior to publication, with provision in the ZooBank record of a permanent archive in which the the published work will be held,

(2) the published work must include evidence of registration, such as the ZooBank registration number, and

(3) the published work must be associated with either an ISSN or ISBN number, so it must be a formal 'book' or 'journal'.

You can read further details here. As is standard for new ICZN requirements, they are not intended to be retroactive, and online-only names from before the new rules were introduced are still invalid.

I don't think that many people will be surprised by this (while you complain about the cost of prescriptions... Mike Taylor is looking very smug). As I've discussed before, I reluctantly came to accept that electronic publication would have to be allowed after I realised that most non-taxonomists (and many actual taxonomists) were finding it increasingly difficult to distinguish what was 'published' from what was not. So what does this mean in practice?

It became clear at an early date that successful management of electronic publication was going to require registration. In the past, most people were talking about registration of names, but the ICZN has decided to go with registration of the actual publication. This avoids any hiccups such as human error leading to some of the names in a publication being 'published' while others are 'unpublished'. I can see potential complications arising with the requirement that registration happen before publication, but ZooKeys has been publishing articles with ZooBank registration numbers for taxa included for a while now, so it would seem that the requirement is not insurmountable. Of course, there would have been potential problems had the requirement been registration after publication. It should be noted that, even though the published work has to include evidence of registration, there is a certain allowance for error, so long as it is clear that the work has indeed been registered (so, for instance, if a transcript error meant that the wrong registration number was included in the publication, that does not automatically invalidate the publication).

The requirement that the publication has either an ISSN or ISBN number means that names cannot be just published carelessly. If I refer to the features of an unpublished species in a blog post, I will not be accidentally 'publishing' that species and potentially confusing the paper trail (electronic trail, in this case). Note also that, while the ZooBank record of a published work must include the ISSN or ISBN, the work itself doesn't directly have to. So, for instance, the ISSN of a journal does not have to be included in every individual article.

One of the biggest concerns raised about allowing electronic publication is that it will make it even easier for would-be taxonomic 'vandals' to ply their irritating trade. The registration and ISSN/ISBN requirements, as well as making it clear what is intended for publication and what is meant to be just an online communication, are intended to impede such behaviour. They won't stop it entirely (as I've noted a few times before, that would be effectively impossible) but they do provide a couple of hoops that must be jumped through.

So all that remains to be said is: Let the games commence!

The Variety of Life turns 1000

I have just published the 1000th entry onto the Variety of Life site. Subject: the weevil subfamily Baridinae.

I started "The Variety of Life" a bit over a year and a half ago to give a broad, more technical sampler of organismic diversity, and to convey sometime of just how extensive that diversity was. On that note, the main thing that strikes me after 1000 entries of higher-level taxa is just how little of it I've touched on. Perhaps the only group that I wouldn't say is completely rudimentary are the mosses, and even then it's pretty ropey.

Still, I'm reasonably happy with how its progressing, and things can only improve. Already, there are some taxa for which "The Variety of Life" comes out #1 in a Google search. Which, considering the rudimentary coverage I've just spoken of, is more of an indictment of just how poorly covered some taxa are in general.

A Brain Explosion

Elliptical star coral Favia speciosa, photographed by Utsunomiya.
For today's random taxon, I drew the Faviinae. This is a subfamily within the Faviidae, commonly known as 'brain corals' and recognised as an important family among the tropical reef-builders. Families of corals have generally been distinguished by the arrangement and morphology of skeletal structures within the coral cup: Faviidae were characterised by having trabeculae (the calcareous fibres forming the basis of the skeletal septa) arranged in one or two fans, with more or less regular marginal teeth at the top of the septum. The Faviidae were divided into two subfamilies, the Faviinae and Montastreinae, based on whether the budding of polyps takes place inside (Faviinae) or outside (Montastreinae) the individual cups in a colony. Several genera recognised within the Faviinae were mostly distinguished by their colony form and how the individual polyps are arranged (Budd & Stolarski 2011).

Leptoria phrygia, photographed by Neville Coleman.
And if any of you were wondering about the use of the past tense in the last paragraph, that is because more recent studies have been pretty unanimous in indicating that the system just described is in need of a significant shake-up. As noted here in an earlier post, molecular studies have indicated that coral taxa distinguished by septal characters are widely problematic. A broad phylogenetic study of corals by Fukami et al. (2008) found that, of sixteen recognised families tested, eleven were polyphyletic. Faviidae, in particular, were scattered between no less than seven of the twelve supported clades identified by Fukami et al. within the broader 'robust clade'. Some of the larger genera, such as the type genus Favia, were also polyphyletic and dispersed between multiple clades. The level of discordance between morphological classification and molecular phylogeny is reflected by the fact that Fukami et al.'s large clade XVII, containing members of the families Faviidae, Merulinidae and Pectiniidae, has since been informally dubbed the 'Bigmessidae' (Huang et al. 2011). The 'Bigmessidae' also includes the genus Trachyphyllia, a morphologically very variable coral that is generally found free-living, either solitary or colonial, among the sand at the very base of coral reefs (Best & Hoeksema 1987). Trachyphyllia has been treated by some authors as its own family, or regarded by others as an unusual member of the Faviinae.

Maze brain coral Goniastrea australensis, photographed by David Witherall.
As yet, no formal reclassification of the corals has been proposed, but when it eventually is, it is likely that there will be no Faviidae at all. The type species of the family, Favia fragum, is closely related to the type species of another family, Mussidae, and the latter name is the one with priority. Interestingly, both these taxa are found in the Atlantic Ocean, and the molecular phylogenies do support a separation of the Atlantic faviids from the Pacific species. Also, it is still possible that morphological characters will play their part in the coming coral reclassification: even though the broader scale features of the septa and colony form have proven vulnerable to convergence, smaller scale features of the skeletal microstructure promise to be less discordant with molecular phylogenies (Budd & Stolarski 2011).

REFERENCES

Best, M. B., & B. W. Hoeksema. 1987. New observations on scleractinian corals from Indonesia: 1. Free-living species belonging to the Faviina. Zoologische Mededelingen 61 (27): 387-403.

Budd, A. F., & J. Stolarski. 2011. Corallite wall and septal microstructure in scleractinian reef corals: comparison of molecular clades within the family Faviidae. Journal of Morphology 272: 66-88.

Fukami, H., C. A. Chen, A. F. Budd, A. Collins, C. Wallace, Y.-Y. Chuang, C. Chen, C.-F. Dai, K. Iwao, C. Sheppard & N. Knowlton. 2008. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (order Scleractinia, class Anthozoa, phylum Cnidaria). PLoS ONE 3 (9): e3222.

Huang, D., W. Y. Licuanan, A. H. Baird & H. Fukami. 2011. Cleaning up the ‘Bigmessidae’: molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae. BMC Evolutionary Biology 11: 37.