Carnivalia

Berry Go Round #12 is up at Foothills Fancies.

It's also coming up to time for Linnaeus' Legacy, the carnival of biodiversity and how we understand it. This month's edition will be hosted by Greg Laden, so get your posts in to him, me, or use the submission form.

Attercop

Permarachne novokshonovi, a Permian fossil that was similar in appearance to the Devonian Attercopus fimbriunguis. Figure from Selden et al. (2008).

Selden, P. A., W. A. Shear & M. D. Sutton. 2008. Fossil evidence for the origin of spider spinnerets, and a proposed arachnid order. Proceedings of the National Academy of Sciences of the USA 105 (52): 20781-20785.

A new paper published today presents us with a revised description of Attercopus fimbriunguis, the stem-spider (thanks to William Shear, one of the paper's authors, for sending it out). With this redescription, the position of Attercopus is secured as one of palaeontology's great "transitional fossils".

Attercopus is a fossil arachnid from the Middle Devonian (bonus question: what is the connection between Attercopus and Barad-dur?), so dates back to when the terrestrial environment was first finding its feet (and in those invertebrate-dominated days, there were often a lot of them to find). Most modern terrestrial animals were yet to make an appearance - the vertebrates were still keeping to the water, the insects were there but not yet a significant part of the ecosystem. It was the age of the arachnids and myriapods. Even within the arachnids, most of the taxa then present would have been unfamiliar to modern humans, and the currently most familiar group of arachnids, the spiders, had not yet made an appearance. That is where Attercopus becomes so significant.

Spiders are actually not typical arachnids at all. Like all other arthropods, the ancestral arachnid form has the body divided up into segments. These segments are externally visible as the cuticle is divided into plates, with separate dorsal (tergites) and ventral (sternites) plates. In most living arachnid orders (such as scorpions and harvestmen), these external plates are still present. In most spiders, the cuticular plates have become fused, and the segmentation is not externally visible. One small group of spiders that is today restricted to eastern Asia, the Mesothelae or liphistiomorphs, differ from all other living spiders (the Opisthothelae, to which they form the sister group) in retaining visible tergites on the opisthosoma (abdomen), though they do not have visible sternites. Mesothelae also differ from Opisthothelae in lacking poison glands in the fangs. As well as the concealed segmentation (independently acquired by acaromorphs such as mites), spiders are also distinct in their production of silk. Only one other group of arachnids, the pseudoscorpions (as well as numerous groups of insects), produces silk. In pseudoscorpions, the silk-producing glands are in the pedipalps. In spiders, they are at the back end of the underside of the opisthosoma, and open through appendages called spinnerets (photo below from here).



The presence of silk-producing spigots in Attercopus was first established in 1991, when it was connected to an isolated Devonian 'spinneret' described two years previously (Selden et al., 1991). As redescribed by Selden et al. (2008), however, Attercopus shows a number of significant differences from modern spiders. It retains distinct external segmentation, both tergites and sternites. Also, rather than having the silk glands on spinnerets, the spigots are positioned directly on the underside of the opisthosoma (and their status as silk glands is confirmed in one specimen by the presence of a strand of silk preserved in the process of being exuded from one of the spigots!) The 'spinneret' previously described for Attercopus, as it turns out, was an artifact resulting from post mortem folding of the cuticle. Without the guiding control of spinnerets, Attercopus would not have produced silk in well-defined strands like a modern spider, but in more of a shapeless mat. This is not surprising - the distribution of silk use in modern spiders suggests that its use in reproductive functions (constructing egg cases, spermatophores, etc.) or in constructing burrows probably pre-dated its use in prey capture.


Part of a fossilised Attercopus, showing silk preserved while being released from one of the spigots. Figure from Selden et al. (2008).

Attercopus also appears to have lacked poison glands (again, their previously-suggested presence appears to have been an artifact), which tallies well with their absence in living Mesothelae. Perhaps most intriguing of all (at least to me) is that Attercopus possessed a segmented flagellum. The flagellum is a character of the Uropygi (whip scorpions) which, together with the Amblypygi, form the probable living sister group to spiders in the clade Tetrapulmonata (Shultz, 2007). At present, we cannot say whether the flagellum is an ancestral feature of Tetrapulmonata that was lost in spiders and amblypygids, or was independently derived in uropygids and Attercopus. Selden et al. (2008) also identify sternites and a flagellum in a Permian spider-like fossil, Permarachne novokshonovi, and establish a new order, Uraraneida, for the two fossils. This is not a major change in classification, as Uraraneida is still regarded as the stem group to modern spiders. Also, as the characters uniting Attercopus and Permarachne (free sternites and a flagellum) are both probably plesiomorphies, the Uraraneida is not necessarily monophyletic. With the definite exclusion of Attercopus from the crown group, the earliest known true spider is now Palaeothele montceauensis, a liphistiomorph from the late Carboniferous.


Liphistius owadai, a modern species of spider retaining free tergites. Photo from here.

The big change between Attercopus and crown Araneae seems to have been the development of spinnerets instead of bare spigots. Developmental genetic studies show that the spinnerets are homologous to opisthosomal legs, which is remarkable because arachnids don't have legs on the opisthosoma. To find opisthosomal appendages on the arachnid lineage, one has to go to their living sister group, the horseshoe crabs. Because of the derived position of spiders within arachnids, and the fact that all other fossil arachnids lack opisthosomal appendages, it is unlikely that opisthosomal appendages in spiders represent a retained plesiomorphy that was lost in all other arachnids. Selden et al. (2008) suggest that this may represent reactivation of suppressed developmental genes, as supposedly seen in stick insects. But despite my wince at their ill-chosen supporting example, legs-to-spinnerets is perhaps a good candidate for such a process. While obvious opisthosomal appendages are not present in arachnids, developmental studies indicate that the covering plates of the arachnid book lungs are homologous to appendages, and it has been suggested for scorpions that the sternites themselves represent fused appendage remnants.

The sad fact, I feel, is that our understanding of how developmental processes evolve is still all too rudimentary. For all the vast amount of genetic studies that have been conducted in recent decades, most have been focused on a relatively small number of model species - Drosophila melanogaster, Danio rerio, Arabidopsis thaliana,... Consideration of a single species, or even a few closely-related species as has been done for Drosophila, becomes woefully inadequate when considering questions raised when debating the possibility of genetic recurrence. What happens to a developmental gene when it is inactivated for a certain function? Can it be readily reactivated, or does genetic drift seal its fate as a pseudogene? Is genetic reactivation even the only possible explanation - what about those genes that are still developmentally functional elsewhere in the body? Can they become activated elsewhere in the embryo to give rise to novel structures? Could the spinnerets of spiders be not recurrences of the lost opisthosomal appendages, but rather re-deployments of the appendages still present on the prosoma? Or could they somehow represent a combination of the two? Whatever the answers that are yet to be found, fossils such as Attercopus will always be critical in directing our searches for them.

REFERENCES

Selden, P. A., W. A. Shear & P. M. Bonamo. 1991. A spider and other arachnids from the Devonian of New York, and reinterpretations of Devonian Araneae. Palaeontology 34: 241–281.

Shultz, J. W. 2007. A phylogenetic analysis of the arachnid orders based on morphological characters. Zoological Journal of the Linnean Society 150 (2): 221-265.

Streps

Just a quick post for Taxon of the Week this time around - blame it on the time of year (I am definitely one of those who move into full "Bah, Humbug!" mode around this time of year, though personally I always associate the word "humbug" more with The Phantom Tollbooth than A Christmas Carol*). And in this time of year with its tradition of kissing under the mistletoe (or so we're told - that tradition never made it to the Antipodes), what could be more appropriate than an introduction to an organism most commonly associated in the public mind with throat infections?

*Remember that Phantom Tollbooth allusion - hopefully, I will be having cause to make further reference to it within the year.

Streptococcus is one of the most familiar bacterial genera. There was a time when the name was used to refer to almost any spherical, Gram-positive bacterium that grew in a chain-shaped colony, but the old Streptococcus calved off a few genera in the mid-1980s, most notably Enterococcus and Lactococcus. One of the most significant features distinguishing Streptococcus from the latter two genera is that Streptococcus secretes a protective capsule of slimy polysaccharides. In pathogenic species, this capsule apparently mimics the host's connective tissue, allowing the bacterium to pass unnoticed by the host's immune system.

The best-known members of the genus include Streptococcus pneumoniae and S. pyogenes. Streptococcus pneumoniae causes (unsurprisingly) pneumonia. Streptococcus pyogenes causes... well, almost anything that you'd care to mention, really. It's most commonly associated with "strep throat", but it can also cause such dreadful conditions as scarlet fever, toxic shock syndrome and ye olde puerperal fever that caused the death of so many new mothers before Oliver Wendell Holmes suggested in 1843 that getting doctors to wash their hands before delivering a baby was perhaps not such a bad idea. The most infamous (though thankfully, one of the rarest) condition caused by S. pyogenes is necrotising fasciitis - the dreaded flesh-eating bacterium. Yes, it does exist. No, it is not just something invented by B-grade horror movies.

Not all members of Streptococcus are pathogens. Streptococcus thermophilus, for instance, is used in the production of yoghurt. Unfortunately, though all too typically for bacteria, the non-pathogenic taxa have generally been ignored in favour of their more attention-seeking cousins.

REFERENCES

Prescott, L. M., J. P. Harley & D. A. Klein. 1996. Microbiology (3rd ed.) Wm. C. Brown Publishers: Dubuque (Iowa).

When Parsimony Goes Wrong: The Wings of Stick Insects

The stick insect Sipyloidea sipylus opening its wings. Photo by Drägüs.

One of the questions most commonly asked when looking at a phylogenetic tree is what that tree indicates about how the organisms on it evolved. What does it say about what their ancestors were like? What changes happened when? In answering those questions, the most commonly invoked tool is the principle of parsimony - in the absence of any reason to think otherwise, favour the explanation that is the most straightforward, and (in the case of inferring evolutionary history) requires the least number of changes. Parsimony is a popular tool because it's straightforward, relatively easy to apply, and it makes a great deal of intuitive sense - if a red animal occupies a deeply nested position in a clade of blue animals, then it seems fairly obvious that the ancestral animal was blue. However, like all analytical tools, the principle of parsimony is based on certain assumptions, and can be misleading if those assumptions are violated. Parsimony assumes that when comparing changes in a character between two states, change in either direction is equally likely. If, for whatever reason, a change is more likely to happen in one direction than another, then a parsimony analysis might be mislead about the ancestral condition. An elegant demonstration of this limitation of parsimony can be found in Collins et al. (1994) were the results were discussed of using parsimony to infer an ancestral DNA sequence (cytochrome b) for the marine gastropod genus Nucella. Nucella DNA is AT-rich (its base composition includes far more As and Ts than Gs and Cs). Inferring the ancestral sequence using parsimony implies an ancestor even more AT-rich than any of its descendants, despite the fact that the AT-bias remains fairly constant across all living members of the clade. Because GC bases are relatively uncommon for a given position, the parsimony analysis always tends to indicate them to be the derived state.

A few years ago, a paper appeared in Nature presenting a phylogenetic analysis of Phasmatida, stick insects or phasmids (Whiting et al., 2003). Phasmids include both winged and wingless taxa. In those taxa that do have wings, the forewings are greatly reduced and the hindwings are the functional pair. Whiting et al. (2003) found that the various winged phasmids were phylogenetically nested well within a series of wingless taxa. They therefore made the surprising suggestion that the common ancestor of living phasmids was wingless, and that those phasmids with wings had regained them secondarily.


Timema dorotheae, a member of the basalmost genus of Phasmatodea. Photo by David Maddison.

As remarkable as this may sound, it may not be impossible. Studies of embryonic development in animals have found that developmental regulatory genes often act in a hierarchical manner, so that a relatively small mutation in a gene acting on an early stage of development may have a significant effect on later stages of development. It has therefore been suggested that it might be possible for a given feature (such as wings in an insect) to be lost through a mutation causing that feature to start developing in the first place, without any change in the genes that shape how that feature develops once it starts. If the original regulatory gene was then to mutate back to its original condition in a later generation, the missing organ might spring back into its original position as if it had never left. It might be argued that the patterning genes rendered functionless by the original mutation might be suject to genetic drift, and degrade to useless pseudogenes that could not be reactivated even if the original mutation did revert, but Whiting et al. (2003) invoke another of the interesting features of developmental genetics - many genes are pleiotropic (involved in patterning different characters at once). For instance, insects use many of the same genes in patterning their legs as patterning their wings, so even if selective pressure to retain function for the one was removed, there still might be the need to retain function for the other.

While this may be theoretically possible in general, is it the case for phasmid wings in particular? Does the evidence offer strong support for regained wings in stick insects? Despite Whiting et al. (2003) being widely cited as a proven case of evolutionary regain of a complex character, I'm going to have to answer with a no, I don't think so. Stick insects are generally not highly mobile. Even those species that have fully functional wings fly only rarely. They are exactly the type of insect that one would expect to be prone to frequent flightlessness and wing loss. Whiting et al. (2003) themselves state at one point that a winged ancestor for crown phasmids became the most parsimonious reconstruction if wing loss was weighted as six times more likely than wing gain. This does not seem too unlikely a difference. Other potential evidence can be seen in the wings themselves. Whiting et al. argue that genes involved in wing development may have remained potentially functional if they were still being used for other organs. But how far can this argument be taken?



One of the most useful features in characterising insect wings is their venation. A generalised diagram of insect wing venation is given above, but different orders of insects have significantly different wing venation, enough so that relationships can be recognised for fossil insects known from wings alone. Comparisons between wing venation of different orders can also be very useful in establishing their relationships.

Wing venation of phasmids shares a number of distinctive characters with that of Orthoptera (grasshoppers and crickets). Both these orders have the forewings leathery, with the main veins running roughly parallel. It is the hindwings, however, that show the major similarities (Grimaldi & Engel, 2005). In both orders, the cubital veins (the veins marked Cu and in blue in the diagram above) don't run to a point low on the hind edge of the wing as they do in most orders, but instead run fairly straight out to near the distalmost tip of the hindwing. The veins in front of the cubitals, which enclose most of the wing space in other insect orders, are packed into the fairly small space between the cubitals and the front of the wings (this is the hardened part of the wing in the photo at the top of this post). Most of the hindwing in orthopterans and phasmids is composed of the anal fan, reasonably small in other insects but massively expanded in these orders. All veins in both wings are densely connected by numerous crossveins. The close relationship between phasmids and orthopterans suggested by these shared characters has also been supported by molecular analyses (Terry & Whiting, 2005), albeit with the inclusion of the webspinners, which have greatly simplified wings with a much-reduced venation. While pleiotropy might explain how wing-patterning genes remained functional overall, it is difficult to imagine how the form of the potential wings could have been maintained down to their very venation.


Worker of the army ant Eciton burchelli, with the reduced eyes visible. Photo by Alex Wild, via Ant Hill Wood.

For contrast, Alex Wild recently discussed a much better-supported case of character reversal. Army ants of the genus Eciton have functional eyes in the workers despite being descended from an eyeless ancestor. However, while other ants have eyes with well-marked facets and multiple ommatidia (lenses) like those of other insects, Eciton eyes are nowhere near as well organised. The separate ommatidia have become atrophied and fused together, so that unless examined at electron microscopic level they look like a single enlarged ommatidium. Eciton worker eyes resemble the eyes of other insects the way that a six-year-old child's drawing of a horse looks like a real horse. You can see that the idea's there, but the execution is still something of a shapeless blob. What makes this situation even more remarkable is that there can be no doubt that Eciton still possesses the genes for growing fully-formed eyes, because the winged males (which never lost their eyes in the first place) still have perfectly normal insect eyes.

While pleiotropic selection might preserve the overall position and maybe even shape of the wings, there seems little reason for it to preserve the fine detail. After all, there are countless different ways that wing veins could potentially be arranged to give similar shape and function - that's how venation can vary so much between orders in the first place. Even if loss and regain of wings in phasmids might seem the most parsimonious explanation, I just don't think that it is more convincing than the alternative suggestion that phasmids have a repeated bias towards wing loss.

Afterword: I had written all this before I found the commentary on Whiting et al. (2003) by Trueman et al. (2004), and the reply by Whiting & Whiting (2004). I'd recommend reading them.

REFERENCES

Collins, T. M., P. H. Wimberger & G. J. P. Naylor. 1994. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Systematic Biology 43 (4): 482-496.

Grimaldi, D., & M. S. Engel. 2005. Evolution of the Insects. Cambridge University Press: New York.

Terry, M. D., & M. F. Whiting. 2005. Mantophasmatodea and phylogeny of the lower neopterous insects. Cladistics 21: 240-257.

Whiting, M. F., S. Bradler & T. Maxwell. 2003. Loss and recovery of wings in stick insects. Nature 421: 264-267.

The Tomb of the Unknown Honeyeater

Some of the birds referred to in this post. Clockwise from top left - Bombycilla garrulus, the Bohemian waxwing, Bombycillidae; Chaetoptila angustipluma, a Hawaiian honeyeater; two true honeyeaters (Meliphagidae), Anthochaera carunculata (red wattlebird) and Prosthemadera novaeseelandiae (tui); and Moho nobilis, the Hawai'i 'o'o, a Hawaiian honeyeater. Painting by John Anderton.

Fleischer, R. C., H. F. James & S. L. Olson. 2008. Convergent evolution of Hawaiian and Australo-Papuan honeyeaters from distant songbird ancestors. Current Biology 18: 1-5.

GrrlScientist brought my attention yesterday to an interesting new publication on the phylogeny of the Hawaiian honeyeaters. Not, I hasten to explain, the Hawaiian honeycreepers, the Drepanidini clade of birds unique to Hawaii that has become famed for their remarkable adaptive radiation into a whole range of ecological niches, but a smaller clade of five species, Chaetoptila angustipluma and the four species of 'o'o (Moho), that is also unique to Hawaii.

The honeyeaters of the family Meliphagidae are a sizable, fairly heterogenous assemblage of songbirds (Oscines) that are found throughout the Australo-Papuan region, with outliers on various Pacific islands such as New Zealand and Samoa. Despite including a diversity of morphologies, meliphagids are well established as a family, united by features such as a brushed tongue used for taking nectar from flowers (hence, of course, the name "honeyeaters"). The five Hawaiian species share many of these features, and are fairly similar in appearance to Australasian meliphagids, so have always been regarded as meliphagids themselves. The study being discussed here found in a DNA phylogenetic analysis that this was not the case.

Conducting a molecular analysis of Hawaiian honeyeaters is a remarkable achievement in itself because, tragically, not one of the five species remains alive today. All became extinct in the last two centuries. The last surviving species was the smallest, the Kauai 'o'o (Moho braccatus), the last male of which was sighted in 1987 (just to turn the pathos up a notch, a short video of this last individual can be seen here). The Hawaiian honeyeaters therefore join an all-too-long list of birds extinct on the Hawaiian islands since human colonisation, such as the moa-nalo. In the absence of living specimens, Fleischer et al. had to extract DNA from museum specimens, but were able to do so for all five species.

Phylogenetic analysis of these samples showed that, as mentioned above, Chaetoptila and Moho were not related to the true meliphagids. As I've explained elsewhere, recent molecular analyses have consistently identified three large clades within the songbirds (as well as a smattering of smaller clades), the Meliphagoidea (including the meliphagids), Corvoidea and Passerida (including most Northern Hemisphere songbirds). The Hawaiian honeyeaters are not members of the Meliphagoidea, but instead belong to an entirely different clade, the Passerida. Within the Passerida, they belong to an assemblage that includes the Holarctic waxwings (Bombycilla), North American silky flycatchers (Ptilogonatinae) and Caribbean palmchat (Dulus dominicus). Most authors have united these birds in the family Bombycillidae, and the name was recently used in this sense by Spellman et al. (2008). While Fleischer et al. (2008) establish a new family Mohoidae for the Hawaiian honeyeaters, that clade would belong within Bombycillidae in the broad sense. Relationships of the Bombycillidae within the Passerida remain largely unresolved.

The Hawaiian honeyeaters have not been the first birds to abscond from the Meliphagidae in recent years. I have previously discussed the discovery that the New Zealand stitchbird (Notiomystis cincta) is related to the New Zealand wattlebirds, and perhaps a basal member of the Corvoidea. The South African sugarbirds of the genus Promerops, long unsettled as meliphagids, belong to the Passerida and are basal members of the Passeroidea assemblage that includes finches and sparrows (Beresford et al., 2005). The Bonin honeyeater (Apalopteron familiare) is also a member of the Passerida, and falls within the family of white-eyes, Zosteropidae (Driskell & Christidis, 2004) - which I wasn't too surprised to hear because, if you ignore the "meliphagid" brushed tongue, Apalopteron really does look like a big white-eye. Still, the Hawaiian honeyeaters are probably the most typically "meliphagid-like" birds to be recognised as non-meliphagids.

In another interesting recurring theme in oscine phylogeny, the reclassification of Hawaiian honeyeaters, while morphologically unexpected, makes a certain degree of biogeographic sense. Most colonisation of the Hawaiian islands seems to have been derived from North America rather than the western part of the Pacific, with Hawaiian honeycreepers, warblers, geese and violets, among others, all having demonstrated North American (and often northern North American) affinities. As pointed out by a commentator at GrrlScientist's post linked to above, the only Hawaiian bird that still possesses western Pacific affinities is the monarch flycatcher Chasiempis sandwichensis, whose Monarchidae affinities were supported by Filardi & Moyle (2005).

That Hawaiian honeyeaters are such a distinct lineage makes their loss all the more tragic. An extra dose of tragedy that verges on the comic surrounds the most distinct of the mohoids, Chaetoptila angustipluma. Those of my readers who have heard of it before may have noticed that I have deliberately avoided using the vernacular name given to this bird, the kioea. My reason for doing so is that there is reason to doubt whether this name properly belongs to Chaetoptila at all. "Kioea" is actually the Hawaiian name for the bristle-thighed curlew (Numenius tahitiensis), a migratory wading bird and not very much like a honeyeater at all. References to "kioea" as a seabird include the Kumulipo, the epic poem that recited the genealogy of the Hawaiian royal family:

Hanau ke Kioea ka makua,
Puka kana keiki he Kukuluae'o, lele.

The Kioea was born and became parent,
Its offspring was a Kukuluaeo [stilt, Himantopus knudseni], and flew.

--Hawaiian text from here, 1897 translation by Queen Liliuokalani.

Peale (1848) provided no common name for Chaetoptila angustipluma when he first described it (as Entomiza angustipluma - Entomyza is a meliphagid genus). Bryan & Greenway (1944) gave the name "kioea" for this species, but with a question mark, and they also used the name elsewhere for the curlew - I haven't been able to find whether this is the first recorded association between the name and Chaetoptila. Not only has Chaetoptila been cruelly forced out of existence, but it has potentially been subjected to the indignity of a name that is not its own. It truly is the unknown honeyeater.

REFERENCES

Beresford, P., F. K. Barker, P. G. Ryan & T. M. Crowe. 2005. African endemics span the tree of songbirds (Passeri): molecular systematics of several evolutionary ‘enigmas’. Proceedings of the Royal Society of London Series B – Biological Sciences 272: 849-858.

Bryan, E. H., Jr & J. C. Greenway Jr. 1944. Check-list of the birds of the Hawaiian islands. Bulletin of the Museum of Comparative Zoology 94 (2): 92-140.

Driskell, A. C., & L. Christidis. 2004. Phylogeny and evolution of the Australo-Papuan honeyeaters (Passeriformes, Meliphagidae). Molecular Phylogenetics and Evolution 31 (3): 943-960.

Filardi, C. E., & R. G. Moyle. 2005. Single origin of a pan-Pacific bird group and upstream colonization of Australasia. Nature 438 (7065): 216-219.

Peale, T. R. 1848. Mammalia and Ornithology. C. Sherman: Philadelphia.

Spellman, G. M., A. Cibois, R. G. Moyle, K. Winker & F. K. Barker. 2008. Clarifying the systematics of an enigmatic avian lineage: what is a bombycillid?. Molecular Phylogenetics and Evolution 49 (3): 1036-1040.

Flowers from Two to Five

Gunnera, the so-called giant rhubarb (sadly, not edible), one of the most surreal-looking of all plants. Photo from Achamore House.

This Monday's Taxon of the Week post deal with a clade that was formally named only recently, but which had been informally established some time earlier. The name "Gunneridae" was introduced by Cantino et al. (2007) for the flowering plant clade previously referred to as "core eudicots" in publications such as Soltis et al. (2003) and APG II (2003). As yet, the name doesn't appear to have appeared in print outside its original publication - time will tell whether or not it catches on.

The Gunneridae has been mainly supported as a clade by molecular sequence analyses, though other potential characters uniting its members are a number of gene duplications and the production of ellagic acid (offhand, it is intriguing how many molecular relationships within plants that were not predicted by straight morphological data have also been supported by biochemical data). The name "Gunneridae" refers to one of the basalmost divisions within this clade, the small order Gunnerales. The remaining members of the Gunneridae form a clade that Cantino et al. (2007) dubbed Pentapetalae, for reasons that I'll go into in a moment. The Pentapetalae include the vast majority of dicotyledonous flowering plants - from apples to apple cucumbers, from stonecrops to sage - with most falling into the three clades known as Asteridae, Rosidae and Caryophyllales.


Myrothamnus flabellifolius, the African resurrection plant. It starts off looking like this... (Photo from Farm Kyffhäuser)

...and ends up looking like this! (Photo from Flora of Zimbabwe)

The clade Gunnerales contains only two genera, Gunnera and Myrothamnus. Both are wind-pollinated plants with a mostly Southern Hemisphere distribution, but this is about where their similarities end. Myrothamnus are two species (one in sub-Saharan Africa, one in Madagascar) of small arid-living shrubs known as resurrection plants for their ability to dry out then seemingly spring back to life when the rains fall. Other types of plant around the world are also known by this name and share this ability, but Myrothamnus is unique in being the only resurrection plant with a woody stem (Moore et al., 2007). Gunnera is a genus of herbaceous plants found scattered through South America, Africa and south-east Asia, with outliers in Tasmania, New Zealand and Hawaii. Some Gunnera are very small - the New Zealand Gunnera albocarpa has leaves one or two centimetres long - but the genus is best-known for the gigantic South American species known as "giant rhubarbs", which describes their appearance exactly. Some species can have leaves over two metres in length, on two metre stalks (Wikipedia has examples of exact measurements). Gunnera is also the only genus of flowering plants to form a symbiotic association with nitrogen-fixing cyanobacteria (Bergman et al., 1992). Mucus-secreting glands on the stem near the base of the leaves become colonised by the cyanobacterium Nostoc punctiforme. When they first colonise the gland, the Nostoc grow as hormogonia - short filaments that lack differentiated heterocysts (the larger nitrogen-fixing cells). These multiply until they form a film over the opening of the gland. Cyanobacterial cells then migrate deeper into the gland (in complete contradiction to the attraction to light that these photosynthetic organisms show when free-living), where they somehow penetrate and enter the cells of the host Gunnera itself. Once inside the Gunnera cells, they multiply and differentiate, and Nostoc colonies within Gunnera actually contain a higher proportion of heterocysts than any free-living colonies.


Fossilised flower of a Cretaceous rosid, one of the main lineages of Pentapetalae. Fossil by John M. Miller.

The remaining core eudicots, as mentioned before, form the Pentapetalae. In high school, you may have learned that flowering plants are divided between monocots, with parallel leaf-veins and flower parts in multiples of three (trimerous flowers), and dicots, with netted leaf-veins and flower parts in multiples of five (pentamerous flowers). Like so many things we learnt in high school, this was partially correct and partially a load of twaddle. While monocots are indeed a coherent group, the "dicots" are not only paraphyletic with regard to monocots (though the majority of dicots still fall within the clade Eudicotyledoneae, the eudicots), but also include taxa with parallel leaf-veins (the Aristolochiaceae) and taxa which don't have pentamerous flowers. The basal state for flowering plants as a whole appears to be trimerous flowers, which are found in most flowering plants outside the eudicot clade (Soltis et al., 2003). The basal state for the eudicots is equivocal - that for the clade formed by eudicots with the exception of the order Ranunculales appears to be dimerous flowers (parts in multiples of two), but the Ranunculales include both dimerous and trimerous taxa. Pentamerous flowers appear to have arisen three times within eudicots - the Ranunculaceae (the buttercup family), the small family Sabiaceae and the Pentapetalae. As this covers the significant majority of "dicots" that most people are likely to ever come across, it explains how your teachers were able to get away with fudging things like that.

REFERENCES

APG II (Angiosperm Phylogeny Group). 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society 141: 399-436.

Bergman, B., C. Johansson & E. Söderbäck. 1992. The Nostoc-Gunnera symbiosis. New Phytologist 122 (3): 379-400.

Cantino, P. D., J. A. Doyle, S. W. Graham, W. S. Judd, R. G. Olmstead, D. E. Soltis, P. S. Soltis & M. J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56 (3): 822-846 (abridged printed version) or E1-E44 (longer electronic-only version).

Moore, J. P., G. G. Lindsey, J. M. Farrant & W. F. Brandt. 2007. An overview of the biology of the desiccation-tolerant resurrection plant Myrothamnus flabellifolia. Annals of Botany 99 (2): 211-217.

Soltis, D. E., A. E. Senters, M. J. Zanis, S. Kim, J. D. Thompson, P. S. Soltis, L. P. Ronse De Craene, P. K. Endress & J. S. Farris. 2003. Gunnerales are sister to other core eudicots: implications for the evolution of pentamery. American Journal of Botany 90: 461-470.

The newest edition of Linnaeus' Legacy has been installed at Agricultural Biodiversity Weblog. This month's keywords: creationism and sound natural history, onlie begetter, Archie or Jughead, raised from an egg, poisonous bird, Names on Nodes, confused scientists, Gigantosaurus, Kipling, pesticide resistance, medicinal species, English Pupil.

Greg Laden has kindly offered to host the next edition in January.

What's in a Name?

A special issue of Zootaxa has come out in the last week, under the title Updating the Linnaean Heritage: Names as Tools for Thinking about Animals and Plants. As the title indicates, it's a collection of papers discussing various aspects of the role(s) of nomenclature in taxonomy. Some of them are open-access via the link above, if you want to take a look, such as one by Alessandro Minelli discussing reaction to the Strickland Code of 1842, generally regarded as the first formal attempt to propose a set of regulations for taxonomic nomenclature. The Strickland Code was proposed to cover zoology, and Minelli presents a suggestion by Charles Bonaparte, vertebrate zoologist and nephew to the Emperor, that the Strickland Code or some variant thereof be extended to cover all biology, both zoology and botany. That suggestion, sadly, failed (long story short - the botanists felt that their nomenclature was in a pretty good state anyway, and while slack zoologists might need a code, the botanists were perfectly happy following the examples of Linnaeus and de Candolle), and the opportunity was lost to avoid a lot of subsequent irritation.

This post, however, will be devoted to another, more theoretically based paper by Alain Dubois - Dubois, A. 2008. Phylogenetic hypotheses, taxa and nomina in zoology. Zootaxa 1950: 51-86. (All quotes given below are taken from this paper.) Alain Dubois has published a whole series of papers on nomenclatorial theory in recent years, and while I'm guessing that he has probably given a lot more thought to the issues than I have, there were still a couple of things that didn't add up for me.

I should warn you, too, that Dubois (2008) is not an easy read. Dubois suffers from one of the most terrible afflictions to affect a theoretician - neologorrhoea, the overwhelming compulsion to coin new terminology*. The introduction of neologisms is not necessarily a bad thing - the cladistic revolution, for instance, carried a whole swag of new terminology. Some of these terms (e. g. synapomorphy, plesiomorphy) have become part of biology's everyday stock in trade. Others (e.g. adelphotaxon) - not so much. Time will tell how many of Dubois' neologisms gain currency.

*Spot the irony.

At the heart of Dubois' thesis is the superiority of the current hierarchical, onomatophore-based system (onomatophore, "name-bearer", is Dubois' replacement for the arguably more vague term type) over suggested phylogeny-based systems (most prominently the PhyloCode, though there are other such propositions).

Taxonomic paradigms have changed several times during the history of taxonomy, yet a single nomenclatural system, so-called Linnaean, has remained in force all along. It is theory-free regarding taxonomy as it relies on ostensional allocation of nomina to taxa, rather than on intensional definitions of nomina (e.g., “phylogenetic definitions”).

The supposed theory-free nature of the taxonomic codes as they currently stand is often cited as their main advantage. A creationist could follow the ICZN just as happily as anyone else. Phylogeny-based systems, for instance (or maybe, just to be really contrary, a quinarian system), may be closely tied to a particular paradigm of how organisms originate, or a specific model of the best way to interpret diversity. This is one of my personal reasons for doubt about such systems - the PhyloCode, for instance, works best as it currently stands with a branching model of evolution and speciation, and I think that it is worth asking to what extent that is really the best model to be using. However, the current hierarchical systems are not entirely theory-free. For instance, the binomial system that demands organisms be assigned to at least two taxa (genus and species) effectively demands the recognition of at least a certain proportion of paraphyletic taxa, because the common ancestor of two genera must itself be assigned to a genus. Totally ignoring the question of the virtues or otherwise of recognising paraphyletic taxa, I do feel the question needs to be asked whether it is even possible to develop a nomenclatorial system that is completely theory-free. And if not, then the question becomes what implicit theories we can best live with.

Whereas taxa can be cladistically defined by apognoses [apomorphy-based definitions] or cladognoses [tree-based definitions], nomina should remain attached to taxa through onomatophores, combined in some cases with a Principle of Coordination. Under such a system, the allocation of nomina to taxa is automatic, unambiguous and universal, and nomenclature does not infringe upon taxonomic freedom.

And this, I think, is where Dubois is just plain wrong. The allocation of names to taxa under the current system is far from "automatic, unambiguous and universal", as covered here in an earlier post. While designating Homo sapiens as the type of the family Hominidae automatically means that the one is always included in the other, this completely ignores the point that there is no governance on how far that "family" spreads. Hominidae might include H. sapiens only, it may include the bipedal clade only, it might include all apes, it might include all primates if you were feeling perverse enough. One might argue that this is what is meant by "taxonomic freedom" (though I don't think that this is necessarily what Dubois means), but if so, then is "taxonomic freedom" really worth it? This issue is, in my opinion, the major problem with the current systems. I don't actually have too great an issue with different names applying to the same taxon. What does cause no end of hassle is the same name applying to different taxa. Back to this point later.

In conclusion, for the time being, there exists no method for a general standardization of the “meaning” of ranks over the whole of zoology and palaeontology. The “meaning” of the rank family or genus is by no way equivalent in flatworms, beetles and birds. Therefore, any comparison between faunas or taxonomies using the ranks of taxa as a criterion (e.g., quantitative comparisons based on numbers of taxa at some ranks) is unwarranted and misleading (Minelli 2000). This statement was one of the main reasons why several recent authors rejected the use of ranks in taxonomy. But is this reason valid? It would be so only if nomenclatural ranks were viewed as identical with taxonomic categories, an opinion that is shared by many but that is questionable. Dubois (2005c, 2007a) proposed to recognize a basic distinction between these two concepts, stating that one refers to taxonomy and the other one to nomenclature.

The criteria of equivalence between taxa briefly reviewed above are of two kinds: biological and chronological. Biological criteria are all of limited use for equivalence, as they can be used only at low taxonomic levels (species and genus), and are not relevant in various situations. Chronological criteria are potentially general but face three problems (missing data, applicability only for synchronic taxa and taxonomic tradition) that preclude their implementation over the whole of zoology for the time being. This is true, but, as discussed below, the use of such criteria in some situations can however be informative as it allows to obtain useful information regarding the patterns of evolution. Sets of taxa defined by such criteria can be designated as taxonomic categories. Taxonomic categories are categories of taxa that share some common features and are equivalent by some taxonomic criterion. They do not provide information on cladogenetic relationships, but this information can be provided by nomenclatural ranks. On the other hand, nomenclatural ranks are nomenclatural tools which only provide information on the detailed hierarchical structure of a taxonomic hierarchy, but no information on the evolutionary peculiarities of the taxa in this hierarchy.

The first point here is a basic one that I have no quarrel with - ranks are not comparable between non-hierarchically related taxa. A "family" of birds is not comparable to a "family" of plants. This has lead to the suggestion that we should abandon the concept of ranks because too many people have an almost unconscious urge to make exactly that mistake, as shown, for instance, by widely-repeated statements such as "Rodentia is the largest order of mammals". However, Dubois maintains that, despite this, ranks remain useful because of what they can tell us about the relationships between hierarchically related taxa. If I know that Homo sapiens is a member of order Primates, family Hominidae and subfamily Homininae, I automatically know that Homininae is a subset of Hominidae, which is in turn a subset of Primates. The problem is that in order to be able to make that judgement, I have to know that those taxa are hierarchically related in the first place - in which case, I probably already know that Hominidae is a subset of Primates. The only case where this might be useful is if I found one reference that gave one higher taxon (family Hominidae, for instance) and another reference that gave another (subfamily Homininae). I would then be informed that Homininae is a subset of Hominidae, right? Wrong. Because then I come against the issue cited above, that these concepts lack definition. Homininae is always a subset of Hominidae, but how can I assume that the Hominidae of one author is the same as the Hominidae of another author? And if one author uses a broader concept for Hominidae, he might also use a broader concept for Homininae. One author's Hominidae might even be a subset of another author's Homininae. Overall, I think the hierarchical information potentially available from ranks is insignificant compared to the comparative disinformation encouraged by them.

This taxonomic hierarchical representation of phylogeny can be expressed nomenclaturally, and this is the role of ranks. Although ranks were not used for this purpose in the early days of taxonomy, it turned out that they can play this role very well. However, to use the nomenclatural hierarchy as a reflection of the structure of a cladogram or a phylogenetic tree requires a few assumptions. It seems that misunderstanding these assumptions played a role in the recent rejection of ranks by some taxonomists.

The first important assumption is that sister taxa must always be referred to the same nomenclatural rank (Raikow 1985; Sibley & Ahlquist 1990): they are therefore parordinate (Dubois 2006b: 827). Second, any taxon is subordinate to a single upper taxon, which must be referred to the just upper rank. It may be superordinate to two or more taxa of just lower rank. In such a system, the relations between all taxa that are connected by superordination, parordination or subordination are relations of coordination. In the absence of such relations between them, two taxa may be described as being in a relation of alienordination (from the Latin alienus, “foreign”, and ordo, “order”). Thus, in the recent AMPHIBIA, according to the cladistic relationships currently agreed upon by most authors (e.g., Frost et al. 2006), and according to the higher nomenclature of Dubois (2004a, 2005d), the taxon BATRACHIA is the sister-taxon of the GYMNOPHIONA: they are parordinate taxa that must be given the same rank, in this case that of superorder. Both are subordinate to the subclass NEOBATRACHI, and the superorder BATRACHIA is superordinate to the orders ANURA and URODELA. The latter are alienordinate to any other taxon that is not directly related to them by coordination, e.g., the GYMNOPHIONA. [Note that Dubois indicates suprafamilial taxa by printing them in capitals]

To his credit, Dubois is attempting to suggest a system that potentially answers my repeated grievance above - the question of what is a family. The hierarchy, according to Dubois, automatically indicates what taxon goes at what rank. If a family is united with another family in a higher taxon, and the next rank up from family is a superfamily, then that higher taxon has to be a superfamily. You can't skip a few ranks and call it a suborder.

The first complaint that might be made is the supposed shortage of named ranks compared to the total number of levels required. Dubois replies that by searching through the literature, he has collated a hierarchy of some 209 ranks. Aren't you glad we got that one sorted.

Also, the sister taxon of a family has to be another family. Towards the end of the paper, Dubois weighs in at length against what he calls "pseudoranked" classifications. Such classifications are those in which sister taxa are not placed at the same rank. According to Dubois, such "rankings" are meaningless because they are hierarchically uninformative. Hmm, he might have a point there. As an example of a pseudoranked classification, he takes part of the Amphibian Tree of Life of Frost et al. (2006 - poor Frost et al. has become a bit of a whipping-boy in these sorts of situations):

Taxon HYLOIDES 2006
      Taxon NOTOGEANURA 2006
            Taxon AUSTRALOBATRACHIA 2006
                  Familia BATRACHOPHRYNIDAE 1875
                        3 genera
                  Superfamilia MYOBATRACHOIDEA 1850
                        Familia LIMNODYNASTIDAE 1971
                              8 genera
                        Familia MYOBATRACHIDAE 1850
                              13 genera
            Taxon NOBLEOBATRACHIA 2006
                  Familia HEMIPHRACTIDAE 1862
                        1 genus
                  Taxon MERIDIANURA 2006
                        Familia BRACHYCEPHALIDAE 1858
                              15 genera
                        Taxon CLADOPHRYNIA 2006
                              Familia CRYPTOBRANCHIDAE 2006
                                    2 genera
                              Taxon TINCTANURA 2006
                                    Familia AMPHIGNATHODONTIDAE 1882
                                          2 genera
                                    Taxon ATHESPHATANURA 2006
                                          Familia HYLIDAE 1815
                                                Subfamilia HYLINAE 1815
                                                      38 genera
                                                Subfamilia PELODRYADINAE 1858
                                                      1 genus
                                                Subfamilia PHYLLOMEDUSINAE 1858
                                                      7 genera
                                          Taxon LEPTODACTYLIFORMES 2006
                                                Taxon CHTHONOBATRACHIA 2006
                                                      Familia CERATOPHRYIDAE 1838
                                                            Subfamilia CERATOPHRYINAE 1838
                                                                  6 genera
                                                            Subfamilia TELMATOBIINAE 1843
                                                                  1 genus
                                                      Taxon HESTICOBATRACHIA 2006
                                                            Taxon AGASTOROPHRYNIA 2006
                                                                  Familia BUFONIDAE 1825
                                                                        48 genera
                                                                  Superfamilia DENDROBATOIDEA 1850
                                                                        Familia DENDROBATIDAE 1850
                                                                              11 genera
                                                                        Familia THOROPIDAE 2006
                                                                              1 genus
                                                            Familia CYCLORAMPHIDAE 1850
                                                                  Subfamilia CYCLORAMPHINAE 1850
                                                                        11 genera
                                                                  Subfamilia HYLODINAE 1858
                                                                        3 genera
                                                Taxon DIPHYABATRACHIA 2006
                                                      Familia CENTROLENIDAE 1951
                                                            Subfamilia ALLOPHRYNINAE 1978
                                                                  1 genus
                                                            Subfamilia CENTROLENINAE 1951
                                                                  3 genera
                                                      Familia LEPTODACTYLIDAE 1838
                                                            11 genera
      Familia SOOGLOSSIDAE 1931
            2 genera

Dubois then converts this into a "properly" ranked classification using his system:

Anofamilia HYLAIDAI 1815
      Hyperfamilia HYLAIDIA 1815
            Epifamilia MYOBATRACHOIDIA 1850
                  Superfamilia BATRACHOPHRYNOIDEA 1875
                        Familia BATRACHOPHRYNIDAE 1875
                              3 genera
                  Superfamilia MYOBATRACHOIDEA 1850
                        Familia LIMNODYNASTIDAE 1971
                              8 genera
                        Familia MYOBATRACHIDAE 1850
                              13 genera
      Epifamilia HYLOIDIA 1815
                  Superfamilia HEMIPHRACTOIDEA 1862
                        Familia HEMIPHRACTIDAE 1862
                              1 genus
                  Superfamilia HYLOIDIA 1815
                        Familia BRACHYCEPHALIDAE 1858
                              15 genera
                        Familia HYLIDAE 1815
                              Subfamilia CRYPTOBRANCHINAE 2006
                                    2 genera
                              Subfamilia HYLINAE 1815
                                    Infrafamilia AMPHIGNATHODONTINEI 1882
                                          2 genera
                                    Infrafamilia HYLINEI 1815
                                          Tribus HYLINI 1815
                                                Subtribus HYLINA 1815
                                                      38 genera
                                                Subtribus PELODRYADINA 1858
                                                      1 genus
                                                Subtribus PHYLLOMEDUSINA 1858
                                                      7 genera
                                          Tribus BUFONINI 1825
                                                Subtribus BUFONINA 1825
                                                      Infratribus CERATOPHRYITA 1838
                                                            Clanus CERATOPHRYITOI 1838
                                                                  6 genera
                                                            Clanus TELMATOBIITOI 1843
                                                                  1 genus
                                                      Infratribus BUFONITA 1825
                                                            Clanus BUFONITOI 1825
                                                                  Subclanus BUFONILOI 1825
                                                                        48 genera
                                                                  Subclanus DENDROBATILOI 1850
                                                                        Infraclanus DENDROBATISOI 1850
                                                                              11 genera
                                                                        Infraclanus THOROPISOI 2006
                                                                              1 genus
                                                            Clanus CYCLORAMPHITOI 1850
                                                                  Subclanus CYCLORAMPHILOI 1850
                                                                        11 genera
                                                                  Subclanus HYLODILOI 1858
                                                                        3 genera
                                                Subtribus LEPTODACTYLINA 1838
                                                      Infratribus CENTROLENITA 1951
                                                            Clanus ALLOPHRYNITOI 1978
                                                                  1 genus
                                                            Clanus CENTROLENITOI 1951
                                                                  3 genera
                                                      Infratribus LEPTODACTYLITA 1838
                                                            11 genera
      Hyperfamilia SOOGLOSSAIDIA 1931
            Familia SOOGLOSSIDAE 1931
                  2 genera

Not only would this revised classification result in taxa very different from those used in the past - different names for many, and massively changed coverage for a number of names - it would also be highly unstable. For a start, imagine if a new taxon is discovered that is the sister taxon to Hylini exclusive of Bufonini in the classification above. That taxon would have to get its own tribe, and those two tribes together would have to become the infrafamily Hylinei, effectively moving Bufonini out of Hylinei. What was Hylinae would have to become Hylidae, and so on and so forth. What is more, for every taxon that has to move up a step, its sister taxon has to move up a step, so Bufonini becomes Bufoninei, Amphignathodontinei becomes Amphignathodontinae, and so on. And it should also be obvious that even if no new taxa are discovered, such a system is dependent on a stable phylogeny or other concept of relationship.

The Principle of Coordination is a major rule of the Code [i.e. the ICZN], which states that, within a nominal-series, among all the parordinate taxa that are subordinate to the same superordinate taxon, one, called in the Code the “nominotypical taxon”, must bear the same nomen (with the same nomenclatural author and date) as this superordinate taxon...

The existence of the Principle of Coordination in the Code results in this nomenclatural system being partly polysemic. In grammar and linguistics, monosemy applies to a situation where one word has only one meaning, whereas in polysemy one word has several meanings...

A few final words of caution must be added here regarding the meaning of the term eponymy. The situation it describes can be, and has been, confused with two other situations regarding biological nomenclature. Eponymy is the situation where the same nomen (same author, date and onomatophore) is used in the same ergotaxonomy [i. e. classification] as the valid nomen for several distinct, coordinate taxa. In contrast, homonymy is the situation where different nomina (generally with different authors, dates and onomatophores, with a few exceptions, when the same author used the same nomen for naming two different nominal taxa) are nomenclaturally available — which results in one of them, usually the junior one, being rejected as invalid. Finally, a third situation results from the fact that zoological nomina under the Code are not defined by closed intension or extension, but attached to taxa by ostension (Stuessy 2000, 2001; Keller et al. 2003). This results in the same nomen being liable to designate quite different taxa in different ergotaxonomies, the only requirement being that these taxa must include the onomatophore of this nomen. The reasons why this is highly preferable to a system of closed intension or extension were explained in detail elsewhere (Dubois 2005a, 2006c, 2007a): if a nomen corresponded to a strict, unchangeable definition and/or content of the taxon, a new nomen would have to be coined every time a subordinate taxon or even a specimen is added to the taxon or removed from it, so that there would be no continuity in the use of nomina and no simple way to understand the taxonomic history of a group, as is now possible through “synonymies” or more exactly logonymies (see Dubois 2000b). The situation here described, where the same nomen applies to different taxa, but in different ergotaxonomies, is neither homonymy nor eponymy, and its clear distinction from the latter two requires a special designation. For this situation, I propose the term astatonymy (from the Greek astatos, “unstable”, and onoma, “name”). This situation is extremely common in zoology, by far more than the situation where the nomen has always designated exactly the same taxon since its creation, which may be called menonymy (from the Greek meno, “I stay, I am stable”, and onoma, “name”).

Dubois doesn't regard the potential changes in his taxonomic system above as "real" changes, because there is no change in the type taxon. The different names at different ranks are, technically speaking, the same name with different terminations. I'm sorry, but while such a system may work well for establishing priority, it doesn't work as a practical guide. To the non-taxonomist, Homininae and Hominidae are different names, and when they are asked to think of them as identical, confusion is usually the result (trust me, I know). It's bad enough when Hominidae is always equivalent to Homininae - when it's only sometimes equivalent, things stop being just confusing and move on to hopeless. And while one might argue that taxonomists are the best-placed to judge the accuracy of taxonomies, one should never forget that, as often as not, it will be non-taxonomists who are the end-users.

The last part of this is Dubois' reply to my complaint about a "family" being a different thing to different authors, which is basically to say, "define different". If a taxon is effectively defined as the list of organisms (whether real or theoretical) assigned to that taxon, then even the discovery of a new organism could render it a "different taxon". You can smell the straw in this one. Nobody is going to claim that Vertebrata is a "different taxon" because of the description of a new species of rodent. What matters, essentially, are changes in the definition of the taxon - how we decide whether a given organism belongs to a given taxon or not. The current codes supply no working rules on definition.

Definitions of taxa are a matter of taxonomy, not of nomenclature. Different taxonomic “schools” use different kinds of definitions of taxa. Nowadays, no taxonomic school claims to be “Linnaean”, i.e., to use “Linnaean” definitions of taxa. There exist no such things as “ICZN-taxa” (Joyce et al. 2004) because the Code does not provide any guideline for defining taxa, being theory-free regarding taxonomy. In current taxonomy, only two kinds of definitions of taxa are widely used: phenetic definitions or diagnoses; and cladistic or “phylogenetic” definitions, or cladognoses (Dubois 2007a: 43).

Ultimately, I think this sums up the problem I'm having with Dubois' thesis. Dubois claims that the current system is preferable by virtue of being theory-free; my reaction is to ask whether a theory-free system is so great in the first place. Anarchy sounds like a wonderful system - we would all like to be able to live our lives exactly how we choose without anyone else's say-so. But it only works if one person's ideal doesn't clash with another person's ideal. And in an anarchy, no-one wants to be the one to unblock the toilet.

Dubois himself states near the beginning of the paper that "nomenclature is not a science but a technique, a tool at the service of taxonomy". And as I've said so many times before, the use of that tool is communication. In attempting to expunge theory from nomenclature, Dubois ultimately ends up eliminating the usefulness of that nomenclature in communication. It's like being presented with a specially-designed asparagus cooker, and then told that you can't have any asparagus. All you're left with is a complicated device that no-one can agree on how to use it.