Field of Science

When is a Cephalopod Like a Snake?

The tarphycerid Lituites lituus. Photo from here.

When its a snakestone.

Just a quick post on tarphycerids today - haven't much time. The Tarphycerida were the earliest group of cephalopods to develop a coiled shell, back in the lower Ordovician. Sweet et al. (1964) regarded tarphycerids as sharing a common ancestor in the lower Ordovician Bassleroceratidae with the Oncocerida, the lineage ancestral to modern nautilids. Though tarphycerids are therefore more closely related to nautilids than to coleoids (and therefore, unlike the other Palaeozoic cephalopods I've covered so far, have a case to actually be regarded as nautiloids), the fact that the earliest oncocerids were not coiled (Sweet, 1964a) indicates that the coiled form was independently derived in tarphycerids from nautilids. A few tarphycerid lineages later became more loosely coiled, or uncoiled.

Campbelloceras, a more typical tarphycerid. Note the significant size of the body chamber compared to earlier chambers. From

Most tarphycerids were more or less evolute. Closely coiled cephalopod shells can be described as evolute, involute or convolute, though these aren't distinct forms so much as lines on a spectrum. In involute forms, the successive whorls of the shell overlap and cover the earlier whorls to some degree. This is taken to the extreme in convolute forms such as modern Nautilus in which the later whorls entirely conceal the older whorls. In evolute forms, however, the successive whorls lie alongside each other and remain clearly visible. There seems to have been a repeated tendency for evolute forms to be replaced by involute forms - I'm guessing because the involute arrangement was more sturdy and robust. Evolute shells are described as 'serpenticone', which refers to an old English belief that such shells were the petrified remains of coiled snakes. Indeed, it was not uncommon for coiled cephalopod fossils to be sold as 'snakestones' (supposedly protecting against snakebite) with carved snake heads attached to them.

A specimen of the ammonite Dactylioceras commune, modified into a snakestone. Photo from here.

One tarphycerid genus, Lituites, was one of the earliest fossil cephalopods recognised, and though officially published by Bertrand in 1763, Bertrand was merely validating a name that pre-dated Linnaeus (Furnish & Glenister, 1964). Lituitidae started life as coiled shells, but soon changed their growth pattern and grew in a straight line, with the straight segment of shell far larger than the coiled section - lituitids might be up to a foot in length, with the coiled section less than an inch across. While most tarphycerid families were widespread (albeit uncommon), lituitids are only known from northern Europe (and mostly from erratic boulders, which are an absolute bugger to place stratigraphically).

Many tarphycerids showed changes in growth habit through their life. The siphuncle often changed in position - all tarphycerids had ventral siphuncles when young, but for many species they became dorsal with age. Juvenile tarphycerids had standard round apertures, but in many species the aperture changed significantly in form at maturity, becoming contracted by ingrowing lobes of the shell with deep hyponomic and ocular sinuses. Whether and how this change in aperture form was reflected by any change in soft-body morphology can, of course, only be speculated upon. It is worth noting, as well, that the mature body chamber was often spectacularly long - in the family Ophidioceratidae, it may occupy more than an entire whorl of the shell. Again, in the absence of soft-body fossils there is no way of knowing whether the adult body was similarly long, or whether the animal was shorter and able to retreat deep into its shell.

Tarphycerids survived into the mid-Devonian - Sweet (1964b) separated the lineage including all later forms as the order Barrandeocerida, but all more recent authors seem to include the barrandeocerids in the Tarphycerida* (e.g. Turek, 2008). A number of barranderocerids became non-planar coilers (torticones), adopting a more gastropod-like form. Because non-planar coils would not have had such a centred buoyancy distribution compared to planar forms, these species would have probably been benthic in their lifestyle. The tarphycerids disappeared at about the same time as the ecologically similar nautilids and ammonoids were diversifying.

*The concept of paraphyletic taxa in a phylogeny-based classification is a bit like the concept of God in a secular society. People may not actually have anything against the idea, they may argue vociferously for the retention of the idea, but as time goes by they just refer to the idea less and less, and eventually the realisation dawns that there's just no real practical point in hanging on to it.


Furnish, W. M., & B. F. Glenister. 1964. Nautiloidea - Tarphycerida. In Treatise on Invertebrate Paleontology pt K. Mollusca 3 (R. C. Moore, ed.) pp. K343-K368. The Geological Society of America and The University of Kansas Press.

Sweet, W. C. 1964a. Nautiloidea - Oncocerida. In Treatise on Invertebrate Paleontology pt K. Mollusca 3 (R. C. Moore, ed.) pp. K277-K319. The Geological Society of America and The University of Kansas Press.

Sweet, W. C. 1964b. Nautiloidea - Barrandeocerida. In Treatise on Invertebrate Paleontology pt K. Mollusca 3 (R. C. Moore, ed.) pp. K368-K382. The Geological Society of America and The University of Kansas Press.

Sweet, W. C., C. Teichert & B. Kummel. 1964. Phylogeny and evolution. In Treatise on Invertebrate Paleontology pt K. Mollusca 3 (R. C. Moore, ed.) pp. K106-K114. The Geological Society of America and The University of Kansas Press.

Turek, V. 2008. Boionautilus gen. nov. from the Silurian of Europe and North Africa (Nautiloidea, Tarphycerida). Bulletin of Geosciences 83 (2): 141-152.

Open Query – What are Cephalopod Shells For?

Cross-sectioned reconstruction of the Late Cambrian cephalopod Plectronoceras, from

I'm continuing with the "nautiloid" theme here (previous posts on Palaeozoic cephalopods can be found here and here). The primary reason why Palaeozoic cephalopods have been occupying my mind lately is that I am currently working my way through the Treatise of Invertebrate Paleontology volume on "nautiloids" (as explained in an earlier post, the lumping of all non-ammonoid, non-coleoid cephalopods under the name of "nautiloid" is a really unfortunate example of paraphyletic lumping, which is why I'm insisting on the quotation marks). For those unfamiliar with them, the Treatise of Invertebrate Paleontology (or simply the Treatise to its friends) is a series of volumes cataloguing the known genera of fossil invertebrates, and each volume also includes a series of introductory essays describing the anatomy, palaeoecology, etc. of the group it covers. I've commented before that there is something incredibly purgatorial about a Treatise volume. It's a long, painful, torturous slog that hammers you both mentally and physically*, but when you finally come out the other end there can be no doubt that you've done something really worth achieving.

*Anyone who doubts that a book is able to challenge you physically has not had to carry a bag holding the entire 1000 pages plus in three volumes of the Treatise section on crinoids, nor been assualted by a falling copy of the 1100 pages of Roewer's Die Weberknechte der Erde.

The question that is currently residing in my mind also, in a roundabout sort of way, relates to the recent publication of the fossil avialian Epidexipteryx ('Les'). Typically for a Nature article, the revolutionary nature of that fossil has been more than a little exaggerated, but it has publicised the growing consensus among palaeontologists that feathers were not originally used for flight when they first evolved. It is more likely that they were originally used for insulation, and only later became used for other functions such as display and flight*. Gould & Vrba (1982) actually coined a term for this phenomenon, 'exaptation', which was meant to refer to cases where a feature that originally evolved for one function was co-opted for use in another function, as opposed to 'adaptation', when a feature originally evolved directly for its current function. The term 'exaptation' in itself never really caught on, because almost all 'adaptations' are in some way 'exaptations'. However, the verb form 'exapted' remains useful when describing examples of such a process.

*I'm going to speculate a little and suggest that the use of feathers for display may have even been a necessary prerequisite for their use for flight, because the planar surface required for flight may have been less likely to be selected for insulation than for maintaining a stereotyped form for display. This may be why flightless maniraptorans such as Caudipteryx possessed planar tail and arm fans.

Cross-section of the Late Cambrian cephalopod Yanheceras, showing the closely-spaced septa in this 12 mm shell. Image from again.

What is the connection between cephalopods and the origin of feathers? As note before, fossil cephalopods can be distinguished from all other molluscs by their unique shell structure, with the shell divided into a series of internal chambers. In most shelled cephalopods, the chambers would have been/are mostly hollow and filled with gas whose volume can be adjusted to control shell buoyancy. But how and why did this unique structure evolve in the first place? Contrary to first impressions, the chambers were probably not used as floats when they first appeared. The really early cephalopods, such as plectronoceratids and ellesmeroceratids, were small subconical shells, generally only a few centimetres in length. Despite their small size, their shells were divided into relatively large numbers of chambers, with the dividing septa packed close to each other. Even if the chambers were filled with gas (which they may not have been - it is currently unknown just when in cephalopod evolution the chambers became gas-filled), it is unlikely that the volume of the chambers would have been enough to lift the weight of the shell. Plectronoceratids, etc., were almost certainly benthic (Furnish & Glenister, 1964). Because these early forms are mostly outside the cephalopod crown group, there is currently no way of knowing whether they shared any of the soft-body features associated with modern cephalopods, such as tentacles and the siphon, or whether they still had a more primitive, superficially snail-like (though untorted) morphology.

Holland (1987), if I understand correctly, suggests that the septate shell, either by increasing relative buoyancy (even if it did not make the animal actually buoyant) or by changing the distribution of the shell's weight, may have made cephalopod locomotion more energy-efficient, allowing greater mobility. Does this seem like a likely explanation? Can any of you think of an alternative? And how would you suggest we test any likely explanations?


Furnish, W. M., & B. F. Glenister. 1964. Paleoecology. In Treatise on Invertebrate Paleontology pt K. Mollusca 3 (R. C. Moore, ed.) pp. K114-K124. The Geological Society of America and The University of Kansas Press.

Gould, S. J., & E. S. Vrba. 1982. Exaptation; a missing term in the science of form. Paleobiology 8 (1): 4-15.

Holland, C. H. 1987. The nautiloid cephalopods: a strange success. Journal of the Geological Society of London 144 (1): 1-15.

Moore, R. C. (ed.) 1964. Treatise on Invertebrate Paleontology pt K. Mollusca 3. The Geological Society of America and The University of Kansas Press.

Getting Crabs

The purple shore crab Leptograpsus variegatus of the southern subtropical Indo-Pacific ocean. Photo by Benjamint444.

When I was but an ickle lad, and my family would camp over Christmas at the beach by the estuary beneath the house of my great-grandparents, I would spend many hours turning over rocks and catching the crabs that I found underneath them. The most common variety I would find was the tiny grey-brown mud crab (Helice crassa), which could be handled easily, but if I managed to turn over one of the really big rocks then I would be able to find the larger purple shore crabs (Leptograpsus variegatus), which required a more careful approach lest they inflict great pain. One thing I didn't know at the time about either animal, however, was that they were both members of the superfamily Grapsoidea.

Grapsoidea is a grouping of crabs including at least seven families. The classification of Grapsoidea is currently undergoing something of a revision, and has shifted about a little in recent years. While most grapsoids were once included in the single family Grapsidae, the recognition of the latter as paraphyletic to the Gecarcinidae has lead to the elevation of the various prior subfamilies of Grapsidae to separate families. The family Glyptograpsidae was only established in 2002 (Schubart et al., 2002), while the genus Xenograpsus was moved into its own family within the past year (Ng et al., 2007). Other families in the group are Sesarmidae, Varunidae and Plagusiidae. The majority of grapsoids are found on the shoreline, but some (such as the Chinese mitten crab Eriocheir sinensis) move into fresh water. At least one genus, Planes (Grapsidae), is pelagic, while Xenograpsus has been found to depths of 270 m (McLay, 2007). Xenograpsus is found in association with hydrothermal vents, and populations of X. testudinatus living on sulphur vents near Taiwan make their living by feeding on the rain of dead zooplankton killed by toxic discharges from the vents (Ng et al., 2007).

Gecarcoidea natalis, Christmas Island red crab migration. Photo from here.

Some members of the Gecarcinidae live their adult lives terrestrially as adults on tropical islands. Nevertheless, all grapsoids (as far as I can tell) retain the ancestral state of marine planktonic larvae, so all terrestrial gecarcinids must return to the coast to spawn. The Christmas Island red crab, Gecarcoidea natalis has become renowned for the vast numbers that can be seen in its mass migrations, as the entire island's population of crabs (more than 40 million when estimated in 1995 - Adamczewska & Morris, 2001) moves down to the coast over the course of a week or so. Tragically, recent years have seen a population explosion on Christmas Island of the introduced yellow crazy ant* (Anoplolepis gracilipes), which was estimated to have killed off some 15 million-plus crabs by 2003 (O'Dowd et al., 2003), and has essentially eliminated crab populations wherever it has established colonies. Foraging crabs are attacked in large numbers by crazy ants defending their nests, and poisoned with large amounts of formic acid. Crazy ants will also occupy crab burrows, removing their former inhabitants with extreme prejudice. Not only are resident crabs killed, but crabs migrating from elsewhere have been destroyed as they crossed crazy ant-infested locations on their way to the coast. Where red crabs have been eliminated, the forest vegetation structure has begun to change significantly, as seedlings that would have once been grazed by crabs are able to establish a dense undergrowth.

*So called because of the seemingly random way in which they wander about when foraging.

Xenograpsus testudinatus at the base of a sulphur vent. Photo from here.

The Grapsoidea are closely related to another shore-crab family, the Ocypodoidea, and apparently species included in these two superfamilies were once united (back in the 1800s) under the taxon name Catometopa (Schubart et al., 2006), a name that I think deserves resurrection (just try saying it a couple of times - "Catometopa!"). While it seems to be universally accepted that these two superfamilies form a clade, the molecular phylogenetic analysis of Schubart et al. (2006) indicated that each of the "superfamilies" was polyphyletic within this clade, and recommended that they not be recognised as distinct. So far, I haven't been able to find what are the characters that are supposed to separate the two groups. Davie & Ng (2007) stated that morphological data maintained the monophyly of Grapsoidea, but omitted to cite any details in support of this statement.


Adamczewska, A. M., & S. Morris. 2001. Ecology and behavior of Gecarcoidea natalis, the Christmas Island red crab, during the annual breeding migration. Biological Bulletin 200: 305-320.

Davie, P. J. F., & N. K. Ng. 2007. Two new subfamilies of Varunidae (Crustacea: Brachyura), with description of two new genera. Raffles Bulletin of Zoology Supplement 16: 257-272.

McLay, C. 2007. New crabs from hydrothermal vents of the Kermadec Ridge submarine volcanoes, New Zealand: Gandalfus gen. nov. (Bythograeidae) and Xenograpsus (Varunidae) (Decapoda: Brachyura). Zootaxa 1524: 1-22.

Ng, N. K., P. J. F. Davie, C. D. Schubart & P. K. L. Ng. 2007. Xenograpsidae, a new family of grapsoid crabs (Crustacea: Brachyura) associated with shallow water hydrothermal vents. Raffles Bulletin of Zoology Supplement 16: 233-256.

O'Dowd, D. J., P. T. Green & P. S. Lake. 2003. Invasional 'meltdown' on an oceanic island. Ecology Letters 6 (9): 812-817.

Schubart, C. D., S. Cannicci, M. Vannini & S. Fratini. 2006. Molecular phylogeny of grapsoid crabs (Decapoda, Brachyura) and allies based on two mitochondrial genes and a proposal for refraining from current superfamily classification. Journal of Zoological Systematics and Evolutionary Research 44 (3): 193-199.

Schubart, C. D., J. A. Cuesta & D. L. Felder. 2002. Glyptograpsidae, a new brachyuran family from Central America: larval and adult morphology, and a molecular phylogeny of the Grapsoidea. Journal of Crustacean Biology 22(1): 28-44.

The Floating Egg

Reconstruction of a mature ascocerid with the positions of the chambers drawn as visible, from Holland (1999).

Have you ever come across an example of something that looks like an incredibly good idea, but for some unknown reason it just never catches on? In the oceans of the Silurian, the Ascocerida must have seemed to be the ultimate cephalopod. Furnish & Glenister (1964b) described the ascocerids as "almost perfectly adapted for an active nektonic [swimming] mode of life", which, in the normally dry and dusty context of a Treatise on Invertebrate Paleontology volume, comes across as high praise indeed. Despite this, ascocerids never attained a high degree of diversity or wide distribution, and by the end of the Silurian they had disappeared forever.

In some ways, the Ordovician and Silurian were the high points of cephalopod diversity. While the total number of cephalopod species may not have been as high as in later periods, this was more than made up for by the diversity of body forms. Cephalopod shells (internally shelled or shell-less cephalopods were not to appear until much later) ran the gamut from coiled forms similar to later nautilids and ammonoids (also both not yet on the scene) through to completely straight orthocones and everything in between. In older classifications, this diversity is lumped under the heading of "nautiloids", a particularly unfortunate imposition of obscurity that hides just how different the early "nautiloids" were from the modern Nautilus.

One way in which Palaeozoic cephalopods probably did resemble modern taxa is that the majority of cephalopods have probably all been active predators. In actively-swimming modern cephalopods, the main means of propulsion is through the expulsion of water through the hyponome, a muscular tube close to the mouth and tentacles, which shoots the animal through the water. For shelled cephalopods, jet propulsion adds a particular challenge, as the shell must be buoyant to allow the animal to swim freely, and finely balanced to allow the animal to move horizontally. To achieve and control bouyancy, the cephalopod shell is divided into a series of hollow chambers, with the bulk of the animal occupying the anterior body chamber and only a long cord-like extension, the siphuncle, extending into the posterior chambers. The only two cephalopod lineages with external shells to survive into the Jurassic, ammonoids and nautilids, had both independently developed a tightly-coiled form as the most effective way to maintain balance. Straighter-shelled forms appear to have developed complex arrangements of valves, diaphragms and mineral deposits to keep the shell effectively counter-balanced.

Ascocerids, on the other hand, took a different approach. Ascocerids were small for cephalopods - the largest known examples were about fifteen centimetres in length, but some species reached maturity at less than two centimetres. Their shells were lightweight marvels - even the largest examples rarely had shells more than one millimetre thick, while the paper-thin septa dividing chambers within the shell were generally around 0.1 millimetre thick. Ascocerids started their life as fairly ordinary cyrtocones - that is, rather than being perfectly straight their shells were curved like a crescent, but not so curved as to be coiled - with fairly ordinary evenly-spaced concave septa. As an ascocerid reached maturity, though, the mode of growth changed significantly. The shell become inflated and bulbous. The septae became tightly-spaced posteriorly, and sigmoid and extended forward dorsally, so that the gas chambers contained by the septa lay above rather than behind the body chamber. The posterior juvenile part of the shell was then shed, leaving the flask-shaped mature shell only. It is quite likely that there was a concurrent change in lifestyle from more benthic juvenile to fully nektic adult. With their lightweight construction and well-placed dorsal chambers, ascocerids would have been among the most mobile of Palaeozoic cephalopods, probably rivalling modern-day cuttlefish.

Reconstruction of various stages in the life-cycle of the ascocerid Billingsites noquettensis from juvenile cyrtocones (a) to ovoid adult (g), from Kesling (1961).

It might be thought that such marvels of construction would be well-placed to take over the world, but ascocerid fossils are spectacularly rare. Though specimens have been found in a number of localities in Europe and North America, they have generally only been found in very small numbers, and only in localities that have been intensely collected. Holland (1999) noted that he had seen many thousands of cephalopods from the Silurian of Britain, but only eight ascocerids. What is more, most of those specimens that are known from these localities are in very poor condition. The only two localities from which ascocerids have been found in any sort of numbers are in Gotland in Sweden and Bohemia. Gotland is also the only locality from which juvenile ascocerids have been recovered. Modern chambered Nautilus shells are capable of significant floating dispersal after the death of the animal inhabiting them - for instance, specimens have been washed up on the coast of New Zealand roughly a thousand miles south of the limits of their living distribution. Furnish & Glenister (1964a) suggested that was not impossible that the Gotland locality was in fact the only locality that had been inhabited by living ascocerids, and that all other specimens had floated to their eventual point of deposition post mortem.

I am completely at a loss as to why ascocerids remained as restricted as they did. All I can do for now is just write it off as another one of life's little mysteries.


Furnish, W. M., & B. F. Glenister. 1964a. Paleoecology. In Treatise on Invertebrate Paleontology pt K. Mollusca 3 (R. C. Moore, ed.) pp. K114-K124. The Geological Society of America and The University of Kansas Press.

Furnish, W. M., & B. F. Glenister. 1964b. Nautiloidea – Ascocerida. In Treatise on Invertebrate Paleontology pt K. Mollusca 3 (R. C. Moore, ed.) pp. K261-K277. The Geological Society of America and The University of Kansas Press.

Holland, C. H. 1999. The nautiloid cephalopod order Ascocerida in the British Silurian. Palaeontology 42 (4): 683-689.

Kesling, R. V. 1961. A new species of Billingsites, an ascoceratid cephalopod, from the Upper Ordovician Ogontz formation of Michigan. Contributions from the Museum of Paleontology, the University of Michigan 17 (3): 77-121.

Les is More

The avialan theropod previously referred to here as "Les" has now made its official, honest-to-goodness debut in the latest issue of Nature, and I can now reveal the proper name for Les - Epidexipteryx hui (the genus name means "display feather" and refers to the fact that the feathers preserved for Epidexipteryx appear to have been used for display rather than flight). It's a pretty fossil, but Nature has pulled its usual frustrating trick of giving us just enough information to whet the appetite, and leaving us howling frustratedly for more information...

Reconstruction of Epidexipteryx hui above taken from The Loom.

More Tales of the Crunchy

Male of the Sri Lankan cyphophthalmid Pettalus. Photo from Gonzalo Giribet.

This week's Taxon of the Week post had to be delayed a couple of days because I thought the Monday slot was better devoted to the proposed new electronic publication rules for the ICZN. It now being Wednesday, I am perfectly seated to introduce the delayed post. Today's highlight taxon is something not too far from my own research stomping grounds - the harvestman (Opiliones) superfamily Sironoidea.

Sironoidea was one of the three superfamilies of Cyphophthalmi or mite-like harvestmen recognised by Shear (1980). Largely thanks to the work of Gonzalo Giribet and associates, cyphophthalmids have in recent years become the most thoroughly studied of the major groups of harvestmen. I have previously posted on them here, and I'd recommend reading through that post before this one. As originally defined by Shear, Sironoidea included two families, the Holarctic Sironidae and the temperate Gondwanan Pettalidae (the subject of the previous post). Later, Shear (1993) added the New Caledonian Troglosiro to the superfamily. Sironoidea were united by Shear (1980) on the basis of their having a single series of dorsal setae (three groups of setae in other cyphophthalmids), coxae II free from coxae III (vs. fused), and the presence of anal glands and a modified anal region. Sironoidea was the only superfamily in the infraorder Temperophthalmi, the temperate cyphophthalmids, while the other two superfamilies, Stylocelloidea (containing the single south-east Asian family Stylocellidae) and Ogoveoidea (Ogoveidae and Neogoveidae of tropical America and west Africa) in the infraorder Tropicophthalmi, both had tropical distributions. One tropical species, the Kenyan Marwe coarctata, has since been supported by Bivort & Giribet (2004) as forming a clade in the Sironidae with the genera Paramiopsalis and Iberosiro.

More recent studies have broken down Shear's classification. Both of Shear's infraorders are likely to be polyphyletic, but relationships between the various families are difficult to pin down. The molecular analysis of Boyer et al. (2007) identified two possible arrangements - one with Pettalidae sister to the remaining cyphophthalmids in the arrangement Sironidae + (Stylocellidae + (Troglosiro + Neogoveidae)), while the other had Stylocellidae as the basalmost branch and Pettalidae sister to the clade formed by Sironidae and (Troglosiro + Neogoveidae). In contrast, the morphological analysis of Bivort & Giribet (2004) supported a basal position for Stylocellidae with the Ogoveoidea forming a paraphyletic series to a monophyletic Sironoidea. Until recently, the belief that Stylocellidae were the only family of cyphophthalmids to retain eyes was thought to support a basal position for them, but eyes were identified in a species of Pettalidae for the first time by Sharma & Giribet (2006), and have since been shown to be widespread in the family (Boyer & Giribet, 2007). Cyphophthalmid eyes (in those species that have them) are minute, integrated into the ozophore, of doubtful functionality and lack lenses in many Pettalidae, which is how it was possible for them to have gone unnoticed.

Siro carpaticus, a cyphophthalmid species from Poland. Not that while originally described as more closely related to species now included in Siro than to species now included in Cyphophthalmus, this species has not been properly reanalysed since Boyer et al. (2005) divided the two genera, and its generic assignment is not certain. Image from here.

Even the family Sironidae, established by Shear (1980) mainly on the basis of fused anal sclerites, is not necessarily monophyletic. As with Pettalidae (see the earlier post), each of the genera recognised within Sironidae shows a distinct geographical distribution, demonstrating that vicariance has been a significant factor - in fact, the primary factor - in the diversification of these spectacularly poorly-dispersing soil animals. Interestingly, there appears to be a closer evolutionary connection for cyphophthalmids between western Europe and North America (both inhabited by members of the genus Siro) than between western Europe and eastern Europe (the latter inhabited in the Balkan peninsula by the genus Cyphophthalmus - Boyer et al., 2005), which might be regarded as a case of life imitating politics. The Iberian peninsula has been the site of a notable mini-radiation of sironids, being the only home of the monotypic genera Odontosiro lusitanicus, Paramiopsalis ramulosus and Iberosiro distylos while the genus Parasiro is found in Spain, Corsica and Italy. Other sironid genera are the Bulgarian Tranteeva paradoxa and the Japanese Suzukielus sauteri. Boyer et al. (2007) supported the monophyly of a core clade for Sironidae including Siro, Cyphophthalmus and Paramiopsalis, but Suzukielus and Parasiro were not closely associated with this clade - Suzukielus only joined the core Sironidae in the Stylocellidae-rooted tree, while Parasiro never did.

It's worth my adding a bit more about cyphophthalmid eyes. One things arachnids are known for by the general public is their possession of multiple pairs of eyes. Harvestmen, however, stand out in this regard by never having more than a single pair of eyes (the one supposed exception, the "cyphophthalmid" Gibocellum sudeticum, seems never to have existed outside the overactive imagination of its author - Sørensen, 1906). In the Phalangida (the sister clade to Cyphophthalmi containing the majority of harvestmen), the eyes are usually placed on either side of a raised structure called the ocularium or eyemound positioned on the midline of the prosoma (visible in the photo here), but there are a few examples in which the ocularium has disassociated and the eyes are positioned closer to either side of the animal (some examples are visible among the images on this page). The eyes of cyphophthalmids may be homologous to the median eyes of Phalangida. Alternatively, they could correspond to the lateral eyes of other arachnids. Shultz (2007) identified the sister group of Opiliones as scorpions, which have both median and lateral eyes, so no help there. A paper in the most recent Journal of Arachnology (Alberti et al., 2008) apparently identifies the ultrastructure of cyphophthalmid eyes as more like the median eyes of other arachnids, but this paper is so new that I haven't even seen the issue in question as yet.


Alberti, G., E. Lipke & G. Giribet. 2008. On the ultrastructure and identity of the eyes of Cyphophthalmi based on a study of Stylocellus sp. (Opiliones, Stylocellidae). Journal of Arachnology 36 (2): 379-387.

Bivort, B. L. de, & G. Giribet. 2004. A new genus of cyphophthalmid from the Iberian Peninsula with a phylogenetic analysis of the Sironidae (Arachnida: Opiliones: Cyphophthalmi) and a SEM database of external morphology. Invertebrate Systematics 18: 7-52.

Boyer, S. L., R. M. Clouse, L. R. Benavides, P. Sharma, P. J. Schwendinger, I. Karunarathna & G. Giribet. 2007. Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids. Journal of Biogeography 34 (12): 2070-2085.

Boyer, S. L., & G. Giribet. 2007. A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New Zealand. Cladistics 23: 337-361.

Boyer, S. L., I. Karaman & G. Giribet. 2005. The genus Cyphophthalmus (Arachnida, Opiliones, Cyphophthalmi) in Europe: a phylogenetic approach to Balkan Peninsula biogeography. Molecular Phylogenetics and Evolution 36 (3): 554-567.

Sharma, P., & G. Giribet. 2006. A new Pettalus species (Opiliones, Cyphophthalmi, Pettalidae) from Sri Lanka with a discussion on the evolution of eyes in Cyphophthalmi. Journal of Arachnology 34 (2): 331-341.

Shear, W. A. 1980. A review of the Cyphophthalmi of the United States and Mexico, with a proposed reclassification of the suborder (Arachnida, Opiliones). American Museum novitates 2705: 1-34.

Shear, W. A. 1993. The genus Troglosiro and the new family Troglosironidae (Opiliones, Cyphophthalmi). Journal of Arachnology 21: 81-90.

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.

Sørensen, W. 1906. Un animal fabuleux des temps modernes. Analyse critique. Oversigt over det Konigelige Danske Videnskabernes Selskabs Forhandlinger 4: 197-232.

Electronic Publication in the ICZN - new proposals

Hot on the heels of the Les debacle, the ICZN has released its proposed regulations allowing electronic publication. For those interested in the full legalistic details, a complete description of the proposed amendments is openly available at Zootaxa (full reference at the bottom of this post). Because this is (needless to say) A Big Thing, and the proposals affect printed as well as electronic publications, I'm going to give my own comments on a number of points.

Before I do, though, I think that it's important to stress that these proposed amendments are not yet in effect. The Zootaxa paper (and an apparently upcoming release in the Bulletin of Zoological Nomenclature) have been released to publicise the proposals and allow researchers to submit comments before they are voted on by a future meeting of the ICZN. The alterations to the Code that end up coming into force will not necessarily be exactly those proposed in the Zootaxa paper. Some or even all of them may be altered in the process.

On to the paper. Italics in sections quoted below come from the original paper. When presenting ICZN articles, the paper uses normal text to indicate regulations that are in the current Code and italics to indicate proposed text alterations.

In Paris, Commissioners voted separately in favour of three principles relating to publication. None of these passed unanimously, but all had at least a two-thirds majority among the twelve voting.

    • Electronic-only publications should be allowed, if mechanisms can be found that give reasonable assurance of the long-term accessibility of the information they contain.

    • Some method of registration should be part of the mechanism of allowing electronic publication of names and nomenclatural acts.

    • Physical works that are not paper-based (e.g. CD-ROMs, DVDs) should be disallowed.

The primary issue with online publication has always been long-term availability. As noted before, guaranteeing the availability of publications to future researchers is a far more difficult issue for electronic rather than printed formats. The half-life of a website is far shorter than that of a book. Will the electronic publication still be available ten years in the future? Twenty years? Two-hundred years? The ICBN has, to date, avoided the question by refusing to accept electronic publication entirely. The current code of the ICZN attempted to ensure availability by requiring that copies of electronic publications be lodged as compact discs or some other permanent, unalterable electronic format in major libraries. However, this rule has caused a lot of debate. While CDs may be fairly permanent, the problem is that reading something on a CD requires that one have the appropriate equipment to do so, and the rapidly changing nature of electronic equipment could cause problems if CDs become no longer the storage format of choice in the future. When was the last time you saw an ultrafiche reader, for instance? The proposed amendments suggest that the development over the last few years of reliable electronic archiving services "such as Portico, which offers a permanent archive for electronic journals, and LOCKSS (Lots of Copies Keep Stuff Safe), an international, communal initiative based at Stanford University Libraries" may offer a more suitable alternative to CDs.

8.1. Criteria to be met. A work must satisfy the following criteria:

    8.1.1. it must be issued for the purpose of providing a public and permanent scientific record,

    8.1.2. it must be obtainable, when first issued, free of charge or by purchase, and

    8.1.3. it must have been produced in an edition containing simultaneously obtainable copies by a method that assures numerous identical and durable copies (see Article 8.4), or widely accessible electronic copies with fixed content and format (e.g. PDF/A, ISO Standard
      19005-1:2005) (see Article 8.5)

No problems here, but it's necessary background for what comes after. Note in particular the requirement that an electronic publication have "fixed content and format". One of the potential issues with electronic publication is that a document may be altered after its release, which is obviously undesirable for the purposes of a permanent archive. Should an altered edition of an electronic publication become available, then it would be required to be treated as a new publication and archived separately and in addition to the original version.

8.4.2. Works on CD-ROM or DVD. To be considered published, a work on CD-ROM or DVD must have been issued after 1999 and before 2010, and
    must contain a statement naming at least 5 major publicly accessible libraries in which copies of the CD-ROM or DVD were to have been deposited.

Because of the aforementioned potential problems with CD publication, the ICZN is proposing removing the option in favour of electronic archiving. However, the general principle in amending the ICZN is that new regulations should generally not be retrospective, because of the obvious issues that could arise if the availability or otherwise of a publication was to change many years after its publication. Therefore, anything validly published on CD during the period when that publication method was allowed will still retain its availability.

8.5. Works issued and distributed electronically. To be considered published, a work issued and distributed electronically must

    8.5.1. have been issued after 2009,

    8.5.2. state the date of publication in the work itself, and

    8.5.3. be archived with an organization other than the publisher in a manner compliant with ISO standard 14721:2003 for an Open Archive Information System (OAIS), or the successors to that standard. (For documentation of the location of the archive, see Article The archiving organization’s website must provide a means to determine which works are contained in the archive. The archiving organization must have permanent or irrevocable license to make the work accessible should the publisher no longer do so. If it is found that the work was not deposited in an archive within one year after the work’s stated date of publication, or that after the publisher or its successor no longer supports distribution of a work it cannot be recovered from an archive, the case must be referred to the Commission for a ruling on the availability of any names and nomenclatural acts contained in the work.

You got all that? This is the real meat of the discussion, and there are a number of really interesting provisions to try to ensure availability as much as possible. Take note of the proposed Articles and According to the Zootaxa article, "Both [Portico and LOCKSS] are curated, dark archives; “dark” in that a work will be released by the archive only if the publisher no longer supports distribution; “curated” in that the archive takes responsibility for migrating the content to new formats as needed to address changes in technology" (note that the article states that there is no intention to mandate the use specifically of those two archives, simply that they are used of examples of what a suitable archive service might be like). The archive services will not release copies of publications so long as they are available from the publisher - this is comparable to current "fair use" copyright regulations for in-print vs. out-of-print publications. The ICZN requires a guarantee that, should the publisher make a work unavailable direct from them, they will not be able to also prevent the archive from distributing the publication. I can see potential issues with determining exactly when the publisher "no longer supports distribution" (just as, with a printed work, it might be debatable whether a publisher "supports distribution" if one print run has been sold out but the next print run has not yet been started), but this is more a matter for copyright law than the ICZN.

Article is particularly significant. I think that it is quite appropriate that, in the case a supposed "permanent" electronic publication proves to not be so, that the question of how this affects any names published therein should be decided on a case-by-case basis rather than by a blanket rule. For instance, if the validating information (type data, etc.) has been republished in a later source, such as a redescription, it may be possible to conserve the taxon as described in the later publication with priority retained from the original publication, and potentially maintain greater nomenclatural stability than if the name should become unavailable. In a way, this would be comparable to the current procedure of designating neotypes for species whose type specimens are no longer available. What is surprisingly not mentioned in the Zootaxa article is that this could have implications for more than just electronic publications. While I am not aware of any printed publications actually having become permanently unavailable, some very old publications have become exceedingly difficult to obtain. the day may yet come when all available copies of a printed publication have fallen to the ravages of time, and it may be useful for the ICZN to have procedures in place for dealing with such situations.

8.6. New methods of publication and archiving. The Commission may issue Declarations to clarify whether new or unconventional methods of production, distribution, formatting, or archiving can produce works that are published in the meaning of the Code.

This proposed regulation would mean that if further new non-paper methods of disseminating information are developed (say, direct brain-to-brain data downloads), the ICZN would potentially be able to decide whether or not such methods produce nomenclaturally valid results without having to publish a whole new edition of the Code.

Recommendation 8B. Minimum edition of printed works. A work on paper should be issued in a minimum edition of 25 copies, printed before any are distributed.

Can I just say that this is absolutely fantastic? One funny thing about the ICZN to date is that while the current edition laid down very strict guidelines on what constituted a valid electronic publication, the only requirement for a printed publication (except for various formats specifically excluded by Article 9) was that "it must have been produced in an edition containing simultaneously obtainable copies by a method that assures numerous identical and durable copies" (Article 8.1.3), a sufficiently vague phrasing to have caused much debate in the past as to whether or not a given publication counts as taxonomically valid. For instance, Rafinesque's (1815) Analyse de la nature, ou tableau de l'univers et des corps organise's was a privately-published pamplet distributed to only a small number of friends and leading zoologists (Bock, 1994). Or try running an internet search for "Avgodectes". In my opinion, it is long since time for the ICZN to be more explicit on what are the basic requirements for a printed publication.

According to the Zootaxa article, this has become more of an issue in recent years with computer technology leading to the increasing availability of "print-on-demand" publications, where rather than a number of copies being produced in a single print-run, only a small number or even single copies of issues are printed off as ordered. Such "publications" are particularly difficult to assess as regards their availability under the ICZN, especially if the possibility exists for corrections and alterations to be made to the source document between successive printings.

10.8. Availability of names and nomenclatural acts in electronic works. New names and nomenclatural acts cannot be made available in electronic works issued before 2010 (Article 8.5.1; see Article 10.9 for other requirements).

    10.8.1. Where stability of nomenclature would be promoted thereby, a name or nomenclatural act appearing in such a work may be referred to the Commission for a ruling under the plenary power on its availability, if the work otherwise fulfils the requirements of Article 8.5.

This follows on from the principle described earlier that changes in regulations should not be retrospective. So Scansoriopteryx is still Scansoriopteryx, unless someone successfully petitions the ICZN otherwise.

10.9. Registration of names and nomenclatural acts. Registration in the OFFICIAL REGISTER OF ZOOLOGICAL NOMENCLATURE (Article 78.2.4) is required for a new scientific name published in an electronic work (Article 8.5) to be available. Additional requirements for availability of such names are:

    10.9.1. the registration number assigned in the OFFICIAL REGISTER must be cited in the work itself, and

    10.9.2. at least the following information must be recorded in the OFFICIAL REGISTER: for the name of a taxon at any rank, sufficient bibliographic information to identify the work in which the name is proposed, and the name and Internet address of the archiving organization, and for a species-group name, the depository for the name-bearing type and the location of that depository; for a genus-group name, the type species; for a family-group name, the type genus.

    10.9.3. Registration of nomenclatural acts other than the proposal of new names in an electronic work is voluntary.

    10.9.4. Names and nomenclatural acts published on paper may be registered voluntarily and retrospectively; such registration does not affect their availability.

    10.9.5. Registration without publication in conformity with Articles 8 and 9 does not confer availability.

One of the biggest changes that is being proposed for the new edition of the ICZN is the introduction of ZooBank, an online register of all zoological names. While it appears that mandatory registration may not be introduced for new names in printed publications, it is being suggested for electronic publications. I suspect one major reason for this is to facilitate proceedings if situations arise as covered in Article above.

Even though the proposed article explicitly states that a name is not available if it is registered but not published, I can see definite confusion arising in such situations. An alternative is the previous proposal (Polaszek et al., 2005) that had authors releasing publications prior to registration, then having two years to register the name on ZooBank.

21.8.3. Some works are accessible online in preliminary versions before their final publication date. Advance electronic access does not advance the date of publication of a work.

Again, Scansoriopteryx is still Scansoriopteryx. However, as the Scansoriopteryx example shows, this could still lead to problems if the early online version is widely publicised, and personally I think this is one of the more problematic proposals. Harris' (2004) proposal that would allow the date of DOI registration to count as the date of publication might have been preferable.

And finally:

21.9. Works issued on paper and electronically. A name or nomenclatural act published in a work issued in both print and electronic editions is available from the one that first fulfils the relevant criteria of availability.

This seems fairly obvious - however, I'm wondering if researchers could be confused as to how this article interacts with Article 21.8.3 given just above. So online early editions do not count as proper publications, except for cases where they do? Scansoriopteryx might not be Scansoriopteryx after all? Mind you, as pointed out in the Zootaxa article, this issue is not actually unique to electronic publications - "The same situation already exists with repaginated reprints, or second printings that still state “new species”". The Zootaxa article suggests that the new Code will make explicit what sensible researchers have generally been doing all along - when the same content is published twice, it should be counted as a single publication dating from the first valid appearance.


Bock, W. J. 1994. History and nomenclature of avian family-group names. Bulletin of the American Museum of Natural History 222: 1-281.

Harris, J. D. 2004. 'Published works' in the electronic age: recommended amendments to Articles 8 and 9 of the Code. Bulletin of Zoological Nomenclature 61 (3): 138-148.

International Commission on Zoological Nomenclature. 2008. Proposed amendment of the International Code of Zoological Nomenclature to expand and refine methods of publication. Zootaxa 1908: 57-67.

Polaszek, A., M. Alonso-Zarazaga, P. Bouchet, D. J. Brothers, N. Evenhuis, F.-T. Krell, C. H. C. Lyal, A. Minelli, R. L. Pyle, N. J. Robinson, F. C. Thompson & J. van Tol. 2005. ZooBank: the open-access register for zoological taxonomy: Technical Discussion Paper. Bulletin of Zoological Nomenclature 62 (4).

Are You Sucking on a Lemon or a Lime?

The genus Citrus is one of the most significant groups of fruit trees around the world. An overwhelming diversity of fruit varieties are produced by Citrus, such as oranges, lemons, grapefruit, tangelos, citrons, bergamots, mandarins, and the wonderfully-named ugli fruit (and yes, it is). Technically, the fruit of Citrus is a specialised type of berry called a hesperidium, named after the mythical garden of the Hesperides where golden fruit were tended by airy nymphs watched over by a giant serpent, suggesting that Greek prophets had also predicted the eventual appearance of Benny Hill. The hesperidium is distinguished by its leathery, acidic rind and division into segments, and is unique to a clade containing Citrus and a few closely related genera such as Poncirus and Fortunella (kumquats*), both of which have been included by at least some researchers in Citrus (de Araújo et al., 2003). From the taxonomist's point of view, however, Citrus has always been a gigantic headache. The question of how to classify this kaleidoscopic array of varieties, most of them only known as cultivated forms with no record of their origins, presents a quandary perhaps rivalled among plants only by the similarly over-cultivated genus Brassica. In the two main classifications that have been used for Citrus, that presented by Swingle in 1943 recognised sixteen species in the genus, while that of Tanaka in 1977 recognised one-hundred and sixty-two (Jung et al., 2005).

*Some time ago, I commented on the misleadingly obscene sound of words such as "yeast", "moist" and "sphagnum". None of these words, however, comes even close in this regard to the filth innocently suggested by "kumquat".

The citrus variety known as poorman's orange (it's not an orange) or New Zealand grapefruit (it's not a grapefruit, either). Photo by Julian Sauls.

As well as their long history of cultivation, citrus classification is also handicapped by the fact that the different varieties are at one and the same time both highly interfertile and significantly reproductively isolated. This may sound like something of a paradox, but it results from Citrus' distinctive reproductive system, involving a process called nucellar embryony (Moore, 2001). The nucellus is the nutritive tissue surrounding and protecting the ovum in plant ovules. Seed development begins with the ovum being fertilised, and beginning to develop into an embryo. In Citrus, however, the nucellus itself also gives rise to a number of additional embryos that are genetic clones of the parent plant. These nucellar embryos often outcompete the sexually produced embryo, meaning that when the seed germinates the seedling that grows from it will commonly be genetically identical to its parent, and actual sexually-produced offspring are rare. In spite of this, actual direct barriers to reproduction between different species of Citrus are low, so when successful sexual reproduction does occur, the results can be unpredictable.

Kaffir lime (Citrus hystrix), an ingredient that no good curry can do without. Photo from Trade Winds Fruit.

In light of the above, it is perhaps not that surprising that studies conducted on morphology and biochemistry of Citrus species in the 1970s came to the conclusion that of the 100+ potentially recognised species of cultivated Citrus, only three represented true "species" in the sense of deriving from separate domestications of independently evolved taxa. These three primordial species were the citron (Citrus medica), pummelo (Citrus maxima) and mandarin (Citrus reticulata). All other domestic "species" are ultimately derived from crosses, re-crosses and back-crosses of these three species and their derivatives. Oranges, for instance, are probably derived from hybrids of mandarins and pummelos, while the citron is an ancestor for lemons and limes. . A fourth species, the uncultivated Citrus halimii, has also been suggested as a progenitor of cultivated varieties, but Pang et al. (2007) felt that it was not supported as such (apparently - I haven't read the paper, as our library lacks the appropriate subscription). Nicolosi et al. (2000) added another species, the papeda Citrus micrantha, to the mix, representing the subgenus Papeda that includes Citrus micrantha and its close relatives such as the kaffir lime, Citrus hystrix.

Probable relationships between citrus species, from Moore (2001).

I find it quite an impressive thought that the spectacular diversity of citrus fruits we see today should have come from so few progenitors. From pummelos to papedas to Poorman oranges, this is certainly something to keep in mind the next time you down a cocktail.


Araújo, E. F. de, L. P. de Queiroz & M. A. Machado. 2003. What is Citrus? Taxonomic implications from a study of cp-DNA evolution in the tribe Citreae (Rutaceae subfamily Aurantioideae). Organisms Diversity & Evolution 3 (1): 55-62.

Jung, Y.-H., H.-M. Kwon, S.-H. Kang, J.-H. Kang & S.-C. Kim. 2005. Investigation of the phylogenetic relationships within the genus Citrus (Rutaceae) and related species in Korea using plastid trnL-trnF sequences. Scientia Horticulturae 104 (2): 179-188.

Moore, G. A. 2001. Oranges and lemons: clues to the taxonomy of Citrus from molecular markers. Trends in Genetics 17 (9): 536-540.

Nicolosi, E., Z. N. Deng, A. Gentile, S. La Malfa, G. Continella & E. Tribulato. 2000. Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theoretical and Applied Genetics 100 (8): 1155-1166.

Pang, X.-M., C.-G. Hu & X.-X. Deng. 2007. Phylogenetic relationships within Citrus and its related genera as inferred from AFLP markers. Genetic Resources and Crop Evolution 54 (2): 429-436.

More Mysterious Palaeogene Eutherians

A few weeks ago, I wrote a post about some of the distinct groups of eutherian mammals that waddled through the world during the Palaeocene, the time period that followed directly after the end of the Cretaceous. At the time, many of the modern groups of mammals were either still fairly marginalised or yet to put in an appearance, and the relationships of most of those primordial eutherians such as pantodonts and taeniodonts remains a remarkable mystery. In this post, I thought I'd focus on one of those early groups that seems to get given an even shorter shrift than most (in fact, this post will be unillustrated because my attempts to find suitable free images online drew a complete blank) - the Tillodontia.

Tillodonts are known only from the Palaeocene and Eocene of North America and Eurasia. Most authors have recognised a single family, the Esthonychidae, though Lucas & Schoch (1998) positioned the genera Lofochaius and Basalina as a paraphyletic series outside that family*. They were medium to large herbivores (one of the later genera, Trogosus, may have weighed around 150 kg - Lucas & Schoch, 1998). Like most mammals of the time, these would not have been the most graceful of beasts - they would have probably been built more like a barrel on legs, perfect for the moist, densely-forested conditions of the time. One of the most distinct features of the tillodonts was the development of large, rodent-like incisors, which in one later clade became open-rooted and permanently-growing like those of rodents. The powerful dentition this gave tillodonts, together with the sturdy legs and claws found in those few species for which post-cranial material is known, would have allowed them to tackle some pretty resilient food-sources, and it is easy to imagine them gnawing bark off trees or digging up roots. A similar lifestyle appears to have also characterised another group of Palaeogene herbivores, the taeniodonts, which also developed rodent-like gnawing teeth. It was once suggested on this basis that taeniodonts and tillodonts were closely related to each other, but the gnawing teeth in taeniodonts were the canines, not the incisors, so the two groups could not have possibly shared a common gnawing ancestor.

*The authors of the late Palaeocene Chinese genus Yuesthonyx (Tong et al., 2003) established a new family for it, Yuesthonychidae. Not only would this family be redundant with its single genus, but Rose (2006) implies that Yuesthonyx is a more derived form not far from the origin of the Trogosinae (see below), making the recognition of a separate family for it all the more pointless.

The very earliest tillodonts such as Lofochaius and Meiostylinodon come from the Lower Palaeocene of China, and this would appear to represent the place of origin for the clade (Rose, 2006). The early Chinese genera were much smaller than the later trogosines, and had less exaggerated dentition. The first North American tillodonts make their appearance in the very end of the Palaeocene with the similarly generalised Azygonyx which survived into the beginning of the Eocene alongside Esthonyx, the most common genus of tillodonts. These forms all lacked permanently-growing incisors, the appearance of which marks the appearance of the clade Trogosinae in the Eocene. Trogosines are known from both North America (Tillodon and Trogosus) and China (Higotherium and Chungchienia), so their geographic origins are unclear. The Chinese Chungchienia had the most advanced dentition of any tillodont - not only were the second incisors a whopping 26 cm long(!), but the ever-growing rootless condition of the incisors was extended to the cheek-teeth (Chow et al., 1996), implying that it must have had an exceedingly tough diet.

While it is fairly well-established that tillodonts were not related to taeniodonts, it has been a decidedly more difficult prospect to establish exactly what they are related to. Van Valen (1963) suggested a close relationship to Arctocyonidae, a family of "condylarths", but this was based on comparisons with the relatively derived North American Esthonyx rather than the mostly then-undiscovered Asian genera. More recent authors have suggested a relationship with the pantodonts, with which tillodonts share dilambdodont cheek teeth. Basal tillodonts may also be difficult to distinguish from basal pantodonts (Rose, 2006). The Palaeocene North American Deltatherium may also be relevant to the origin of tillodonts. However, none of these groups has yet been subject to a proper cladistic analysis to determine whether their shared features indicate actual relationship or convergence. And even if these taxa do form a monophyletic clade, this still just takes a number of small problematic clades of unknown relationships to modern taxa and turns them into one big clade of unknown relationships to modern taxa!


Chow, M., J. Wang & J. Meng. 1996. A new species of Chungchienia (Tillodontia, Mammalia) from the Eocene of Lushi, China. American Museum Novitates 3171: 1-10.

Lucas, S. G., & R. M. Schoch. 1998. Tillodontia. In Evolution of Tertiary Mammals of North America (C. M. Janis, K. M. Scott & L. L. Jacobs, eds.) pp. 268-273. Cambridge University Press.

Rose, K. D. 2006. The Beginning of the Age of Mammals. JHU Press.

Tong Y.-S., Wang J.-W. & Fu J.-J. 2003. Yuesthonyx, a new tillodont (Mammalia) from the Paleocene of Henan. Vertebrata PalAsiatica 41: 55-65.

Van Valen, L. 1963. The origin and status of the mammalian order Tillodontia. Journal of Mammalogy 44 (3): 364-373.


Today marks another first for Catalogue of Organisms - for the first time, the Taxon of the Week post is focusing on a single species. Specifically, the tropical fish Dendrochirus zebra (Cuvier, 1829)*, commonly known as dwarf lionfish, zebra turkeyfish, zebra butterfly-cod and doubtless a whole host of others of which I'm not even aware. And a very attractive animal it is too, as you can see in the photo above by K. Uchino. Dendrochirus zebra is a widespread species on reefs in the tropical Indian and Pacific Oceans. A map, as well as a whole heap of other information, can be found on FishBase.

*Things are a little confusing regarding the authority of this species - some sources (including FishBase) cite Cuvier (1829), while others such as Munro (1958) point to Quoy and Gaimard (1824). I have no idea which is correct.

The lionfishes or firefishes are two genera (Pterois and Dendrochirus) forming the subfamily Pteroinae of the family Scorpaenidae, the scorpionfishes (though Smith & Wheeler, 2006, found the pteroines to be more closely related to the Sebastidae rather than the Scorpaeninae). The differences between the two genera are fairly minimal, and a molecular phylogenetic analysis of seven (of thirteen) species of pteroines by Kochzius et al. (2003) failed to resolve their relative monophyly. Dendrochirus zebra was actually originally described as a species of Pterois (Munro, 1958), and it seems a return might be in order - proving once again that vertebrate workers tend to oversplit their genera. The name Dendrochirus ("tree-hand") refers to one of its supposed distinguishing characters, that some of the upper rays in the pectoral fin are branched. The other distinguishing character is that, unlike Pterois, Dendrochirus never has the upper pectoral rays free from the membrane.

The spectacular coloration of the pteroines makes them instantly recognisable, though the above photo of Dendrochirus zebra by Richard Ling shows quite well how the fish are not quite so obvious against a colorful reef background as one might expect. Like other scorpaenids, lionfish are slow-moving ambush predators. Their somewhat glum expression is the result of their relatively gigantic maws, which open up to inhale just about anything that can fit. Lionfish also resemble other scorpaenids in the presence of painfully venomous spines in the dorsal, ventral and anal fins. This toxicity has not prevented D. zebra from becoming popular in the marine aquarium industry. While D. zebra has spawned in captivity (FishBase), the majority of captive specimens would appear to be wild-caught. Unfortunately, FishBase suggests that this species is a relatively slow breeder and moderately vulnerable to overfishing.

One last thing which, though it relates not to Dendrochirus zebra but to another pteroine, is something I stumbled across while researching this post that is just too cool not to share. Take a look at the two photos below:

The above photos come from Fishelson (2006). The upper photo shows a typical individual of Pterois volitans, the red firefish. The lower photo shows a variant with the supraoral tentacles flattened into feather-like ornaments. Such a variant was first sighted near the southern end of the Sinai peninsula in the early 1980s. Since then, records of variant individuals have slowly spread southwards, and have since been recorded as far south as Kenya and the Comoros. While variant individuals remain extremely rare, they do seem to be slowly increasing in abundance...


Fishelson, L. 2006. Evolution in action-peacock-feather like supraocular tentacles of the lionfish,
Pterois volitans – the distribution of a new signal. Environmental Biology of Fishes 75: 343-348.

Kochzius, M., R. Söller, M. A. Khalaf & D. Blohm. 2003. Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 28 (3): 396-403.

Munro, I. S. R. 1958. The fishes of the New Guinea region: A check-list of the fishes of New Guinea incorporating records of species collected by the Fisheries Survey Vessel “Fairwind” during the years 1948 to 1950. Papua and New Guinea Agricultural Journal 10 (4): 97-369 (reprinted 1958. Territory of Papua and New Guinea Fisheries Bulletin no. 1).

Smith, W. L., & W. C. Wheeler. 2006. Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes): evidence from mitochondrial and nuclear sequence data. Molecular Phylogenetics and Evolution 32 (2): 627-646.

Chain, Chain, Chain

Hou, X.-G., D. J. Siveter, R. J. Aldridge & D. J. Siveter. 2008. Collective behavior in an early Cambrian arthropod. Science 322: 224.

Fossils can offer fascinating insights into the lives of long-extinct organisms. Sometimes, the lifestyles suggested are so different from anything found in living taxa that we may be at something of a loss to understand their function and significance. The new publication linked to above reports on the fascinating discovery of a collection of early arthropods from the famed Chengjiang fauna of China. (For those unfamiliar with it, the Chengjiang is similar to the Burgess Shale of North America, but even more impressive - it is only the fact that the latter was discovered earlier that gets it more press).

The fossils are of an animal very similar to Waptia, a previously-known, superficially shrimp-like animal of uncertain affinities. Waptia is not uncommon as a Cambrian fossil - according to Taylor (2002), it is the third-most common animal in the Burgess Shale, with over 1000 specimens held by the American National Museum of Natural History. Despite this abundance, Waptia has not been described in detail since Walcott's original preliminary description in 1912 (Taylor, 2002, says that he is working on a revision, but this doesn't seem to have appeared in print yet). Hou et al. (2008) refer to it as a stem-crustacean, but do not specify on what grounds. It could just as easily be a stem-chelicerate, as are the majority of known Cambrian arthropods (Cotton & Brady, 2004).

What makes this new finding so remarkable can be seen in the figure below from Hou et al. (2008). A group of 22 individuals is preserved together, each arranged head to tail in a long chain. As shown in the close-up in fig. 1C, each individual has the tail-end of the individual ahead of it cavered by its carapace. There is no evidence that the animals were lined up in a burrow, so they were most likely living above the sediment surface. The fact that the chain has not broken apart as the animals were buried indicates that they must have had an extremely firm hold on each other in life. Hou et al. interpret the chain as having been pelagic, but that seems unlikely to me - the sheer abundance of Waptia in the Burgess shale seems more consistent with a life close to the sediment surface, which would offer more opportunities for burial. Cambrian animals more likely to be pelagic, such as Amiskwia and Nectocaris, are very rare as fossils.

What on earth were these animals doing lined up like that? Hou et al. claim that such behaviour is unique, but I'm not sure just how unique. Hou et al. claim that lines formed by modern arthropods such as crayfish (for migration) and some caterpillars (feeding) are "more trains than chains", but don't explain exactly what is the difference (the curse of the super-compressed Science format strikes again?) Certainly, I've seen fireblight caterpillars here in Perth form very closely-linked chains, and one of the most horrifying sights I've ever seen was a mass of about twenty fireblights, so closely coiled that it was hard to tell where one finished and another began, moving as one. The waptiid assemblage is unlikely to be connected to feeding, as the close proximity of the mouth of one and the anus of another makes such an arrangement rather too horrible to consider. Hou et al. favour a connection to migration, probably for defense, which is a distinct possibility. I would suggest that the chain could have also been related to mating behaviour. Some animals, such as some marine gastropods, can form chains of multiple intermating individuals. Hou et al. (2008) dismiss this possibility on the grounds that "there is no precedent of arthropods of comparable aggregation for fertilisation". However, living arthropods show an absolutely enormous diversity of mating behaviours. Is it that much of a stretch to entertain the possibility that extinct forms may have shown even more?


Cotton, T. J., & S. J. Braddy. 2004. The phylogeny of arachnomorph arthropods and the origin of the Chelicerata. Transactions of the Royal Society of Edinburgh: Earth Sciences 94: 169-193.

Taylor, R. S. 2002. A new bivalved arthropod from the Early Cambrian Sirius Passet Fauna, north Greenland. Palaeontology 45 (1): 97-123.

Tortoise Resurrection

In a subsequent portion of this narrative I shall have frequent occasion to mention this species of tortoise. It is found principally, as most of my readers may know, in the group of islands known as the Gallipagos... They are frequently found of an enormous size... They can exist without food for an almost incredible length of time, instances having been known wher they have been thrown into the hold of a vessel and lain two years without nourishment of any kind - being as fat, and, in every respect, in as good order at the expiration of that time as when they were first put in... They are excellent and highly nutritious food, and have, no doubt, been the means of preserving the lives of thousands of seamen employed in the whale-fishery and other pursuits in the Pacific.

--Edgar Allen Poe, The Narrative of Arthur Gordon Pym of Nantucket

For sailors in tropical oceans before the invention of refrigeration, keeping supplies of food was a serious issue. It was a permanent challenge to keep supplies fresh and edible, and indeed, much of the time stores failed at both. Under such conditions, the giant tortoises of the Galapagos islands and the Mascarenes and other islands in the Indian Ocean would have been seen as nothing short of miraculous. Tortoises could be captured easily and kept in the hold of a boat for extended periods without feeding, only slaughtered when they were actually required for eating. As a result, ships that were in a position to do so often took on tortoises in large number, and Charles Darwin apparently recorded single vessels taking up to 700 individuals at a time. By modern standards the idea of seven hundred starving tortoises crammed into a single hull seems unthinkably cruel, but doubtless the sailors who otherwise faced another six months of decomposing ship's biscuit saw things differently.

Geochelone becki, the Volcano Wolf tortoise. Photo by Joe Flanagan.

Unfortunately, such intense harvesting took an inevitable toll. Tortoise numbers declined rapidly, and many went extinct. Honneger (1981) lists three extinct species of tortoise from the Galapagos (including Geochelone abingdoni from Pinta island, which is technically not yet extinct but which only survives in the form of a single captive male) and at least six extinctions from the Seychelles and Mascarenes. Extinct populations on the Galapagos islands of Rabida and Santa Fe may have represented further undescribed species.

However, a paper published yesterday in the Proceedings of the National Academy of Sciences adds a remarkable coda to the history of one of the "extinct" species, the Floreana tortoise Geochelone elephantopus. Using DNA extracted from museum specimens collected on Floreana before the population disappeared, Poulakakis et al. (2008) have demonstrated that G. elephantopus may not be quite as extinct as previously thought. Instead, anomalous genetic haplotypes previously identified in some living individuals of Geochelone becki, a species found on the Volcano Wolf at the northern end of Isabela, the largest island in the Galapagos, indicate descent from G. elephantopus. These individuals would appear to be descendants of past hybridisations between native Volcano Wolf tortoises and introduced Floreana tortoises.

Such a situation is quite believable. As a result of the widespread transport of tortoises for food, many tortoises ended up on islands to which they were not native*. Tortoises were regularly imported to Réunion in the Mascarenes after the native population became extinct. Living populations of giant tortoises on the Granitic Islands of the Seychelles probably descend from imports from Aldabra rather than representing the species originally found there (Honegger, 1981). According to Poulakakis et al. (2008), some 40% of the Volcano Wolf tortoises tested showed evidence of Floreana ancestry, so the genetic legacy of Geochelone elephantopus is alive and well, at least in hybrid form.

*Potentially a serious issue for taxonomy, as researchers cannot assume that species names based on inadequate type material necessarily represent the species native to the island the type was collected on. Honegger (1981), for instance, cast doubt on whether Geochelone gouffei, known from a single specimen found on Farquhar Island in the Seychelles, actually originated there.

This still leaves a significant problem - most conservation policies do not cope well with hybrids. A number of species worldwide, such as the black stilt (Himantopus novaezelandiae) in New Zealand, are regarded as endangered because of the risk of hybridisation with related species. The red wolf (Canis rufus) and the Florida panther (Puma concolor coryi) represent two 'endangered' taxa in the United States for which the suggestion that their histories could have been compromised by hybridisation led to the suggestion that they should be abandoned as worthwhile conservation targets. However, the disappearance or decline of a species in its pure form due to hybridisation with another species is a different proposition from its decline due to replacement by that species. The genetic legacy of the declining species may still persist. Overemphasis on species "purity" may actually hinder the conservation of endangered taxa, especially if natural hybrid zones with related taxa exist in the first place (Allendorf et al., 2001). If there are no purebred Florida panthers, should that mean that there is no place for panthers in Florida?


Allendorf, F. W., R. F. Leary, P. Spruell & J. K. Wenburg. 2001. The problems with hybrids: setting conservation guidelines. Trends in Ecology and Evolution 16 (11): 613-622.

Honegger, R. E. 1981. List of amphibians and reptiles either known or thought to have become extinct since 1600. Biological Conservation 19: 141-158.

Poulakakis, N., S. Glaberman, M. Russello, L. B. Beheregaray, C. Ciofi, J. R. Powell & A. Caccone. 2008. Historical DNA analysis reveals living descendants of an extinct species of Galápagos tortoise. Proceedings of the National Academy of Sciences of the USA 105 (40): 15464-15469.

Linnaeus' Legacy #12 - The Legacy gets crossed by a Black Cat

The newest edition of Linnaeus' Legacy has been put up by Podblack Cat. This month's keywords: Dante's Inferno, sex, mysteries, bet your ass, ants, ants, ants, ants and more ants, stand back and let rip, expensive varieties, tragic tale, goose almost the size of a small plane, Komodo dragons. Enjoy!

Of Macros and Micros

Vorticella, a sessile ciliate of the intramacronucleate class Oligohymenophora. Photo from here.

Today's Taxon of the Week is the ciliate subphylum Intramacronucleata. Ciliates, one of the most famous groups of protozoa, have been touched on previously at the Catalogue of Organisms. They are certainly one of those groups of organisms that get progressively cooler the further one looks. Admittedly, there are few groups of organisms to which that wouldn't apply.

Intramacronucleata is the largest of the two primary subdivisions within the ciliates recognised in the recent years, and includes most well-known ciliates such as George (Paramecium) and George (Tetrahymena), as well as the Georges (Spirotricha) discussed at the post linked to above (names due to an ex-partner of mine who decided that Paramecium was far too unwieldy a word, and henceforth all microbes should be known as George). The other subphylum goes by the even more unwieldy moniker of Postciliodesmatophora (Lynn, 2003). The name refers to one of the more intriguing features of ciliates, the macronucleus. Ciliate cells always contain at least two nuclei, the reproductive micronucleus and the transcriptional macronucleus. Depending on species and life-cycle stage, a ciliate may have between one and twenty micronuclei, and from one to several hundred macronuclei (McGrath et al., 2006). The vast majority of transcription happens from chromosomes contained in the macronuclei. However, when conjugation (sexual reproduction) occurs, the macronuclei break down and only the micronucleus is propagated. Two conjugating ciliates each generate a pair of haploid micronuclei, one of which they donate to the other. The donor and recipient micronuclei then fuse to form the new diploid micronucleus, which gives rise to the daughter cells' macronuclei. (In the post linked to above, I originally said that the macronuclei break down during cell division, but I was wrong. It only happens in conjugation).

Reproductive cycles in ciliates. Diagram from here.

Despite being derived from the micronucleus, the macronucleus is genetically very different from its progenitor. As well as being replicated, the original genome is subjected to an intense processing programme (described in detail by McGrath et al., 2006). The fewer standard chromosomes contained in the micronucleus are fragmented into a larger number of much smaller chromosomes, each of which is usually present in a large number of chromosomes. The most extreme examples are found among the spirotrichs, some of which start with 120 micronuclear chromosomes which they divide up into as many as 24,000 macronuclear chromosomes. Each of these macronuclear chromosomes may comprise only a single gene, and there may be up to 15,000 copies of each one. New telomeres are generated and tacked onto each of the newly-produced chromosomes. Non-functional sections of DNA in the original micronuclear genome such as repetitive elements, introns and transposons (up to 95% of the original sequence) are brutally excised from the daughter chromosomes, which are stitched back together to form unbroken transcriptional templates.

Intramacronucleata get their name because the microtubules involved in macronuclear division form within the nuclear envelope, while the Postciliodesmatophora include one class (the Heterotrichea) in which the microtubules form outside the macronucleus, and one (the Karyorelictea) in which the macronuclei do not undergo division. While micronuclei divide like respectable nuclei by a process of mitosis, macronuclei are anarchists to the core and divide by a poorly-understood process called amitosis. Amitosis differs from mitosis in that there is no mitotic spindle. As a result, the division of chromosomes between amitotically-produced nuclei is not necessarily even, and in some species of ciliate one daughter nucleus will regularly contain more than twice as many chromosomes as the other. This may explain why ciliate macronuclei may contain such a ridiculous number of copies of each chromosome. When one also factors in that macronuclei are not necessarily evenly distributed during cell division, individual ciliates can vary significantly in their functional genetic makeup even if they descend asexually from the same ancestral cell.

Trichodina, another member of the Oligohymenophora, and a parasite of fish. Image from here.

There is an intriguing paradox at work as a result of all this. Because of their unique disconnect between the products of reproduction and the functional template, one can't help wondering if ciliates are, to some extent, able to dodge the consequences of natural selection. Does the ruthless excision of non-functional sequences prior to transcription mean that the ciliate genome may accumulate more such sequences than it could normally? The uneven assortment of chromosomes during amitosis means that not every macronucleus will necessarily contain all alleles present in the micronucleus. Does this mean that deleterious mutations can persist in the micronucleus even if they would impair function in the macronucleus? Zufall et al. (2006) demonstrated that ciliates showed significantly higher rates of genetic evolution than other eukaryotes, and suggested that such potential persistance of deleterious alleles increased the chance of compensatory mutations appearing in the genome before selection took its toll. As Zufall et al. put it, ciliates were therefore free to "explore protein space" to a higher degree than was possible for other eukaryote groups.


Lynn, D. H. 2003. Morphology or molecules: How do we identify the major lineages of ciliates (phylum Ciliophora)? European Journal of Protistology 39 (4): 356-364.

McGrath, C. L., R. A. Zufall & L. A. Katz. 2006. Ciliate genome evolution. In Genomics and Evolution of Microbial Eukaryotes (L. A. Katz & D. Bhattacharya, eds.) pp. 64-77. Oxford University Press.

Zufall, R. A., C. L. McGrath, S. V. Muse & L. A. Katz. 2006. Genome architecture drives protein evolution in ciliates. Molecular Biology and Evolution 23 (9): 1681-1687.