Field of Science

Request for a Citation

Recently I obtained a pile of duplicate reprints from the museum library, and I've since been entering them into my Endnote. Unfortunately, one of the reprints doesn't have the journal volume number and pagination, and I haven't been able to find them online. Does anyone out there have the details for:

Ride, W. D. L., & A. J. Cain. 1961. On the transfer of the name Anas punctata Burchell from the Hottentot teal to the Maccoa duck by the S.A.O.S. List Committee. Ostrich.

In the meantime, enjoy this sweet little video courtesy of The Other 95%:

Update (13/12/2007): A massive thank you to Darren Naish who finally supplied me with the answer:

Ride, W. D. L., & A. J. Cain. 1961. On the transfer of the name Anas punctata Burchell from the Hottentot teal to the Maccoa duck by the S.A.O.S. list committee. The Ostrich 32: 91-92.

He even gave me the reference for a follow-up paper:

Winterbottom, J. M. 1961. Transfer of the name Anas punctata Burchell from the Hottentot teal to the Maccoa duck. The Ostrich 32: 134-135.

Now I am content.

Is it a sponge, or is it a plant?

Welcome to the first (but hopefully not the last) conjointly envisioned post on Catalogue of Organisms. Today's post is on the problematic fossil Receptaculites, and Kevin Z is providing a musical background (or foreground if you prefer) to accompany it.

The fossil order Receptaculitida occurs from the Ordovician to the Carboniferous, possibly to the Permian (Nitecki et al., 2004 - image above comes from Wikimedia). They are quite spectacular fossils, with a striking geometric arrangement of plates on a globose body. Complete fossils are rare, but we have a reasonably good idea of overall structure.

One end of the fossil (shown above in an image from Gould & Katz, 1975) provided the centre that the plates radiated from (the nucleus), and is the most often preserved section. The other end (the lacuna) appears to have been open at the tip (Nitecki et al., 1999). The plates radiated off a central axis to which they were attached by lateral branches known as meroms.

The relationships of receptaculitids have been debated ever since they were discovered. Various authors have regarded them as giant foraminifera, sponges or algae. Part of the problem is that, as with Stylophora, receptaculitids are a group of fossil taxa different enough from anything still living that authors have disagreed on which end was up and which down. Those who would see the receptaculitids as algae have argued for an orientation with the closed nucleus upwards, while an uncalcified stalk would have attached the organism to the substrate through the lacuna. On the contrary, if receptaculitids are to be sponges, the orientation is reversed - the nucleus becomes the lower, while the open lacuna corresponds to the osculum of other sponges, the ejection point of filtered water. Also, like a palaeontological version of the famous two faces vs. vase optical effect, some authors have seen the meroms as solid branches supporting the plates, while others would see them as hollow canals. Authors have also disagreed about whether the nucleus or the lacuna represented the growing end of the receptaculitid, but the existence of specimens with secondarily fused plates at the nucleus, in contrast with the less calcified plates at the lacunar end, strongly implies that the lacuna is the growing end.

A word of caution at this point - the term "alga" is often a difficult one in palaeontology. It is well-known that the various groups of living algae (green, red, brown, etc.) are a polyphyletic group, with multicellularity arising multiple times from unicellular ancestors. Unfortunately, the characters distinguishing the various groups are usually fine scale features, often at the cellular level. At the macroscopic level, the simple organisation of many algae means that members of different groups may be superficially quite similar in appearance, and may be indistinguishable as fossils. As a result, referring to fossils of completely extinct groups as "algae" often implies a certain degree of agnosticism about their actual relationships. At worst, the term "fossil alga" sometimes seems to be a shorthand for "sessile organism that we haven't a clue where else to put it". In the case of receptaculitids, fortunately, an actual modern algal analogue has been suggested in the form of the Dasycladales, an order of calcified green algae that also possess a radial arrangement of side-branches around a central stem (image above of Acetabularia from here). However, there are problems in attributing receptaculitids directly to Dasycladales, as that would effectively require the nucleus to be the growing end.

Nevertheless, an algal interpretation (whatever that might mean) of Receptaculitida does seem more likely than a sponge. The solid outer casing of receptaculitids doesn't compare that well to the more porous structure of sponges. The question of the life-orientation of receptaculitids is even harder to comment on - while an open lacuna-upward position does seem more appealing if the lacuna is the growing tip, an attached lacuna-downwards position is still not impossible, though receptaculitids would then be perhaps the only group other than grasses to have evolved a basal meristem.

In 1972, Zhuravleva and Myagkova assigned receptaculitids to an association with other Palaeozoic sessile problematica such as Archaeocyatha in a new extinct kingdom Archaeata unrelated to both plants and animals (Rowland, 2001). Archaeocyaths were cup-shaped Cambrian organisms that are now almost universally agreed to be sponges of some form. The concept of Archaeata never gained much recognition outside Russia, though it must be admitted that at least part of this may have been due to the inaccessibility of Russian publications in the West.

The Cyclocrinales are another group of Palaeozoic "algae" found from the Middle Cambrian to the Lower Devonian (Nitecki et al., 2004). Cyclocrinales are superficially similar to receptaculitids, with a similar basic body plan (image of Cyclocrinites from Dry Dredgers. They differ in having a less organised nucleus, generally lacking a lacuna, and branching laterals that come off the axis in certain areas rather than over the entire length as in receptaculitids. Cyclocrinales are more easily accepted as related to Dasycladales, and most authors appear to have done just that.


Gould, S. J., & M. Katz. 1975. Disruption of ideal geometry in the growth of receptaculitids: a natural experiment in theoretical morphology. Paleobiology 1: 1-20.

Nitecki, M. H., H. Mutvei & D. V. Nitecki. 1999. Receptaculitids: A phylogenetic debate on a problematic fossil taxon. Springer.

Nitecki, M. H., B. D. Webby, N. Spjeldnaes & Zhen Y.-Y. 2004. Receptaculitids and algae. In The Great Ordovician Biodiversification Event (B. D. Webby, F. Paris, M. L. Droser & I. G. Percival, eds.) Columbia University Press.

Rowland, S. M. 2001. Archaeocyaths - a history of phylogenetic interpretation. Journal of Paleontology 75 (6): 1065-1078.

Interesting Animals Viral Chain Letter... I mean, Meme

I've had this one passed on to me by Julia.

An interesting animal I've had

My misfortune with cats has become something of a running black joke in the family - I've had two hit by cars and two disappear (one of them only a few months after I'd spent $1400 getting her brought back to life after being hit by a car). My most recent cat did technically outlive me - when I left New Zealand, I sent him to live at my parent's. Unfortunately, that rather elderly cat (I had inherited him from someone else who had gone overseas) took to peeing around the house, and after my mother injured her back slipping on one of the puddles, my father took the cat outside and shot him. At the moment my partner and I are catless, but we do have a year old retriever/bull terrier cross dog by the name of Sammy, also known as Master of Destruction, He of the Inescapable Tongue, and Digger-up and Devourer of Unspeakable Things. Sammy has been known to eat wood.

An Interesting Animal I Ate

There is very little that I won't try at least once, but outside of crustaceans and molluscs, there are surprisingly few tasty invertebrates. The only thing that I've found almost completely inedible were silkworms (they taste exactly like mushrooms picked after they've become too old and gone to spore), which were sold in copious amounts from street-stands in Korea. I have tried witchetty grubs, which have a very rich taste something like butter and something like snot. Jack says they used to catch locusts in the season in Thailand and eat them fried, but I've not yet had the pleasure.

One thing I haven't yet tried - a number of years ago the Department of Conservation tent at the local Field Days was selling pies made from possum, but they were all gone by the time my sister and I got there.

An Interesting Animal in a Museum

I already mentioned the Auckland Museum moa earlier this week, which despite its vast inaccuracies is an old familiar. For a great many years, visitors coming into the foyer of Auckland Museum were greeted by "Rajah". Rajah had been resident in Auckland Zoo in the 1930s, but increasingly erratic behaviour (in a time when zoo elephants were expected to be available to be ridden by visitors) lead to his being regarded as a danger to public safety and put down, after which he was mounted and put on display at the museum. By the time the museum was refurbished about ten years ago, long years of display had taken their toll on Rajah, who was beginning to look decidedly tattered and moth-eaten, and the decision was made to take him off display (it may have also been a factor that Rajah had a decidedly colonial air, and was associated with an outdated mindset that the museum was trying to escape the taint of). He was moved into storage, but the size of the mount was such that the movers ended up sawing of his legs in order to fit him onto the truck (seven months to prepare the mount, a matter of minutes to destroy it). I was an occassional volunteer in the museum at the time, and there was a story circulating that the sight of an elephant travelling down the road on the back of a truck had severely disconcerted a passing drunk in Newmarket.

Rajah has since been somewhat restored, and has been returned to the Auckland Museum as part of a display on the history of children's icons in the country. If you look closely at the photo on the museum's website, you can still see the scars of past indignities in the seams were his legs had to be sewn back on.

An interesting thing I did with or to an animal

I have been thrown by a bull once in my life. When my parents first moved from dairy to beef, the first time I helped in taking the bulls into the stockyards I was not yet used to working with these animals that were so much bigger than the cows I was used to. When one of them turned and tried to head back in the direction he'd come from, my nervousness rather compromised my attempts to shoo him in the direction he was supposed to go. The bull made a dash for it with me standing in the gateway, picked me up with the dish of his head and tossed me onto the fence. I rolled off the fence and came away completely unharmed. For the record, I am now more aware that it is spectacularly easy you get a bull to do what you want - you just need to shout louder than they do.

An Interesting Animal in its Natural Habitat

Pretty much all of them, I'd say. I have rather fond memories of the first time I found a scorpion, though.

I suppose I should pass this on. Okay, Kevin, Aydin, Bug Girl, she's all yours.

Larry Moran on What Evolution Is

This was written some months ago, but I just found it and I think it's worth highlighting. Larry Moran of Sandwalk posted an essay in January on the definition of evolution. The importance of definitions in science almost can't be overstated - far too much ink has been wasted on arguments between people who didn't realise that they were using a different definition.

Linking past the language barrier

I just found through eXTReMe Tracking that I've been linked to by Avtor Franc at MIKROB(io)LOG, and I'd just like to say thank you for the link. Unfortunately, I can't comment on Avtor's blog because I'm afraid I can't read the language it's written in. I think it's an Eastern European language - if anyone out there can identify what it is, I'd appreciate the help.

Which brings me to comment on another thing - this is a non-English blog that has no apparent qualms about linking to sites in English. Many if not most non-English speakers seem to have no issues with the idea of at least attempting other languages, and I sometimes just get embarressed by the arrogance of English speakers in automatically writing off material in other languages. In the name of my race, I bow down to those who are more willing to leave their comfort zone.

Taxon of the Week: Leg or Breast?

This week's highlight taxon is one that is very familiar to me as a New Zealander, except it's not really. I've heard of these creatures since I was a little lad, and representations of them have been almost everywhere I've gone. I've never actually seen one. I don't know anyone who's every seen one. Probably no-one has seen one for hundreds of years, in fact. The Dinornithiformes are but a memory these days, long since converted into quarter-pack meals for Polynesian settlers. Ka ngaro i te ngaro a te moa - lost as the moa is lost.

The taxonomy of moa is complicated, but at present there are eleven species recognised as valid*. The order was unique to New Zealand - the "Australian" Dinornis queenslandiae De Vis, 1884, was based on a partial femur in the Queensland Museum, but this bone is now believed to have come from New Zealand and is assigned to Pachyornis elephantopus. In the past, Dinornithiformes has been divided into two families - the lightly built, more cursorial genus Dinornis in its own family and the other smaller and/or more heavily built genera in the Emeidae, but phylogenetic analysis has shown that Dinornis is nested within the Emeidae (Worthy & Holdaway, 2002).

*Eleven species were recognised in Worthy & Holdaway (2002), the most recent major review of Dinornithiformes. Bunce et al. (2003) reduced the number of species of Dinornis from three to two (see below), but Baker et al. (2005) increased the number of species of Megalapteryx from one to two.

The photo at the top of the page (from Wikipedia) shows the reconstructed Dinornis in the Auckland Museum. This specimen has been around for some time - it was built in 1913, though when the Natural History section of the museum was rebuilt it lost the tussock-land diorama it had previously inhabited (if I recall correctly) and moved into a glass case. The Auckland Museum moa stands about three metres tall, and modern interpretations would, unfortunately, label this a severely inaccurate reconstruction. It has been mounted in an unnaturally elevated stance, and should have been much more low-slung. A more realistic reconstruction was shown on a recent stamp issue, shown below (from New Zealand Birds):

Such a lowered reconstruction significantly lowers the height, but we're still looking at about two metres for the tallest Dinornis specimens. A moa of this size may have wighed over 150 kg (Worthy & Holdaway, 2002). Other species were smaller - the smallest was Megalapteryx didinus at probably about 40 kg. The super-heavy Pachyornis elephantopus was considerably shorter than large Dinornis, but may have weighed about the same amount. The image below comes from Nature, and shows three moa species against a 1.8 metre tall human. From left to right, the moas are a female Dinornis novaezealandiae, Megalapteryx didinus and Pachyornis elephantopus.

Despite their extinction prior to European settlement in New Zealand, a surprising amount of molecular data has been gleaned from ancient DNA studies of moa. Among other things, said molecular analyses have demonstrated that Dinornis displayed the highest degree of size dimorphism known from any bird (Bunce et al., 2003). Previously Dinornis had been divided into three species on the basis of size. Bunce et al. tested DNA from Dinornis remains for female-specific markers (birds differ from mammals in that it is the female that possesses different sex chromosomes [ZW], while the male has identical sex chromosomes [ZZ]). They found that all specimens that had been assigned to the smaller 'species' Dinornis struthoides were male, while all specimens of the larger 'species' D. novaezealandiae and D. giganteus were female. Molecular phylogenetic analysis also showed that these specimens were intermingled, with the major divide in the genus being not by size but by geography - the North Island and South Island populations (both containing representatives from all three 'species') were distinct, and were recognised as the separate (but morphologically indistinguishable) species Dinornis novaezealandiae (North Island) and D. robustus (South Island). While females showed a great deal of variation in size, the largest females would have been about 280% of the weight and 150% of the height of the largest males.

There is very little reliable information on the life habits of moa. By the time of European settlement, it had been long enough since the extinction of the moa that records of it in Maori oral tradition were seemingly few and far between, and those that were present had become significantly mythologised. Early researchers such as Owen and Haast interpreted moa as birds of open country, comparing them to modern ostriches and emus. However, the extensive New Zealand grasslands and fernlands these authors pointed to hadn't existed prior to human settlement, so moa were undoubtedly forest birds, foragers rather than grazers as also shown by preserved gizzard contents. Dinornis and Pachyornis seem to have had more fibrous diets with gizzards containing twigs and fibrous plants such as Phormium (the New Zealand flax) while Emeus and Euryapteryx with less robust bills had more selective diets of fruit and leaves. Interestingly, a well-preserved specimen of Euryapteryx geranoides showed a massive intrathoracic loop in the trachea, 1.2 metres long. In other birds such loops are associated with the ability to make loud, far-carrying calls, so moa (or at least Euryapteryx) would have been quite vocal birds in life.


Baker, A. J., L. J. Huynen, O. Haddrath, C. D. Millar & D. M. Lambert. 2005. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas of New Zealand. Proceedings of the National Academy of Sciences of the USA 102(23): 8257-8262.

Bunce, M., T. H. Worthy, T. Ford, W. Hoppitt, E. Willerslev, A. Drummond & A. Cooper. 2003. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425: 172-175.

Worthy, T. H., & R. N. Holdaway. 2001. The Lost World of the Moa: Prehistoric life of New Zealand. Indiana University Press: Bloomington (Indiana).

More little tubes - not just tons but tonnes

At the end of my previous post on tubular problematica, I said that I was leaving the subject while I still had my dignity. But then I remembered that I have no dignity. Besides, I remembered a couple more that I really wanted to look at. Neil from Microecos suggested that "Tubular Problematica" was a good name for a band. I beg to differ - a much better one would be "The Coleolus Effect".

Coleolidae: Coleolus and related taxa are found from the latest Proterozoic (McMenamin, 1985) to the early Carboniferous (Yochelson, 1999). As you can see in the picture above (from Yale University), they are small tapering tubes. They were most likely sessile in life with most of the tube projecting above the surface of the sediment (Yochelson & Hlavin, 1985).

Despite their long stratigraphic range and despite seeming to be reasonably common, the affinities of Coleolidae are completely unknown. Yochelson & Goodison (1999) noted that, "The literature on ancient "worm tubes" is scattered and scant, specimens are uncommon, and even a well-preserved one has few diagnostic characters and virtually no aesthetic interest" (ouch!) They have often been compared to Scaphopoda (tusk shells), a recent class of infaunal molluscs with superficially similar tubular shells, and more than one member of the Coleolidae has been initially identified as a scaphopod (Yochelson, 1999; Yochelson & Goodison, 1999). However, the shell structure is inconsistent with a mollusc, and the single known specimen with an intact tip shows that the apex was closed, unlike scaphopods which are open at both ends (Yochelson & Goodison, 1999). Yochelson & Hlavin (1985) considered Coleolus to be an annelid tube, but by 1999 Yochelson was admitting that "Except for formation of a calcareous tube, there is no basis for assignment of the family to Annelida".

Anabaritidae: I've saved the best for last, I can assure you. Anabaritids (shown in a picture from Palaeos) are known from the latest Proterozoic to the earliest Cambrian, and like Cloudina were one of the earliest animals to develop a skeleton (Kouchinsky & Bengtson, 2002). What's really cool about them, though, is what's shown in the cross-section (a) above the side view (b) - anabaritids had triradial symmetry. Triradial symmetry is exceedingly rare in modern taxa, but was found in a small assortment of Ediacaran and Cambrian organisms that have been suggested on this basis to form a grouping known as the Trilobozoa (Fedonkin, 1985). The affinities of the Trilobozoa are uncertain, but most authors interpret them as coelenterate-grade. Most interestingly, Ivantsov & Fedonkin (2002) suggested that the Conulata might have a trilobozoan ancestry. The Conulata (typified by Conularia) were a class of sessile problematica that survived until the Triassic, which would represent a significant increase in time-span for the Trilobozoa. Conularia has a four-fold symmetry, which has led most authors to interpret it as related to the modern Scyophozoa (jellyfish), but the Ediacaran Vendoconularia has a six-fold symmetry which Ivantsov & Fedonkin (2002) compared to the three-fold symmetry of Trilobozoa.

Tribrachidium heraldicum, another member of the Trilobozoa (from

Reconstruction of the possible live appearance of Conularia (from Dry Dredgers).

An alternative to the Trilobozoa interpretation of Anabaritidae was revived by Kouchinsky & Bengtson (2002), who interpreted anabaritids as polychaete worm tubes. This was based on the presence in anabaritids of a chevron-like wall structure, previously unknown except in serpulid polychaetes. However, there is a significant gap in time between the Cambrian anabaritids and the earliest definite serpulids in the Mesozoic. Also, many anabaritid shells preserve internal tooth-like projections that suggest that whatever animal lived in them was fixed in place - if it had been able to move back and forth in the manner of a serpulid worm, it would have probably filleted itself.


Fedonkin, M. A. 1985. Precambrian metazoans: the problems of preservation, systematics and evolution. Philosophical Transactions of the Royal Society of London Series B - Biological Sciences 311: 27-45.

Ivantsov, A. Y., & M. A. Fedonkin. 2002. Conulariid-like fossil from the Vendian of Russia: A metazoan clade across the Proterozoic/Palaeozoic boundary. Palaeontology 45 (6): 1219-1229.

Kouchinsky, A., & S. Bengtson. 2002. The tube wall of Cambrian anabaritids. Acta Palaeontologica Polonica 47 (3): 431-444.

McMenamin, M. A. S. 1985. Basal Cambrian small shelly fossils from the La Ciénega Formation, northwestern Sonora, Mexico. Journal of Paleontology 59 (6): 1414-1425.

Yochelson, E. L. 1999. Rejection of Carboniferous Quasidentalium Shimansky, 1974, from the phylum Mollusca. Journal of Paleontology 73 (1): 63-65.

Yochelson, E. L., & R. Goodison. 1999. Devonian Dentalium martini Whitfield, 1882, is not a mollusk but a worm. Journal of Paleontology 73 (4): 634-640.

Yochelson, E. L., & W. J. Hlavin, 1985. Coleolus curvatus Kindle ("Vermes") from the Cleveland Member of the Ohio Shale, Late Devonian (Famennian) of Ohio. Journal of Paleontology 59 (5): 1298-1304.

Best on the Web?

TheScientist (the lack of a space there seems to be deliberate, I'm afraid) is asking for votes for the best biology blogs out there. Below are the five that I voted for in no particular order - they've all been mentioned here before, I believe, and they're all in the blogroll down the side (along with many other worthwhile sites), but I'm always happy to recognise their superiority:

Laelaps: Brian Switek mostly writes on vertebrate palaeontology, and seems to go from strength to strength. Check out his recent posts on horse evolution and Thylacoleo. He's so good he makes the rest of us just feel inadequate in comparison. I don't know whether to bow down in front of him or kick him in the teeth.

The Ethical Palaeontologist: Julia's posts are always worthwhile, and she gets extra credit for knowing how to spell "palaeontologist".

Living the Scientific Life (Scientist, Interrupted): GrrlScientist's main subject is ornithology, but she has many other interests - I especially liked here recent post on breeding trout from salmon. I would also like to applaud the great courage she's shown in writing regularly on mental illness (including her own) and living with mental illness. While I have not been affected personally by the issues she discusses (touch wood), I have had to deal with the aftershocks as they affected people close to me, and I wish GrrlScientist every bit of luck as she continues to set an example for us all.

The Other 95%: Kevin Z, my fellow aspondylologist (spot the neologism). Just be careful with that guitar.

Tetrapod Zoology: Darren Naish works on British dinosaurs, and writes on everything four-legged with the crunchy bits on the inside.

Three honourary mentions that I'd like to make:

Snail's Tales: Aydin has a passion for gastropods that must be recognised.

The Lord Geekington: Cameron is another undergrad producing fine work.

Bug Girl's Blog: Another excellent contribution to aspondylology. And I realise as I write this that I have omitted to add a link to her on the right. I'll have to correct that at once. I'm sorry, Bug Girl! Please don't send your attack Hemiptera after me!

You know, I'm not that happy that three of the five best sites out there are by vertebrate palaeontologists - I am a full subscriber to the rule that invertebrate workers must be resentful about the disproportionate amount of attention that vertebrates receive - but I have no choice but to recognise excellence when present. In the meantime, all you entomologists, helminthologists, botanists, protistologists, etc. out there - show yourselves!

Addendum: Arguably more worthy of comment than the shortage of non-vertebrate blogs, Sheril Kirshenbaum at The Intersection and GrrlScientist have both asked why the blog-lists are so biased towards male rather than female bloggers. All I can say in reply is "beats me". A glance at my own blogroll shows more links to blogs by men than women, though I don't believe I've had any conscious bias in selecting one rather than the other. This seems particularly odd for biology - while there are probably still more male professors, my impression as an undergraduate was that, if anything, there are more female biology students arriving these days than male students, and I see no real signs of female students thinning out at the postgraduate level either. Why is scientific blogging seemingly less appealing for women? Or are there plenty of scientific blogs by women out there that I haven't had the fortune to come across?

Taxon of the Week: Apodemus (no Pliers)

The rodents are the most numerous of the traditional mammalian orders by a significant margin, making up about 40% of recent mammal species. Within that species diversity, over half belong to the Muroidea, the rats and mice. You thought a mouse was just a mouse and a rat was a slightly bigger mouse? Well, no. There are literally hundreds of species of mouse - about 1,300 to be more precise (if not necessarily accurate). And safe in the knowledge that the thought of so many rats is going to give some of you raving heebers, allow me to introduce today's Taxon of the Week - the mouse genus Apodemus, the field mice (the image above is the wood mouse Apodemus sylvaticus, and comes from Wikipedia).

Apodemus contains about twenty species distributed in broadleaf forests throughout the Palaearctic, and are the commonest rodents in said forests (Serizawa et al., 2000). Based on molecular clock studies, the genus has been estimated to have originated about eight million years ago, which is consistent with the presence of the fossil species Apodemus primaevus in Europe at the end of the Miocene (about seven million years ago - Michaux et al., 2002). Apodemus primaevus is believed to have been ancestral to the modern Balkan and Middle Eastern species A. mystacinus, a distinctive species that has been suggested to belong to its own genus, Karstomys. The majority of modern European Apodemus species were a later immigration, with their ancestor (A. dominans) arriving at the end of the Pliocene. Serizawa et al. (2000) also inferred that the various Asian species had split from each other earlier than the European species, and suggested that this may have reflected the different histories of broadleaf forest cover during the Pleistocene ice ages. Some broadleaf cover survived in Asia during the ice ages, allowing for the survival of wood mice over that time, while Europe became a broadleaf no-go zone.

Oh yes, and species of Apodemus possess supernumerary chromosomes, like the ones I mentioned for Leiopelma frogs. Interestingly, Zima et al. (2003) found that there was a relationship between number of B chromosomes and body size in male Apodemus flavicollis, suggesting that males with more B chromosomes had a selective advantage, probably in terms of their ability to survive winters. Some individuals may show variation in the number of B chromosomes in individual cells, but Kartavtseva (1999) found that such mosaic individuals dropped in abundance in autumn relative to individuals with constant chromosome numbers, suggesting that for some reason they were less hardy.


Kartavtseva, I. V. 1999. Seasonal observations on supernumerary chromosomes, mosaicism, and dynamics in two populations of the eastern-Asian wood mouse Apodemus peninsulae (Rodentia) from Primorskii Krai. Genetika 35: 949-955 (transl. Russian Journal of Genetics).

Michaux, J. R., P. Chevret, M.-G. Filippucci & M. Macholan. 2002. Phylogeny of the genus Apodemus with a special emphasis on the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA. Molecular Phylogenetics and Evolution 23 (2): 123-136.

Serizawa, K., H. Suzuki & K. Tsuchiya. 2000. A phylogenetic view on species radiation in Apodemus inferred from variation of nuclear and mitochondrial genes. Biochemical Genetics 38 (1-2): 27-40.

Zima, J., J. Piálek & M. Macholán. 2003. Possible heterotic effects of B chromosomes on body mass in a population of Apodemus flavicollis. Canadian Journal of Zoology 81 (8): 1312-1317.

The Boneyard is Available for Digging!

The newest edition of the Boneyard, a roundup of palaeontological posts, is up at The Ethical Palaeontologist (note the spelling). Julia's done an excellent job of putting this week's edition together, and I recommend a look (then take a look around the rest of Julia's site). She's even included the tubular fossil post I did a couple of days ago that I hadn't even submitted*. Enjoy!

*Damn, now I'm going to have to think of something else for the next one.

Tons of Little Tubes

It is a widely-known secret that the fossil record is heavily biased towards hard parts of organisms. Soft body parts generally rot away before they can be fossilised, and usually only a shell, a bone, a piece of wood or something else reasonably crunchy has a chance of lasting long enough to be preserved. This is why sites that do preserve soft body parts, such as the Burgess Shale, Mazon Creek or Liaoning, cause such a sensation and are so significant, because the remains they present us with are so rare.

But for the vast majority of cases, we must make do with the occassions when the fossil record is willing to throw us a bone (ha bloody ha). And while palaeontologists are sometimes able to claw a simply amazing amount of detail out of just the hard parts of an organism, sometimes the information available is frustratingly incomplete. What can you say if all you have is a tube?

Take a look at the pictures at the top of the post. They look to show pretty similar organisms - in fact, if you know how to tell one from the other, you're more than a few steps ahead of me. Yet you've probably guessed already that they don't*. These are not examples of the same family - they don't even belong to the same phylum. The shells on the left (from here) belong to molluscs (gastropods) of the family Vermetidae, while those on the right (from here) are annelid worms of the family Serpulidae. Both have adopted a fairly simple tubular habit, with little in the way of extravagant ornamentation.

*After all, why would I have brought in all the rhetoric if they did?

Were you to find a fossil example of either one of these, however, all would not be lost. Molluscs and tube-worms lay down their shells in different ways, so if you knew what to look for you could tell them apart. Once you had identified your fossil as one of the above, then you could infer a lot more about what the soft parts of the animal may have looked like. Both Vermetidae and Serpulidae are around today, and the soft anatomy of the living species has been well-studied. But there are other tubular shells in the fossil record that don't have modern representatives. One might be tempted (and many have done so in the past) to compare them with modern tubular shells in molluscs and/or annelids. But mineralised skeletal structures have evolved independently at least in foraminiferans, cnidarians (multiple times), annelids, molluscs, bryozoans, brachiopods, echinoderms and vertebrates - it is quite believable that they may have evolved in other clades as well. So for now, most of these tubular fossils get relegated to the howling wasteland of incertae sedis (Malinky et al., 2004).

Hyolitha: Hyoliths (the name means "tongue stones") are conical shells found from the Early Cambrian to the Mid Permian. The illustration (from the Smithsonian) shows Haplophrentis, a member of the hyolith order Hyolithida, which possessed a ventral projecting ligula and two projecting side-arms called helens (structures unique to hyolithids that, in the absence of an appropriate descriptive term, Charles Doolittle Walcott apparently named after his daughter). Members of the other order, Orthothecida, lack these structures. Both orders have an operculum closing off the main shell - retractable in Orthothecida but external in Hyolithida. The function of the helens is rather uncertain - muscle scars close to them suggest that they were quite mobile and might have been used to move the animal across the sea floor (Mus & Bergström, 2005), but this seems in contradiction to their delicate structure. They may have been used to hold the animal upright on soft sea-bed. They have also been suggested as supports for an external tissue system for feeding, respiration or other nefarious purposes.

As for the affinities of hyoliths, most authors have associated them with molluscs, due to similarities in shell structure and composition. One genus of hyolith, Gompholites, preserves serial muscle scars that might indicate a segmented structure that would be inconsistent with molluscan affinities (though at least some molluscs possess/ed serial structures - viz. Neopilinida and Acaenoplax), but other hyoliths do not show such an arrangement and the features seen in Gompholites are generally interpreted as representing successive scars left by chances in the muscle attachment site as the animal grew (Mus & Bergström, 2005). Some remains of hyoliths show signs of a looped gut similar to that of the modern Sipuncula (peanut worms), and some authors have suggested a relationship of hyoliths to the latter (Runnegar et al., 1975). However, more basal fossil sipunculans possess a straighter gut (Huang et al., 2004).

Tentaculitoidea (Cricoconarida): Tentaculitoids are known from possibly the Ordovician (Malinky et al., 2004 - the Ordovician fossils are not definitely tentaculitoids) to the earliest Permian (Niko, 2000 - image from here). The type genus, Tentaculites, was originally identified (somewhat presciently - see later) as spines of brachiopods, and the name refers to the belief that they were appendages of crinoids (Schlotheim, 1820). Tentaculitoids are narrow conical fossils that are radially symmetrically along the long axis. There are two major orders - the Tentaculitida had heavier shells and were probably benthic, while the thinner-shelled Dacryoconarida may have been planktonic (there are also a number of smaller orders that have been counted as tentaculitoids, but authors have differed on these). Tentaculites has an annulated structure (as shown in the photo), and once it was recognised as an independent animal it was interpreted as an annelid due to these. Other tentaculitoids do not all show these annulations, and authors have also suggested a mollusc affinity (Yochelson's [1964] review of a book on tentaculitoids is extremely telling in its reference to the "molluscan-annelid question", seemingly overlooking that there might have been other alternatives). The microstructure of tentaculitoid shells is very different from molluscs, and a similarity and potential affinity with Brachiozoa has been suggested (Herringshaw et al., 2007), though doubt has apparently been cast on whether a phoronid-style lophophorate feeding system is compatible with a planktonic life-style.

Cloudina: Cloudina has the distinction of being one of the earliest shelled animals to have ever existed, dating from the Ediacaran (drawing from Palaeos). It is constructed from a series of internested cup-shaped tubes. The affinities of Cloudina are completely obscure. In a seemingly not-yet-published manuscript available online, Miller compares Cloudina to annelid tubes, but with quite a bit of uncertainty.

Hyolithelminthes: Hyolithelminthes are elongate phosphatic tubes from the early Cambrian (image from Clausen & Álvaro, 2006). They are part of a sizable collection of phosphatic taxa from that time, though over time these forms mostly became extinct and were replaced by taxa with carbonate skeletons - today, relatively few taxa (such as linguloid brachiopods) possess skeletons of calcium phosphate. For a long time it was believed that fossils such as Mobergella represented opercula of hyolithelminthes, but these are now regarded as independent animals (Bengtson, 1992). The affinities of hyolithelminthes are unknown - a recent paper apparently aligns at least one hyolithelminth genus with cnidarians, but I haven't read the paper in question (Vinn, 2006).

Though this has turned into something of a major post, I could still cover many more examples of tubular problematica. Cornulitids, sphenothallids, paiutiids - the list goes on and on. But in the interests of sanity (and not wasting my entire weekend), I'll get out while I still have my dignity.


Bengtson, S. 1992. Proterozoic and earliest Cambrian skeletal metazoans. In The Proterozoic Biosphere: A multidisciplinary study (J. W. Schopf & C. Klein, eds.) Cambridge University Press.

Clausen, S., & J. J. Álvaro. 2006. Skeletonized microfossils from the Lower–Middle Cambrian transition of the Cantabrian Mountains, northern Spain. Acta Palaeontologica Polonica 51 (2): 223-238.

Herringshaw, L. G., A. T. Thomas & M. P. Smith. 2007. Systematics, shell structure and affinities of the Palaeozoic problematicum Cornulites. Zoological Journal of the Linnean Society 150 (4): 681-699.

Huang, D.-Y., J.-Y. Chen, J. Vannier & J. I. Saiz Salinas. 2004. Early Cambrian sipunculan worms from southwest China. Proceedings of the Royal Society of London Series B - Biological Sciences 271: 1671-1676.

Malinky, J. M., M. A. Wilson, L. E. Holmer & H. Lardeux. 2004. Tube-shaped incertae sedis. In The Great Ordovician Biodiversification Event (B. D. Webby, F. Paris, M. L. Droser & I. G. Percival, eds.) pp. 214-222. Columbia University Press.

Mus, M. M., & J. Bergström. 2005. The morphology of hyolithids and its functional implications. Palaeontology 48 (6): 1139-1167.

Niko, S. 2000. Youngest record of tentaculitoids: Hidagaienites new genus from near the Carboniferous-Permian boundary in central Japan. Journal of Paleontology 74 (3): 381-385.

Runnegar, B., J. Pojeta, N. J. Morris, J. D. Taylor, M. E. Taylor, & G. McClung. 1975. Biology of the Hyolitha. Lethaia 8: 181–191.

Schlotheim, E. F. von 1820. Die Petrefactenkunde auf ihrem jetzigen Standpunkte durch die Beschreibung seiner Sammlung versteinerter und fossiler Überreste des Thier- und Pflanzenreichs der Vorwelt erläutert. Gotha. 15 pls.

Vinn, O. 2006. Possible cnidarian affinities of Torellella (Hyolithelminthes, Upper Cambrian, Estonia). Paläontologische Zeitschrift 80 (4): 383-388.

Yochelson, E. L. 1964. Book review: The Tentaculites of Bohemia: Their morphology, taxonomy, phylogeny and biostratigraphy. Journal of Paleontology 39 (3): 509-510.


I need to buy some phylogenetic analysis software to conduct analyses of morphological characters in Windows. At the moment, I think the main contenders are the old standard of PAUP* and the more recent TNT. Does anyone have any advice on how these two compare? Also, does anyone have a couple of good references for me to learn what all the analysis parameters (branch-addition, branch-swapping parameters, etc.) actually mean?

Taxon of the Week: So Many Arms

I haven't covered a fossil taxon for Taxon of the Week before, but that's exactly what I'm going to do today. Behold, therefore, the majesty of the Rhodocrinitidae! The photo here shows fossils of Rhodocrinites kirbyi and Cribanocrinus watersianus, both Rhodocrinitidae, and comes from the Smithsonian.

The Rhodocrinitidae are a family of the Camerata, a clade of crinoids restricted to the Palaeozoic. For those not in the know, crinoids (or "sea lilies") are a class of echinoderms, the phylum including such beasties as starfish and sea urchins, and like all echinoderms they have a skeleton of calcareous plates. The majority of fossil species were permanently attached to the sea-bed by a stalk, but the majority of recent species belong to a clade that has lost the stalk as adults and is free-living (actually, even stalkless forms start their lives attached to the substrate, but before they reach maturity they break off their stalk - Breimer, 1978a). Crinoids are filter-feeders, usually with large numbers of feathery arms that are used to sieve the surrounding water (the common name for the stalkless forms is "feather star"). Even the stalkless forms seemingly never move more than is strictly necessary to occupy the optimum position for filter-feeding - as commented by Breimer (1978b), "Seemingly, the stemless crinoids have only gained the vagile capacity of active movement in order to gain efficiency as sedentary animals".

The Camerata were characterised by the development of a calyx (the cup-shaped part of the body that the arms come off) with the skeletal plates rigidly sutured together. The tegmen (the upper covering of the central body - calyx below, tegmen above, if I understand correctly) forms a vaulted ceiling that conceals the mouth and the proximal parts of the ambulacra (the tube-foot-lined grooves that run down the arms and transport food particles to the mouth). The only external opening to the tegmen is the anus, which is usually raised on a tube (doubtless to carry food particles further from the mouth). Extra plates between the bases of the arms incorporated them into the calyx (Ubaghs, 1978b), though in later camerates these were reduced, freeing the arms (Ubaghs, 1978a). The Camerata are divided into two orders, Diplobathrida (including Rhodocrinitidae) and Monobathrida, distinguished by the number of rings of plates making up the calyx.

Rhodocrinitidae were around from the Middle Ordovician to the Lower Carboniferous. They were a heterogenous group encompassing a variety of forms (Eckert & Brett, 2001). The calyx was globular (Ubaghs, 1978), obconical or bowl-shaped (Eckert & Brett, 2001), and the arms could be uniserial or biserial (Eckert & Brett, 2001).

The largely immobile calyx and increased numbers of pinnules (side-branches of the arms) in camerates appear to be adaptations to a rheophilic lifestyle - living in high-current environments (Breimer, 1978c). Also as a probable adaptation to high currents, rhodocrinitids were attached to the substrate by coiling the end of the stalk around an anchoring object. This may have allowed for a less rigid attachment, allowing a certain degree of slippage around the anchor.

The Rhodocrinitidae were the only family of Diplobathrida to survive the Devonian, along with a number of families of Monobathrida. While the Rhodocrinitidae became extinct during the Carboniferous, the Monobathrida trickled along until the end of the Permian, which sounded the final death-knell for the camerates (Ubaghs, 1978a).


Breimer, A. 1978a. General morphology - recent crinoids. In Treatise on Invertebrate Paleontology pt. T. Echinodermata 2. Crinoidea (R. C. Moore & C. Teichert, eds.) vol. 1 pp. T9-T58. The Geological Society of America, Inc.: Boulder (Colorado), and The University of Kansas: Lawrence (Kansas).

Breimer, A. 1978b. Ecology of recent crinoids. In Treatise on Invertebrate Paleontology pt. T. Echinodermata 2. Crinoidea (R. C. Moore & C. Teichert, eds.) vol. 1 pp. T316-T330. The Geological Society of America, Inc.: Boulder (Colorado), and The University of Kansas: Lawrence (Kansas).

Breimer, A. 1978c. Paleoecology - Autecology. In Treatise on Invertebrate Paleontology pt. T. Echinodermata 2. Crinoidea (R. C. Moore & C. Teichert, eds.) vol. 1 pp. T331-T343. The Geological Society of America, Inc.: Boulder (Colorado), and The University of Kansas: Lawrence (Kansas).

Eckert, J. D., & C. E. Brett. 2001. Early Silurian (Llandovery) crinoids from the Lower Clinton Group, western New York State. Bulletins of American Paleontology 360: 1-88.

Ubaghs, G. 1978a. Evolution of camerate crinoids. In Treatise on Invertebrate Paleontology pt. T. Echinodermata 2. Crinoidea (R. C. Moore & C. Teichert, eds.) vol. 1 pp. T281-T292. The Geological Society of America, Inc.: Boulder (Colorado), and The University of Kansas: Lawrence (Kansas).

Ubaghs, G. 1978b. Camerata. In Treatise on Invertebrate Paleontology pt. T. Echinodermata 2. Crinoidea (R. C. Moore & C. Teichert, eds.) vol. 2 pp. T408-519. The Geological Society of America, Inc.: Boulder (Colorado), and The University of Kansas: Lawrence (Kansas).

The Week of the Microbe

Deep Sea News is having a Microbe Week, though as I've said before, we're not in a Microbe Week, we're in a Microbe Eternity. I heartily support this drive - the diversity of micro-organisms in the world is all too often overlooked. Environmental DNA suggests that probably less than 1% of the world's bacteria have been described.

And the introductory post linked to above contains a comment to really show just how ubiquitous micro-organisms are - "there are approximately 1 million bacteria and 10 million viruses in a milliliter of seawater. There are approximately 0.00000000000000000002 sperm whales per milliliter of seawater."

You have been told.

Is Any of this Garbage Fit to Print?

Coturnix at A Blog Around the Clock is taking submissions for a collection of science-blog posts to be published at the end of the year. Even though I've not been at this game for long and not written much of significance, I was considering putting in a submission. Before I do, I thought I'd ask you, my readers, if you thought I've written anything worth submitting? Is there anything that stood out for you from the general dross and drek? If anyone has any feedback, it'd be greatly appreciated.

Relict Frog Sex

At least one piece of genetics that almost everyone is familiar with is how our sex is determined - that women possess two X chromosomes while men produce an X and a Y chromosome. What may not be so familiar to most people is that this system is far from universal. Different animals exhibit a wide range of methods of sex determination, both genetic (like our own system) and environmental (such as temperature in crocodiles). In Hymenoptera (ants, bees and wasps) unfertilised eggs produce haploid males, while fertilised eggs produce diploid females. In birds, it is the females that possess two different forms of sex chromosomes (referred to as W and Z), while the male possesses two Z chromosomes. But perhaps the oddest little tale of sex determination (and one I only discovered recently) involves the strange relictual frog genus Leiopelma (the species Leiopelma archeyi is shown in a photo from the page of Dr. Bruce Waldman).

Leiopelma is a small genus of four living species of frog restricted to New Zealand (a further three species are known from sub-fossil remains - Bell et al., 1998). They represent a basal grade of frogs of which the only other member is the "tailed frog" Ascaphus truei from western North America (different studies disagree as to whether Leiopelma and Ascaphus form the sister clade to or are paraphyletic to all other living frogs - Green & Cannatella, 1993; Hay et al., 1995). Leiopelma and Ascaphus retain a number of primitive features that have been lost in other frogs, such nine vertebrae in front of the sacrum and tail-wagging muscles (though the 'tail' of male Ascaphus is actually the copulatory organ). Leiopelma also lack a tadpole stage in their life-cycle, hatching straight out into froglets.

The really remarkable thing about Leiopelma, though, is that of the four species living today, at least three have different methods of sex determination from each other. And within two of those species, there are even different populations that differ in their mode of sex determination!

The most primitive state is perhaps that shown by Leiopelma archeyi, in which most populations don't have distinguishable sex chromosomes. This is the condition in most amphibians, though it has been shown that even in taxa that don't have heteromorphic chromosomes, sex is still determined genetically (Hayes, 1998). However, a heteromorphic W sex chromosome has been recorded in one population of L. archeyi from Whareorino in the King Country (Green, 2002). In other features (including genetic features) the Whareorino L. archeyi are almost indistinguishable from Coromandel populations that lack the W chromosome.

The Whareorino Leiopelma archeyi are therefore more like L. pakeka in sex differentiation. Leiopelma pakeka also has a female-ZW/male-ZZ set-up (Green, 1988)*. There is only a single population of L. pakeka, restricted to Maud Island, which diesn't give much scope for variation.

*The species Leiopelma pakeka was recognised only recently (Bell et al., 1998). Previously it had been regarded as a population of the genetically distinct but morphologically almost identical L. hamiltoni, and its genetic structure was described under the latter name. Leiopelma hamiltoni proper is uber-rare, with a population of less than 300 individuals restricted to less than one hectare of habitat on Stephens Island, and does not seem to have yet been investigated for sex chromosomes.

The ultimate wierdness, however, comes when we look at Leiopelma hochstetteri. Most populations of L. hochstetteri have a single sex chromosome in females, while males lack a sex chromosome. This female-0W/male-00 system is unique - no other animal has it. Not one. In fact, it's so bizarre that not even all L. hochstetteri have it - females of the population on Great Barrier Island lack the lonely W chromosome, and like Coromandel L. archeyi this population does not have morphologically distinct sex chromosomes (Green, 1994). The Great Barrier population also lacks the non-sex-related supernumerary chromosomes (or "B" chromosomes) found in other populations (Green et al., 1993). B chromosomes are small, seemingly dispensable chromosomes that are found in a broad scattering of taxa. In species where they are found, numbers of B chromosomes can vary significantly within and between populations, probably because their lack of significant function means a lack of selective control on their propagation. This variation is also seen in L. hochstetteri, where up to 15 B chromosomes were found in individuals of five different populations. The variation in chromosomes between populations is shown below in a figure from Green (1994).

So how did all this come about? I am not aware of any other group of closely-related organisms showing this much variation in so few species. However, it is possible to imagine ZW chromosomes evolving through differentiation of morphologically indistinct sex-determining chromosomes, and this is what appears to have occurred in Leiopelma pakeka and Whareorino L. archeyi. Leiopelma hamiltoni appears to be more closely related to L. archeyi than L. pakeka (Bell et al., 1998), so it would be very interesting to know whether or not it has distinct sex chromosomes.

As for Leiopelma hochstetteri, the sister taxon to all other Leiopelma, phylogenetic analysis of chromosome characters shows that the Great Barrier population, without the extra W chromosome, is probably sister to all other populations. Green et al. (1993) suggest that the 0W/00 system could evolved from a ZW/ZZ system. Either the Z chromosome may have been lost, or (as the authors of the latter study think more likely) it could have been duplicated, giving a ZZW/ZZ pattern that would be karyotypically indistinguishable from 0W/00.


Bell, B. D., C. H. Daugherty & J. M. Hay. 1998. Leiopelma pakeka, n. sp. (Anura: Leiopelmatidae), a cryptic species of frog from Maud Island, New Zealand, and a reassessment of the conservation status of L. hamiltoni from Stephens Island. Journal of the Royal Society of New Zealand 28 (1): 39-54.

Green, D. M. 1988. Heteromorphic sex chromosomes in the rare and primitive frog Leiopelma hamiltoni from New Zealand. Journal of Heredity 79 (3): 165-169.

Green, D. M. 1994. Genetic and cytogenetic diversity in Hochstetter's frog, Leiopelma hochstetteri, and its importance for conservation management. New Zealand Journal of Zoology 21: 417-424.

Green, D. M. 2002. Chromosome polymorphism in Archey's frog (Leiopelma archeyi) from New Zealand. Copeia 2002 (1): 204-207.

Green, D. M., & D. C. Cannatella. 1993. Phylogenetic significance of the amphicoelous frogs, Ascaphidae and Leiopelmatidae. Ecol. Ethol. Evol. 5: 233-245.

Green, D. M., C. W. Zeyl & T. F. Sharbel. 1993. The evolution of hypervariable sex and supernumerary (B) chromosomes in the relict New Zealand frog, Leiopelma hochstetteri. Journal of Evolutionary Biology 6 (3): 417-441.

Hay, J. M., I. Ruvinsky, S. B. Hedges & L. R. Maxson. 1995. Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. Molecular Biology and Evolution 12 (5): 928-937.

Hayes, T. B. 1998. Sex determination and primary sex differentiation in amphibians: Genetic and developmental mechanisms. Journal of Experimental Zoology 281 (5): 373-399.

Mitochondria: Much Stranger than You Think

"Any view of things that is not strange is false" - Neil Gaiman, The Sandman.

Moselio Schaechter has a post at Small Things Considered on fission and fusion of mitochondria that's well worth a look - it certainly managed to teach me a lot in a short time. I didn't know how much the mechanics of division differed between mitochondria of different eukaryotes. I didn't even know there was such a thing as mitochondrial fusion. Enjoy!

Circus of the Spineless

Circus of the Spineless, the monthly round-up of notable recent blog-posts on non-craniate animals, is up at Naturalist Notebook. Even if you had a look when this first went up a couple of days ago, look again - a bunch more have been put up.

Taxon of the Week: Pick from a wide range of pathogens

Pick up almost any popular palaeontology book, and you'll be introduced to various 'ages' of life on this planet. We're told that we are currently in the Age of Mammals. The Mesozoic is dubbed the Age of Reptiles. The Devonian was the Age of Fishes, and so on and so forth. The names of all these ages are supposed to reflect the dominant life-form at the time, the pinnacle of evolutionary achievement. They are, of course, complete hooey. Pretty much ever since life even came into existence on this planet, there has been one group of life-forms whose hegemony has never been broken, and almost certainly never will be. There is only one true age - the Age of Bacteria. And with that piece of flowery writing, let me introduce today's Taxon of the Week: the bacterial suborder Corynebacterineae.

Bacterial taxonomy is a particularly murky subject. Though higher classificatory systems have been provided in many cases, very few of them get used in practice. At present, this is probably wise. There are relatively few well-defined clades of prokaryotes, and bacterial phylogeny is almost entirely genetics-based. Some clades of bacteria can be identified by their production of unique biochemicals, such as chlorophyll in Cyanobacteria. In the case of Corynebacterineae, the clade including such well-known bacteria as Corynebacterium and Mycobacterium, the distinguishing feature seems to be their production of mycolic acid (Portevin et al., 2004), the mild and unassuming molecule shown at the top of the page (image from Wikipedia).

Corynebacterineae are Gram-positive*, non-sporulating bacteria that are well-known as pathogens, though this overlooks the wide variety of non-pathogenic species in the clade (the image above shows Corynebacterium diphtheriae, the causative agent for diphtheria, and comes from MicrobeWiki). The clade is diverse in appearance - Corynebacterium and Mycobacterium are rod-shaped, Rhodococcus are spherical, while Nocardia form aerial hyphae. Corynebacterium and Mycobacterium, at least, reproduce by what is known as snapping division - the individual cell increases in length until it divides into two daughter cells which end up at a sharp angle to each other, as shown below in an image from (though the actual prokaryote shown is not a member of Corynebacterineae, but the thermophilic archaeon Thermoproteus). This gives a distinct angular appearance to the resulting colonies, that has been referred to as "Chinese calligraphy".

*Technically, the structure of the cell envelope (see further on) means that Gram-staining doesn't really work as it should on Corynebacterineae, as they are impermeable to the acid used to wash out the Gram stain - hence they are referred to as acid-fast bacteria. Corynebacterineae are still phylogenetically Gram-positive bacteria.

Now I bet you've been hankering to know just what the significance of the mycolic acid is. The mycolic acid binds to other molecules in the cell wall, and also produces a thick waxy membrane outside the cell wall with other lipids. This waxy membrane greatly reduces the permeability of the bacterium, and makes them highly resistant to penetration by antibiotics (among other things - Portevin et al., 2004). Inability to synthesise mycolates is fatal for Mycobacterium, but appears to be less of an issue for Corynebacterium species - indeed, at least one Corynebacterium, C. amycolatum, does not naturally produce mycolates (Tropis et al., 2005).


Portevin, D., C. de Sousa-D'Auria, C. Houssin, C. Grimaldi, M. Chami, M. Daffé & C. Guilhot. 2004. A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms. Proceedings of the National Academy of Sciences of the USA 101 (1): 314-319.

Tropis, M., X. Meniche, A. Wolf, H. Gebhardt, S. Strelkov, M. Chami, D. Schomburg, R. Krämer, S. Morbach & M. Daffé. 2005. The crucial role of trehalose and structurally related oligosaccharides in the biosynthesis and transfer of mycolic acids in Corynebacterineae. Journal of Biological Chemistry 280 (28): 26573-26585.