Sometimes, the history of people's misconceptions about organisms are nearly as interesting as the organisms themselves - not so much because of what it says about the organism itself, but what it says about us as people. One common pattern is the "pendulum swing" in conceptions about certain organisms. An originally negative over-simplification about a given organism ("wolves are savage human-killers that should be exterminated before they exterminate us"/"whales and dolphins are just fish and can be hunted as such") is replaced by a reactionary viewpoint which is more positive, but arguably just as erroneous an oversimplification ("wolves are completely harmless to humans, and would never attack somebody"/"whales and dolphins are super-intelligent, and, like, just filled with spiritual wisdom"). It is only as our attitudes mature, and the question becomes less politically charged, that opinions settle towards the generally more accurate but usually more complex middle ground.
Sexual cannibalism is one behaviour that has fallen victim to the human tendency to mythologise. Many people are aware of the idea that female spiders, mantids and other such carnivorous arthropods have a habit of eating the male during mating. Any feminist readers I have out there might be interested to consider how the popularity of this concept reflects our own attitudes on the relationship between the sexes (the female eating the male seems scandalous because, of course, we live in a society that tells us it should be the other way around). However, if you open a textbook you will probably be told that this story is generally not true. Bug Girl has recently corrected Isabella Rossellini on just this point*. For the most part, Bug Girl is right - sexual cannibalism is a fairly rare occurrence that usually only happens when things go wrong (for instance, if the male makes his move before properly placating the female). However, there is at least one species in which sexual cannibalism is an integral part of the mating process.
*Actually, speaking of societal attitudes, perhaps the most remarkable thing about the video Bug Girl has posted - other, of course, than the fact that Isabella Rossellini is making videos about arthropods in the first place - is the obvious cultural differences when it comes to talking about sex. The American interviewer with her giggling prudishness does not compare well to Rossellini's far more relaxed attitude.
That species is Latrodectus hasselti, the redback spider. The image at the top of the page (from here) shows two redbacks. The larger individual is a mature female, while the smaller white individual is a male. The genus Latrodectus has a wide distribution around the world, including the black widow (L. mactans) of North America (which does not regularly engage in sexual cannibalism), with most species having a well-deserved reputation for toxicity. The redback had done particularly well out of human civilisation - it is unclear where exactly in Australia it originated*, but it has since been spread throughout the continent, as well as establishing populations in other countries such as New Zealand and Japan. Latrodectus hasselti specialises in constructing its webs between hot, dry, facing surfaces, and humans are very good at building hot, dry, facing surfaces.
*Some people have suggested that the redback is not a native to Australia because of the absence of early records of this species, and its close association in most areas with humans. Conflicting with this is the absence of redbacks in any other part of the world, apart from areas where it has obviously been imported in Australia. It is far more likely that the redback had a much more restricted distribution in Australia prior to European settlement (probably somewhere west of the Great Dividing Range) and has since been spread to the remainder of the country.
In other Latrodectus species, the small male first climbs onto the female's web and approaches her cautiously with regular stops to vibrate the web. The female will usually chase him away a few times, but eventually she calms down and the male is able to climb onto the underside of the female as she hangs upside-down on the web, as shown above in Latrodectus hesperus (image from here). The female remains largely immobile while the male mates with her, and he is able to make his escape quite easily. In the redback, the male approaches and mounts the female as in other Latrodectus but once he has inserted his pedipalp into her he performs a back-flip that brings his abdomen alongside her mouthparts. The female, seemingly unable to resist the temptation, bites into the male and begins chewing. After a while, the male pulls away from the female and rips his badly damaged abdomen out of her grasp. Nevertheless, after a period of grooming the male returns to the female, and inserts and repositions himself as before. This time, the female does not allow him to escape - the male does not survive the second mating.
Why does the male submit himself to this fatal attack? There are a few possibilities that have been suggested. The nutrients the female receives from eating the male may aid in the development of the eggs he has fertilised. Also, the female remains mating with the male for longer while feeding on him than she would have otherwise. Not only does this allow the male more time to fertilise her eggs, it also denies other males the chance to mate with her in this time. A thesis abstract available here indicates that some males try to escape the role of victim, attempting to sneak in and mate with the female without offering themselves. However, females react even more aggressively to such cheaters, who were much more likely to be cannibalised before mating was successfully completed.
Forster, R., & L. Forster. 1999. Spiders of New Zealand and their Worldwide Kin. University of Otago Press: Dunedin, in association with Otago Museum.
As I've commented before on this blog, taxonomy holds an unusual position in the biological sciences in that it fills two equally significant roles. On the one hand, it is a science in its own right, investigating the best way to describe and express the relationships between organisms. On the other hand, it supplies the means for communication between biologists in all fields. For the most part, these two aims compliment each other, but sometimes they can clash. The first aim implies continual change, as our understanding of the relationships between organisms changes and (hopefully) improves. Wheeler (2007) commented in a recent editorial that "Doing taxonomy as an independent science advances simultaneously both the aims
of taxonomy and its users", a sentiment that I agree with fully (be warned, though, that the general tone of Wheeler's editorial is fairly incendiary). To fulfil the second aim, however, a certain amount of stability is usually desired, as researchers who are not working in taxonomy may have trouble keeping up with the changes (or, for that matter, appreciating their necessity).
All of the codes of nomenclature have a central commission to regulate taxonomy - zoology has the International Commission on Zoological Nomenclature, botany has the International Association for Plant Taxonomy. One of the main roles of these commissions is to allow suspension of the usual rules in cases where their strict application would cause more trouble for communication than otherwise. In the case of zoology, applications for rulings on such cases that are submitted to the ICZN are published in the journal Bulletin on Zoological Nomenclature, allowing researchers the opportunity to comment on submissions before the Commission decides on them. One submission that appeared in the December 2007 issue of the BZN involves a case that could affect a large number of researchers in many fields - the impending revision of the fly genus Drosophila.
Drosophila is a very large genus, containing about 1500 species. However, phylogenetic studies (e. g. Robe et al., 2005) have found that Drosophila as currently defined is significantly paraphyletic with regard to a number of other genera in the family Drosophilidae. There are two options to resolve this situation. One is to sink all the smaller genera arising from Drosophila into the larger genus. However, this is not regarded as a suitable solution - not only would it leave Drosophila with over 2000 species, but it would result in over a hundred secondary homonyms (two or more species ending up with the same name as a result of change in genus assignment) that would require correction. The other option, that seems much more likely to be used, is to divide Drosophila into a number of smaller genera. The name Drosophila would then be restricted to a smaller group of species closely related to the type species.
All this would be fairly routine, except that one of the species affected happens to be one of the most widely used model organisms in genetics - the "fruit fly" Drosophila melanogaster (the inverted commas are because Drosophila isn't really a fruit fly proper, but a vinegar fly). So familiar is this species that many people simply refer to it as Drosophila without invoking the species name. One might be forgiven for expecting D. melanogaster to be the type species of Drosophila, but it's not. That honour goes to Drosophila funebris (shown at the top of the post in a photo from here). And as it happens, the two species are not that closely related. If Drosophila is divided up, the Drosophila melanogaster everyone knows and loves becomes a far less familiar Sophophora melanogaster. How will geneticists respond to the loss of their favourite organism?
To avert an apocalypse in evolutionary biology, van der Linde et al. (2007) have made a submission to the ICZN to redefine the type species of Drosophila. They suggest that that honour be given to D. melanogaster rather than D. funebris, meaning that D. melanogaster would remain forever more Drosophila. But if this is accepted, what will become of D. funebris and its close friends and relatives? Will the ICZN exalt D. melanogaster to the position of type species? Or will the geneticists just have to learn to refer to Sophophora, and like it?
I just arrived home from our camping trip over the long weekend (which, offhand, led to Jack and I deciding that next camping trip we'll be just going by ourselves and leaving the kids at home - it would be nice to have a trip that didn't involve exchanges along the lines of: [Kids:] We're bored! [Jack and Chris:] Then get out of the tent and do something! [Kids:] We don't want to! [sound of molars cracking as Jack and Chris grit their teeth beyond their dentition's breaking point]) to find that two blog carnivals have appeared in my absence:
The first ever round of plant carnival Berry Go Round is up at Seeds Aside. You may recall me mentioning this one a few weeks ago, and I'm happy to say that it's debut is any indication, the carnival can only go from strength to strength.
Welcome to the last post for Scleritome Week. I hope you've enjoyed reading it as much as I've enjoyed writing and researching it, and that it's brought a few surprises (it has for me - I actually expected chancelloriids to be a lot more like sponges, and if you look closely you might notice that I actually referred to them as such in the machaeridian post). This week I've brought you mystery fish, armoured worms, and an animal that one researcher reconstructed looking like one of the Ophanim*. Most of the animals I've covered have become well-known throught the fortunate discoveries of articulated specimens, but I thought I'd end with a little reminder of just what made the scleritome animals so fascinating - the fact that for so many of them we don't yet know what the animal looked like.
*Third choir, comes after the Seraphim and Cherubim.
Eurytholia was described in 2001 (Sutton et al., 2001) for small sclerites the authors described as "hat-like" found from scattered locations in Europe and North America. Eurytholia sclerites are more or less oblong in shape, with a central ridge running parallel with the shorter sides. The figure above from Sutton et al. (2001) shows an assortment of specimens from different angles.
As yet, no articulated specimens showing what the rest of the animal looked like have been found, but the authors were able to make some inferences about it. The sclerites were exterior rather than interior - their microstructure indicates that they were secreted from the underside only, and some specimens show evidence of having been damaged while the animal was alive. They were unlikely to have functioned as teeth due to their unsuitable morphology. They also don't appear properly shaped to have overlapped each other. Due to the relative abundances of sclerites of different sizes, Sutton et al. suggest an "armoured slug" appearance rather like that known for Wiwaxia (reconstruction also from Sutton et al., 2001):
Personally, I can't help thinking it looks like a headless, limbless, tail-less ankylosaurian. But the wonderful thing is that we just don't know if Sutton et al. got it right. Their reconstruction seems plausible enough, but until we find an articulated specimen, who knows what kind of tentacled monstrosity Eurytholia might actually turn out to have been?
They may be a day late, but I promised chancelloriids and here they are!
Chancelloriids are arguably the most frustrating group of animals I'm going to be covering for Scleritome Week. in the cases of machaeridians, Microdictyon and palaeoscolecidans, the identification of articulated specimens revolutionised our understanding of the sclerite-bearing animal. In the case of chancelloriids, despite the availability of a number of well-preserved articulated specimens, we remain very much in the dark. We know what the animals looked like, we have a reasonably good idea of how they were put together, we can infer a lot about their probable life-style. And after all that, we're left with something that just doesn't make a lot of sense.
As you can see in the figure above from Bengtson (2004), chancelloriids were sessile animals, probably filter feeders, with an external covering of star-shaped sclerites. Bengtson (2004) compares their appearance to a cactus, which sounds like a pretty good description to me. Different species varied somewhat in overall shape, from the cylindrical Chancelloria to the more globular Allonnia. Chancelloriids were restricted to the Cambrian, and became extinct by the end of that period (Janussen et al., 2002). Some specimens show a root thickening at the base of the animal that probably served to anchor it in soft sediment.
When first described, chancelloriids were regarded as sponges, with the sclerites compared to sponge spicules. It is true that their overall appearance would have been very sponge-like, but the finer details don't stack up. Sponge spicules are internal structures, secreted by an enveloping layer of sclerocyte cells. In contrast, the chancelloriid sclerites appear to have been at least partially external (the base may have been embedded in the animal's body, with only the spines protruding) and possessed a hollow central cavity that in life probably contained soft tissue (the figure above from Janussen et al., 2002, shows the basal foramina in each individual spine that would have connected the spicule tissue with the rest of the body). Well-preserved specimens from Chengjiang show evidence of a thick epidermis, completely different from the thin and undifferentiated pinacoderm of sponges. On this basis, Janussen et al. (2002) decided that chancelloriids must at least belong to the Epitheliozoa, the clade of all animals except for sponges (Trichoplax plus Eumetazoa). However, as I've recently learnt from Palaeos, one group of sponges, the Homoscleromorpha, does possess a true eumetazoan-like epithelium, though spicules are still of typical sponge construction and nothing like the chancelloriid sclerites.
In 1981, Bengtson and Missarzhevsky suggested an alternative position for chancelloriids as a member of their Coeloscleritophora, along with two order groups of sclerite taxa, the siphonoguchitids and wiwaxiids. The three groups were united by the possession of a hollow sclerite with no evidence of accretionary growth (that is, the sclerite was probably secreted as a unit rather than being added to over the course of the animal's life). Later, Bengtson was to suggest a molluscan affinity for coeloscleritophorans due to similarities in shell secretion.
As far as I know, siphonoguchitids have not yet been found as articulated fossils, but finds from the Burgess Shale mean that the living appearance of wiwaxiids is well-known (picture above from Palaeos). In stark contrast to the sessile chancelloriids, wiwaxiids were mobile animals, a bit like an armoured slug. Authors have differed over whether wiwaxiids were more closely related to annelids or molluscs, but their position somewhere within the trochozoans seems secure. It is a lot more debatable whether the Coeloscleritophora is a monophyletic group, or if the coelosclerite has arisen polyphyletically in unrelated groups. Even before the identification of the wiwaxiid body form, doubts had been cast based on the bilateral nature of individual wiwaxiid and siphonoguchitid sclerites compared to the radial arrangement of chancelloriid sclerites. I can't help asking myself, though, if sea squirts were only known from adult fossils, without any understanding of their development, would any connection be made to other chordates?
Bengtson, S. 2004. Early skeletal fossils. In Neoproterozoic-Cambrian Biological Revolutions (J. H. Lipps & B. M. Waggoner, eds.) The Paleontological Society Papers 10: 67-77.
Janussen, D., M. Steiner & Zhu M. 2002. New well-preserved scleritomes of Chancelloriidae from the Early Cambrian Yuanshan Formation (Chengjiang, China) and the Middle Cambrian Wheeler Shale (Utah, USA) and paleobiological implications. Journal of Paleontology 76 (4): 596-606.
Unfortunately, I can't touch the chancelloriids until tomorrow, but they will be here, I promise.
So far, all the animals I've shown you in relation to Scleritome Week (see here, here and here) have all been definitely in the class of organisms dismissed by the sadly vertebrate-centric as "creepy-crawlies". Nevertheless, the disarticulated scleritome issue is not unique to invertebrates.
The figure at the top of the post (from Valiukevičius & Burrow, 2005) shows scales of Silurian fish of the family Tchunacanthidae. This family was originally described by Karatajute-Talimaa & Smith (2003) as a new order, distinct from all others previously described (while Valiukevičius & Burrow seem a little sceptical of such a high ranking, they do still maintain the family's distinctiveness). The interesting thing for this post is that, so far, tchunacanthids are known only from scales.
Tchunacanthidae are member of the Acanthodii, an extinct class of vertebrates found from the Silurian to the Permian (a couple of examples are shown above in an illustration from here). Acanthodians are sometimes referred as "spiny sharks", a name that probably survives more because it sounds neat than because of its appropriateness for the actual animals. While generally regarded as more closely related to modern bony fishes and tetrapods than actual sharks, acanthodians resembled sharks in having a cartilaginous rather than a bony skeleton. As a result, acanthodian skeletons were rarely fossilised, and usually only the hard mineralised parts survived - teeth, scales and spines. Without the soft tissue holding them together, however, the fossils became disarticulated, just like the sclerites of a scleritome animal. Tchunacanthids are far from being the only family of non-bony fish known only from scattered pieces of armation - articulated specimens (except in those taxa that developed large bony plates) are the exception rather than the rule. Beyond the general features shared by all acanthodians, we are doomed to ignorance about what a living tchunacanthid looked like unless some day we are lucky enough to find one of those rare articulated fossils.
I've started improving the home site for the Linnaeus' Legacy blog carnival. Up to now it's been little more than a place-holder, but I'd like to make it into more of a proper resource, in the way the site for Circus of the Spineless is. I've added links for the blogs that have hosted and those that have contributed (and remember, if you'd like your blog to be elevated from a mere contributor to the higher position of host, then volunteer!) I've also started adding links for websites offering good sources on taxonomy and systematics, and I need to know what you the reader think I need to link to.
Also, is there anyone out there that would be willing to contribute a banner? I know there's some pretty decent artists out there that have contributed to Linnaeus' Legacy in the past. Personally, I haven't the artistic ability of a fungus gnat.
Unlike the other animals I'll be covering as part of Scleritome Week, the Palaeoscolecida were actually known as entire animals long before their dermal armation was described, but they still meet the Scleritome Week qualifications because said armation was described as isolated problematic fossils before a connection was made between the animal and its armour (Ivantsov & Wrona, 2004). The photo above (from here) shows one of the isolated sclerites, originally described under the name Hadimopanella. Palaeoscolecid sclerites are round and button-like, with a central array of nodules that vary in different species from low and rounded to higher and pointed. Opinions on the nature of these microfossils (to appreciate how small they are, the scale bar on the photo above represents 0.03 mm) varied from some sort of dermal armour to the remains of reproductive cysts (Repetski, 1981). The dermal armour theory, of course, won out when the connection was made between the isolated sclerites and ornamentation on the compressed body fossils almost simultaneously by different authors in 1989 (Ivantsov & Wrona, 2004).
Palaeoscolecidans were a successful group of burrowing worms in the early Palaeozoic, when they were probably even more significant than the annelids (the image above of the holotype of Tabelliscolex hexagonus comes from Han et al., 2007). Originally interpreted as annelids, the segmented appearance is apparently only superficial, and results from alternating bands of larger and smaller plates (Ivantsov & Wrona, 2004). Well-preserved specimens from the Chengjiang Fauna possess an anterior spiny proboscis like that of the modern priapulids, and palaeoscolecidans have most often been regarded as priapozoans*. Other authors have suggested relationships with the modern nematomorphs, or as stem-panarthropods (Han et al., 2007). At the very least, a position within the Ecdysozoa, the clade uniting these three groups, seems well-established.
Tomorrow, I'll move on to chancelloriids.
*Bring on the nomenclatorial quibble. Most authors supporting this affinity have simply referred to palaeoscolecidans as "priapulids". The modern priapulids are a small, well-defined group of worms, while the various Palaeozoic taxa regarded as stem-priapulids show a much higher diversity of body plans (many of them, for instance, were far more elongate than any living priapulid, while no living priapulid possesses a dermal armour like that of palaeoscolecidans). Personally, I'd prefer to only refer to the crown group as priapulids, and use the name Priapozoa to cover the larger group including the stem forms.
I'm still pretty excited about the articulated machaeridian I wrote about last week. So excited, in fact, that to commemorate that significant discovery I'm declaring this week to be Scleritome Week here at Catalogue of Organisms. Each day this week I'll introduce you to a new Palaeozoic fossil animal of a kind no longer with us today. Not all of them will be scleritome animals in the proper sense of the word, but they will all share a common characteristic - they were all described from disarticulated pieces of dermal armour that gave us little idea of what the entire animal originally looked like. In many cases, more complete specimens have been found that show us the animal's true form. In others, the identity of the original animal remains a near-insoluble mystery.
My first subject is a classic example of just little these isolated elements can sometimes tell us about their source. Microdictyon was first known from tiny roundish to oblong-ish sclerites. The name means "tiny net" and refers to the net-like structure of the sclerites, clearly visible in the example above from here. Differences in appearance between sclerites led to the description of a number of species (Bengtson et al., 1986), but the identity of the animal bearing them was a complete mystery.
It wasn't until the discovery of the Chengjiang Biota in China that a fossil showing the soft anatomy of Microdictyon was discovered, and it's probably fair to say that no-one could have predicted what it looked like (image of fossil and reconstruction from Palaeos):
It turns out that Microdictyon was a lobopod, one of a number of Cambrian marine animals not unlike the modern terrestrial onychophorans*. Paired sclerites sat above each pair of legs. It is most likely that these sclerites served a defensive purpose, but other functions have also been suggested - Jerzy Dzik (2003), a man who has not been above suggesting heterodox interpretations of Cambrian animals in the past (some of which have even turned out to be accurate), suggested that Microdictyon sclerites were similar in structure to trilobite eyes, and might even be homologous. He therefore reconstructed Microdictyon as an elongate animal with a pair of eyes on each segment!
*"Lobopod" is a collective name for tardigrades and onychophorans, which have a soft body with stumpy tubular legs. Some authors have interpreted tardigrades and onychophorans as forming a monophyletic group, but others hold that the lobopod form is the ancestral grade for panarthropods (the clade joining lobopods and arthropods). In the past, the Cambrian lobopods have been interpreted as stem-onychophorans, but beyond the superficial similarities in appearance, it is not unlikely that the shared features are also plesiomorphic for panarthropods in general and a specific relationship to onychophorans should be regarded sceptically (Liu et al., in press).
Bengtson,S., S. C. Matthews & V. V. Missarzhevsky. 1986. The Cambrian netlike fossil Microdictyon. In Problematic Fossil Taxa (A. Hoffman & M.H. Nitecki, eds.) pp. 97–115. Oxford University Press, New York.
Dzik, J. 2003. Early Cambrian lobopodian sclerites and associated fossils from Kazakhstan. Palaeontology 46 (1): 93-112.
Okay, so I'm only doing this to beat Rick MacPherson. A recent publication in Zootaxa (Smith et al., 2008) has given us a new species of moray eel, Gymnothorax baranesi.
The new species has only been collected so far from a small area of the Gulf of Aqaba in the northern Red Sea, in moderately deep water. The picture above (from the paper) shows the male holotype, which is not quite mature but at ~86 cm long is quite big enough to not want to mess with. Full adults would probably be even larger. Gymnothorax baranesi* is distinguished from closely related species by details of the colour pattern and the arrangement of teeth.
*The authors don't suggest a vernacular name, but being a vertebrate someone's probably going to insist that it needs one. I suppose the main options are Baranes' Moray after the species name (named for Albert Baranes, a researcher on fishes of the Red Sea), or Aqaba Moray after the locality.
The discovery of this species highlights just how little we know about the world's biodiversity in another way, too. As the authors note in the paper, "The fact that the new species was collected in an area that has been well studied... for many years (and in fact, directly in front of a major marine laboratory) indicates how much we still have to learn..."
A few months back, I wrote a post on the group of bacteria known as Corynebacterineae. Today, I'm going to delve a little deeper into one of the best-known genera in this group, Mycobacterium.
The most famous members of this genus, of course, are the human pathogens Mycobacterium tuberculosis (the cause of, well, tuberculosis - image above from here) and M. leprae (causing leprosy). Back home in New Zealand, though, the most significant species is possibly M. bovis, which causes bovine tuberculosis, and a whole host of other species infect various other mammals and birds. Mycobacterium also includes a number of non-pathogenic forms such as M. smegmatis. In culture, mycobacteria are clearly divisible into fast-growing and slow-growing taxa - phylogenetic analyses suggest that the slow-growing taxa (which include the major pathogens) may form a single clade (Devulder et al., 2005).
Mycobacterium leprae is a very strange organism, even if we leave aside its apparent ability to survive on only two host species, humans and armadillos. As prominent human pathogens, M. tuberculosis and M. leprae have both been subject to genome-sequencing projects. The differences between the two species can only be described as remarkable. Bacterial genomes tend to be fairly streamlined things, probably because the rapid generation times and hence rapid evolutionary rates mean that non-functional genetic elements would soon be pruned from the genome. The genome of M. tuberculosis is no exception - ~91% of the genome is made up of protein-coding sequences, with only 6 pseudogenes (Cole et al., 1998). That of M. leprae, however, is an entirely different affair (Cole et al., 2001). Not only is it much smaller than that of M. tuberculosis (~3000 ORFs* in M. leprae as opposed to ~4000 in M. tuberculosis) but it also contains a much higher proportion of junk. Less than half of the genome appears functional, with a whopping 1116 pseudogenes. Even those genes that retain the appearance of functionality may not actually be so - comparative proteome analysis recovered only 391 soluble protein species in M. leprae, as opposed to ~1800 in M. tuberculosis.
*ORF - Open Reading Frame. An ORF is a section of the genome that has characteristics suggesting that it might be a functional gene (such as an copy initiation site) but may or may not have been definitely connected to a functional product.
(from Cole et al., 2001) (a) Diagram of the prolyl-tRNA synthetase gene (proS) regions in the genomes of Mycobacterium leprae (above) and M. tuberculosis (below). Arrows represent genes or operons, crosses indicate pseudogenes. Note the different positions of proS in the two species. (b) Domain structures of the proteins of the two species. Note the significantly different structure of the M. leprae synthetase, which may have been acquired through horizontal gene transfer from the eukaryote host.
It is not hard to imagine how this situation arose. Many obligately parasitic organisms such as Mycobacterium leprae show reduction in functionality - why invest time and energy into producing something yourself when your host provides it ready-made? Leprosy (and hence probably the organism that causes it) may have originated quite recently - palaeopathological evidence does not indicate its presence prior to the development of urbanisation, and it is difficult to imagine how M. leprae, with its combination of obligate parasitism yet extremely low communicability, could have maintained a viable population without a dense host population (Pinhasi et al., 2006). It seems that with M. leprae we might be seeing reduction in action - the non-vital factors have lost their function, but their remnants have not yet been purged from the genome*.
*It occurs to me that my wording in describing the loss of non-functional elements from bacterial genomes makes it sound like an active process - as if some factor in the organism's metabolism was directly seeking out and removing unneeded pieces of DNA. This is not necessarily the case. Even if the loss of pseudogenes and such was completely random, there would probably still be a tendency for populations to lose them over time, as bacteria with smaller genomes but no loss of viability would probably have a selective advantage over those with larger genomes because they would be able to grow and replicate faster.
As regards the non-pathogenic mycobacteria, probably the best known is the aforementioned Mycobacterium smegmatis, shown above growing as a biofilm on water (image from ScienceDaily). This species is generally a soil bacterium, though it can cause opportunistic infections (generally in patients already suffering from immuno-suppression) - the name "smegmatis" refers to its initial isolation from human genital secretions. Because M. smegmatis, as a fast-growing Mycobacterium, is far easier to culture than the slow-growing pathogenic species, is has become widely used as a model organism in the study of mycobacteria.
After something of a hiatus, the palaeontological blog carnival The Boneyard has returned and is up at When Pigs Fly Returns.
Also, a new carnival is in the making. Berry Go Round will cover all aspects of plant life, and the first installment will be up at the end of the month at Seeds Aside. Get your submissions in by the 25th!
I'm back from holiday, and a very good one it was too. Two weeks free from work, free from children, free from responsibilities or restrictions (unless being forced to eat Rocquefort cheese in the hotel room en suite because Jack refused to share a room with the malodorous delicacy counts as a restriction) - what more could one ask? However, the one downside of going away (apart, of course, from the e-mail backlog lurking in wait upon my return) is that I always seem to miss the announcement of some fantastic discovery, and this trip was no exception. Indeed, the publication notice that I found waiting in my in-box was something so huge, so absolutely incredible, so much something that I've been dreaming of for years that I'm worried that the greatest announcement of 2008 has already happened less than two weeks into the year, and it may only be downhill from here. 150 years after their initial discovery, we finally have soft-body remains of a machaeridian!
(from Vinther et al., 2008) a, Holotype YPM 221134, part. b, Camera lucida drawing of the part. Colours indicate the trunk (yellow), parapodia (red), chaetae (gray), attachment of shell plates (green), gut (purple) and dorsal linear structure (blue). Abbreviations: os, outer shell plate; is, inner shell plate; aos, anterior outer shell plate; ls, linear structure; cw, cuticular wrinkles; r, rami evidenced by divergent bundles of chaetae. Scale bar, 5 mm.
Machaeridians were small invertebrate animals found from the Ordovician to the Carboniferous. Like a number of other Palaeozoic shelled taxa, they possessed a body armour composed of multiple sclerites rather than a single solid shell. Despite often being implicitly dismissed as ultimately inferior or primitive with regard to the more familiar shelled animals that we see around us today, the scleritome body plan was actually very successful (the Ordovician to the Carboniferous was no small stretch of time) and survives to this day in groups such as the chitons. Vinther et al. (2008) state that machaeridian sclerites are near-ubiquitous in benthic marine assemblages of the appropriate time period. The problem is that because scleritome plates are not directly fused to each other, on death the scleritome generally becomes disarticulated and it can be exceedingly difficult if not impossible to reconstruct the appearance of the entire animal in life. As a result, scleritome animals have been swept into the too-hard basket in the past and not received the attention that they probably deserve. Even with the massive renaissance of interest in problematica that popularised the Cambrian explosion and the Ediacara fauna in the 1990s, the Machaeridia retained their internationally ignored status. Guesses as to their affinity ranged from molluscs to annelids to arthropods (specifically barnacles) to echinoderms.
(from Caron, 2008) Top, a complete machaeridian scleritome from 425-million-year-old deposits in New York state. Length, 5.4 mm. Bottom, dorsal reconstructions of presumed complete scleritomes (not to scale) showing the diversity of scleritomes within the three families of machaeridians — running upper to lower, the Lepidocoleidae, Turrilepadidae and Plumulitidae. The fossil specimen (top) is a lepidocoleid; that described by Vinther et al. is a plumulitid. All scleritomes are shown with the presumed head to the right. (Top image courtesy of A. Högström; bottom images courtesy of J. Dzik.)
Hence my excitement at the publication of Vinther et al. (2008), which gives us our most complete picture of a machaeridian to date, in the form of an articulated specimen of Plumulites bengtsoni from the Lower Ordovician of Morocco preserving soft body parts. The specimen is not perfect - the preserved soft parts are a little smeared, and the head is missing - but what we have is very informative. Most significant are what seem to be bristle groups running down each side of the body, which the authors feel are probably parapodia. Parapodia are groups of chitinous bristles (chaetae) found in polychaete annelids, and their presence in machaeridians is about as clear as indication of annelid affinities as you can get. Polychaete parapodia are divided into upper and lower clusters of chaetae, and a few of the apparent parapodia in P. bengtsoni do appear to show branching compatible with such an arrangement.
Accepting that machaeridians are closer to annelids than other living animal phyla, it still remains difficult to establish their exact position relative to that group, whether as a stem outgroup or derived ingroup. Phylogeny of living annelids remains almost totally unresolved - annelids possess relatively few phylogenetically useful morphological characters, while molecular analyses are so far unable to even recover their monophyly relative to other phyla (Rousset et al., 2007). A possible relationship to the annelid order Phyllodocida, some members of which possess dorsal plates as shown below in an image of Iphione ovata from here, in Vinther et al.'s phylogenetic analysis was dependent on coding the mineralised machaeridian sclerites as homologous with the chitinous phyllodocidan elytra. Leaving this character as uncertain caused the annelid interrelationships to collapse to a polytomy, with the possibility remaining that machaeridians sit on the annelid stem. As it has also been suggested that phyllodocidans represent a paraphyletic grade relative to other annelids, the two results are not necessarily incompatible.
Machaeridians are but one of a number of groups of Palaeozoic scleritome animals that appear to occupy basal positions on the trochozoan family tree - other examples include the sachitids, tommotiids, wiwaxiids and halkieriids*. Interestingly, there is no indication that these groups all form a clade. Halkieriids (shown at left in an image from Palaeos) may be related to brachiopods (Holmer et al., 2002), to which tommotiids are also ultrastructurally similar (Vinther et al., 2008). Wiwaxiids have been interpreted by different authors as related to molluscs and/or annelids, while molluscs of course include chitons (one extinct order of which - the Multiplacophora - possessed a more complex scleritome than modern species - Vendrasco et al., 2004). It seems not unlikely that the scleritome animals as a whole represent the ancestral group of a brachiopod-annelid-mollusc clade, with the three modern lineages arising independently from scleritome ancestors**. The scleritome would have been reduced and lost in the annelids, while brachiopods and molluscs each independently evolved towards more consolidated armation (if halkieriids are brachiopod relatives, then the two larger terminal plates were expanded in the ancestral brachiopod to the expense of the other plates; the mode of evolution in molluscs is a bit more obscure due to more uncertain phylogeny). Of course, this scenario is still pretty provisional, and there are a number of basal shell-less taxa involved such as Odontogriphus, phoronids and aplacophorans that could still potentially cause it to collapse into a quivering heap. As I've so often said in relation to matters of phylogeny, watch this space.
*Many of these groups have been included in a taxon called Coeloscleritophora that was also suggested to include the strange Cambrian organisms called chancelloriids. Individual sclerites of chancelloriids do have a similar structure to those of other "coeloscleritophorans", but articulated specimens indicate a radically different body plan for the entire animal with sclerites arranged radially over a vase-shaped form. It seems most likely that chancelloriids were sponge-grade animals unrelated to the other "coeloscleritophorans", but the question is complicated by the complete absense of a living sponge group that is even remotely similar to chancelloriids beyond superficial appearance.
**Recent genetic analyses show that these three phyla fall within a clade called Spiralia (or Lophotrochozoa, a name which is used often but for various reasons gives me grief, so I try to avoid it) that also includes a number of other taxa such as nemerteans and platyzoans. Relationships within Spiralia have not been satisfactorily sorted out. It is possible that some other spiralian taxa may fall within the annelid-brachiopod-mollusc clade, which would even further complicate my scenario.